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MODDE

By Umetrics

Version 9

© 1992-2009 MKS Umetrics AB, all rights reserved

Information in this document is subject to change without notice and does not

represent a commitment on part of Umetrics. The software, which includes

information contained in any databases, described in this document is

furnished under license agreement or nondisclosure agreement and may be

used or copied only in accordance with the terms of the agreement. It is

against the law to copy the software except as specifically allowed in the

license or nondisclosure agreement. No part of this user guide may be

reproduced or transmitted in any form or by any means, electronic or

mechanical, including photocopying and recording, for any purpose, without

the express written permission of Umetrics.

Umetrics patents and trade marks:

OPLS/O2PLS®, SWE-9802229-6, USA-6754543,

OSC®, SWE-0000563-7, USA-6853923

PLS-TREE®, Pending

SEQUENTIAL MODELING, Pending

DESIGN SPACE, Pending

MODDE®, RED - MUP®, VALUE FROM DATA®, OPLS®, O2PLS®, O2-

PLS®, OPLS-DA®, O2PLS-DA™

PLS-TREE™, S-PLOT™, EZinfo®, SBOL®, FABSTAT®, BATCH

FINGERPRINT®, SIMCA®.

ID # 2038

MKS Umetrics AB

Stortorget 21

SE-211 34 Malmö

Sweden

Phone: +46 (0)40 664 2580

Email: info@umetrics.com

Welcome

Welcome to the user guide for MODDE 9. This is your guide to MODDE and

its capabilities.

Assumed prior knowledge

We assume that you are already familiar with Windows. You should be

familiar with the topics discussed in your Microsoft Windows User's Guide,

including how to use the mouse select, click, shift-click, control-click, press,

drag, and choose from a menu. You should also know how to search through

directories to find files.

Content

This user guide is divided into 21 chapters. Chapter 1 gives a short

introduction of how to use MODDE. Chapter 2 presents an introduction to

experimental design. Chapter 3 is an overview of the program. Chapters 4 - 20

provide step-by-step procedures for creating and using experimental designs

with MODDE. Chapter 21 describes how the Help function works.

Appendix A, "Statistical notes" presents short explanations of statistical

methods used by MODDE.

Appendix B, “Designs” presents short descriptions of the designs available in

MODDE.

Appendix C: "Optimizer" describes the optimizer feature and the properties of

the different optimizer objectives.

Appendix D: "Design Space" describes the design space estimation feature.

References are available on the references page.

User guide edition Tuesday, September 22, 2009.

Table of Contents

How to get started with MODDE 1

Installation ..................................................................................................................... 1

Starting MODDE ........................................................................................................... 1

Experimental cycle ........................................................................................................ 1

Design phase .................................................................................................................. 2

Defining factors................................................................................................................... 2

Defining responses .............................................................................................................. 2

Defining objective ............................................................................................................... 2

Analysis phase ............................................................................................................... 2

Explore the data (Worksheet menu) .................................................................................... 2

Evaluate the design ............................................................................................................. 3

Fit ........................................................................................................................................ 3

Review the fit using plots and lists ...................................................................................... 3

Diagnostics .......................................................................................................................... 3

Interpret the model .............................................................................................................. 3

Refine the model ................................................................................................................. 4

Prediction phase (using the model) ................................................................................ 4

Introduction to MODDE and experimental design 5

General description ........................................................................................................ 5

What is modeling and experimental design? ................................................................. 5

Objectives of modeling and experimental design .......................................................... 5

Screening models and designs ....................................................................................... 5

Number of factors in screening designs .............................................................................. 6

Number of factors with split objective ................................................................................ 6

Response surface modeling (RSM) designs................................................................... 6

Number of factors in RSM designs ..................................................................................... 6

Number of factors in Split objective ................................................................................... 7

Fit methods .................................................................................................................... 7

Multiple Linear Regression (MLR) ..................................................................................... 7

Partial Least Squares (PLS)................................................................................................. 7

Results ................................................................................................................................. 8

Analysis phase ............................................................................................................... 9

Review the model fit ........................................................................................................... 9

Assess model adequacy ....................................................................................................... 9

Prediction - using the fitted model ................................................................................. 9

Convention................................................................................................................... 10

Limitations in investigation names.................................................................................... 10

Limitations in factor and response names ......................................................................... 10

Case sensitivity ................................................................................................................. 10

Menu reference syntax ...................................................................................................... 10

Suggestions for further reading on experimental designs ............................................ 10

Overview 11

Application icon and symbol ....................................................................................... 11

i

User Guide to MODDE

Managing investigations ................................................................................................... 11

Compatibility with older MODDE versions ...................................................................... 12

Organization ................................................................................................................ 12

Command menu bar ..................................................................................................... 13

File menu .......................................................................................................................... 13

Edit menu .......................................................................................................................... 14

View menu ........................................................................................................................ 14

Design menu ..................................................................................................................... 14

Worksheet menu ............................................................................................................... 15

Analysis menu ................................................................................................................... 15

Prediction menu ................................................................................................................ 15

Show menu........................................................................................................................ 16

Window menu ................................................................................................................... 16

Toolbars ....................................................................................................................... 16

Plots and lists ............................................................................................................... 16

File 17

Introduction.................................................................................................................. 17

New.............................................................................................................................. 17

Traditional designs ............................................................................................................ 18

Advanced designs.............................................................................................................. 18

Import design from file ..................................................................................................... 21

Open............................................................................................................................. 21

Save and save as .......................................................................................................... 21

Delete investigation ..................................................................................................... 21

Save plot/list as ............................................................................................................ 21

Revert........................................................................................................................... 22

Send by E-Mail ............................................................................................................ 22

Generate HTML report ................................................................................................ 22

Complement design ..................................................................................................... 23

Available complementing methods ................................................................................... 24

Fold over ........................................................................................................................... 24

Estimate squares of selected factors in factorial designs ................................................... 24

D-Optimal ......................................................................................................................... 25

Complement Doehlert ....................................................................................................... 27

Screening to RSM Rechtschaffner .................................................................................... 28

Plackett Burman Super-Saturated to Plackett Burman ...................................................... 28

Protect investigation .................................................................................................... 29

Encrypt/password protect an investigation ........................................................................ 29

Lock investigation ............................................................................................................. 29

Print Setup ................................................................................................................... 30

Print Preview ............................................................................................................... 30

Print ............................................................................................................................. 30

Print format for plots ......................................................................................................... 30

Exit............................................................................................................................... 30

Edit 31

Introduction.................................................................................................................. 31

Undo ............................................................................................................................ 31

Cut, copy, paste, delete, select all ................................................................................ 31

ii

Table of Contents

Add factor, add response, add experiment, insert rows ............................................... 32

Sort............................................................................................................................... 32

Sorting the candidate set ................................................................................................... 33

Model / reference mixture............................................................................................ 34

Model ................................................................................................................................ 34

Reference mixture ............................................................................................................. 36

Generators .................................................................................................................... 37

Edit the model and/or generators before creating the worksheet ................................. 38

View 39

Introduction.................................................................................................................. 39

Toolbars ....................................................................................................................... 39

Standard toolbar ................................................................................................................ 39

Spreadsheet toolbar ........................................................................................................... 41

Plot toolbar ........................................................................................................................ 41

Model toolbar .................................................................................................................... 44

Window toolbar................................................................................................................. 44

Status bar........................................................................................................................... 44

Dockable windows....................................................................................................... 44

Analysis advisor ................................................................................................................ 45

Audit trail .......................................................................................................................... 45

Favorites............................................................................................................................ 45

Output ............................................................................................................................... 50

Notes ................................................................................................................................. 50

Add to Favorites .......................................................................................................... 51

Add to Report .............................................................................................................. 51

Full Screen ................................................................................................................... 51

Changing the default options using Investigation Options .......................................... 52

Plot labels .......................................................................................................................... 52

Number format .................................................................................................................. 52

Audit trail .......................................................................................................................... 53

Alpha level ........................................................................................................................ 54

Coefficients ....................................................................................................................... 55

Blocking ............................................................................................................................ 56

Confidence level ............................................................................................................... 56

List presentation ................................................................................................................ 57

R2 in plots ......................................................................................................................... 57

Residuals ........................................................................................................................... 58

Select Factor...................................................................................................................... 58

General Options ........................................................................................................... 58

General page ..................................................................................................................... 59

List Options ....................................................................................................................... 60

Restore .............................................................................................................................. 61

Customize .................................................................................................................... 61

Customize toolbars ............................................................................................................ 61

Customize commands ....................................................................................................... 61

Customize options ............................................................................................................. 62

Customize options ............................................................................................................. 62

Design 63

Introduction.................................................................................................................. 63

iii

User Guide to MODDE

Responses .................................................................................................................... 63

Constraints ................................................................................................................... 63

Inclusions ..................................................................................................................... 64

Objective ...................................................................................................................... 64

D-Optimal .................................................................................................................... 64

Design wizard .............................................................................................................. 64

Factors 65

Introduction.................................................................................................................. 65

Factor definition dialog ................................................................................................ 65

Factor name ....................................................................................................................... 66

Abbreviation...................................................................................................................... 66

Units .................................................................................................................................. 66

General page ..................................................................................................................... 66

Advanced .......................................................................................................................... 69

Factor definition spreadsheet ....................................................................................... 72

Printing the factor spreadsheet .......................................................................................... 72

Factor manipulations in short....................................................................................... 73

Opening the factor definition spreadsheet ......................................................................... 73

Adding a factor.................................................................................................................. 73

Modifying a factor............................................................................................................. 73

Updating the worksheet..................................................................................................... 73

Copying a factor ................................................................................................................ 73

Deleting a factor ................................................................................................................ 74

Responses 75

Introduction.................................................................................................................. 75

Response definition dialog........................................................................................... 75

Response name .................................................................................................................. 76

Abbreviation...................................................................................................................... 76

Units .................................................................................................................................. 76

Selecting type of response ................................................................................................. 76

Limits ................................................................................................................................ 76

Regular responses ........................................................................................................ 77

Transformation .................................................................................................................. 77

MLR scaling...................................................................................................................... 77

PLS scaling ....................................................................................................................... 77

Derived responses ........................................................................................................ 78

Defining derived responses ............................................................................................... 79

Modifying a derived response ........................................................................................... 80

Copying or deleting a derived response ............................................................................ 80

Using sets of variables in derived responses ..................................................................... 80

Syntax for derived responses............................................................................................. 81

Operators and functions in derived responses ................................................................... 81

Qualitative factors in derived responses ............................................................................ 82

Linked responses ......................................................................................................... 82

Response definition spreadsheet .................................................................................. 83

Printing the response definition spreadsheet ..................................................................... 83

Response manipulations in short ................................................................................. 84

Opening the responses spreadsheet ................................................................................... 84

iv

Table of Contents

Modifying a response ........................................................................................................ 84

Deleting a response ........................................................................................................... 84

Copying and pasting a response ........................................................................................ 84

Constraints ................................................................................................................... 85

Specifying constraints ....................................................................................................... 85

Constraints supported ........................................................................................................ 86

Defining constraints in the spreadsheet ............................................................................. 86

Defining a constraint graphically ...................................................................................... 87

Modifying a constraint graphically ................................................................................... 88

Candidate set with a constraint.......................................................................................... 89

Constraints in qualitative or quantitative multilevel factors .............................................. 89

Inclusions ..................................................................................................................... 90

Inclusions vs. complement design ..................................................................................... 90

Inclusions added to the worksheet..................................................................................... 90

Inclusions as part of the design ......................................................................................... 91

Generating inclusions ........................................................................................................ 92

Modifying inclusions ........................................................................................................ 92

Introduction.................................................................................................................. 93

Selecting the objective ................................................................................................. 94

Screening objective ........................................................................................................... 94

RSM objective................................................................................................................... 94

Split Objective................................................................................................................... 94

Paste Data.......................................................................................................................... 95

Selecting model and design ......................................................................................... 95

Designs in MODDE .......................................................................................................... 95

Recommended designs ...................................................................................................... 96

Runs in design ................................................................................................................... 96

Model ................................................................................................................................ 96

Screening models .............................................................................................................. 96

RSM models...................................................................................................................... 96

Split models ...................................................................................................................... 96

Pseudo resolution for blocked designs .............................................................................. 97

Design runs ....................................................................................................................... 97

Center points ..................................................................................................................... 98

Replicates .......................................................................................................................... 98

Total runs .......................................................................................................................... 98

Settings.............................................................................................................................. 99

Description ...................................................................................................................... 101

Blocks ............................................................................................................................. 102

D-Optimal 103

What are D-Optimal designs? .................................................................................... 103

When do I use D-Optimal designs? ........................................................................... 103

D-Optimal pages in the design wizard ....................................................................... 104

Design generation criteria section ................................................................................... 104

Design alternatives section .............................................................................................. 106

Candidate set section ....................................................................................................... 107

v

User Guide to MODDE

D-Optimal on the Design menu ................................................................................. 109

Generate .......................................................................................................................... 109

Candidate set ................................................................................................................... 109

Evaluate........................................................................................................................... 110

Onion plot, onion 3D scatter ........................................................................................... 110

Design plot ...................................................................................................................... 110

D-Optimal onion design............................................................................................. 111

Candidate set ................................................................................................................... 111

Generating the design ...................................................................................................... 112

D-Optimal on the Design menu with Onion .................................................................... 113

Evaluate........................................................................................................................... 114

Onion plots ...................................................................................................................... 115

Introduction................................................................................................................ 117

Defining factors ......................................................................................................... 117

Defining responses..................................................................................................... 119

Selecting the objective ............................................................................................... 120

Selecting model and design ....................................................................................... 121

D-Optimal pages in the design wizard ....................................................................... 122

Worksheet 123

Introduction................................................................................................................ 123

Worksheet menu ........................................................................................................ 123

Opening the worksheet spreadsheet ................................................................................ 123

Setting run order.............................................................................................................. 124

Curvature diagnostic plot ................................................................................................ 125

2D and 3D scatter plots ................................................................................................... 126

Histogram ........................................................................................................................ 127

Descriptive statistics........................................................................................................ 128

Correlation ...................................................................................................................... 129

Replicate plot .................................................................................................................. 130

Worksheet spreadsheet .............................................................................................. 131

Description of the worksheet........................................................................................... 131

Missing values in the worksheet ..................................................................................... 131

Deleting the worksheet .................................................................................................... 131

Displaying the worksheet ................................................................................................ 131

Adding experiments in the worksheet ............................................................................. 132

Sorting the worksheet ...................................................................................................... 132

Colors in the worksheet ................................................................................................... 132

Analysis 133

Introduction................................................................................................................ 133

Organization of the Analysis menu............................................................................ 133

Evaluate ..................................................................................................................... 134

Condition number ........................................................................................................... 134

Runs, terms and degrees of freedom ............................................................................... 134

Analysis Wizard......................................................................................................... 135

Open the Analysis Wizard............................................................................................... 135

Analysis Wizard content ................................................................................................. 136

vi

Table of Contents

Fitting the model to the data ...................................................................................... 136

Selecting fit method ........................................................................................................ 137

Fitting the model ............................................................................................................. 137

Next component (only PLS) ............................................................................................ 138

Displaying the summary of fit ................................................................................... 139

Summary of fit plot ......................................................................................................... 139

Summary of fit list .......................................................................................................... 141

PLS summary plot (only PLS) ........................................................................................ 141

PLS response plot (only PLS) ......................................................................................... 142

PLS summary list ............................................................................................................ 142

Saturated models ............................................................................................................. 142

Investigating diagnostics............................................................................................ 143

Normal probability plot of residuals................................................................................ 143

Residuals ......................................................................................................................... 144

Distance to the model in the Y space – DModY (only PLS) ........................................... 146

Box Cox Plot (MLR only) ............................................................................................... 147

Observed vs. predicted .................................................................................................... 148

Lack of fit plot................................................................................................................. 149

Analysis of Variance (ANOVA) ..................................................................................... 150

Reviewing and interpreting the fit ............................................................................. 152

Coefficient plots and lists ................................................................................................ 152

Effects plots and list ........................................................................................................ 155

Variable importance in the projection – VIP (only PLS) ................................................ 161

PLS score and loading plots....................................................................................... 162

Score plots (only PLS) .................................................................................................... 162

Score plot examples (only PLS) ...................................................................................... 163

Loading plots (only PLS) ................................................................................................ 163

Loading plot example (only PLS) ................................................................................... 164

Prediction 165

Introduction................................................................................................................ 165

Contour plot wizard ................................................................................................... 166

Inner plot type ................................................................................................................. 166

Selecting responses ......................................................................................................... 166

Using constraints ............................................................................................................. 166

Plot options ..................................................................................................................... 167

2D contour ...................................................................................................................... 167

4D contour ...................................................................................................................... 169

Response Surface ............................................................................................................ 172

Prediction plot wizard ................................................................................................ 173

Prediction plot wizard first page selections ..................................................................... 173

Axes and constants .......................................................................................................... 174

Overlay prediction plot ................................................................................................... 174

Response prediction plot ............................................................................................ 175

Factor type ...................................................................................................................... 175

Prediction list ............................................................................................................. 176

Scatter plot ................................................................................................................. 176

Sweet spot plot ........................................................................................................... 177

Creating a sweet spot plot ............................................................................................... 177

Optimizer ................................................................................................................... 180

Factor spreadsheet in the Optimizer ................................................................................ 181

vii

User Guide to MODDE

Run list ............................................................................................................................ 183

Optimizer context menu .................................................................................................. 184

Optimizer buttons ............................................................................................................ 185

Design Space Validation ............................................................................................ 190

Design Space 191

Introduction................................................................................................................ 191

Design Space Estimation around the selected setpoint .............................................. 191

Design Space Validation for robustness testing ......................................................... 192

Design Space window ................................................................................................ 192

Factor spreadsheet ........................................................................................................... 193

Response spreadsheet ...................................................................................................... 194

Design Space buttons ...................................................................................................... 194

Design Space Properties .................................................................................................. 195

Factor histogram ........................................................................................................ 196

Response histogram ................................................................................................... 197

Design Space Statistics list ........................................................................................ 197

Final factor adjustments ............................................................................................. 198

Show 199

Introduction................................................................................................................ 199

Objective .................................................................................................................... 199

Design matrix............................................................................................................. 200

Design region ............................................................................................................. 201

Design region properties ................................................................................................. 201

Design region for mixture designs ............................................................................. 202

Confoundings............................................................................................................. 202

Summary D-Optimal.................................................................................................. 203

Model ......................................................................................................................... 204

Reference mixture ...................................................................................................... 204

Plots and lists 205

Introduction................................................................................................................ 205

Properties page........................................................................................................... 205

Opening property page by right-clicking......................................................................... 205

Making a change in the property page ............................................................................ 205

Automatic update of plots and lists ............................................................................ 205

Saving plots and lists ................................................................................................. 205

Generating multiple plots or lists ............................................................................... 206

Plot settings................................................................................................................ 206

Axis ................................................................................................................................. 207

Header and Footer ........................................................................................................... 209

Plot Area ......................................................................................................................... 210

Saving plot settings ......................................................................................................... 212

Customizing contour plots using the property page ................................................... 213

Resolution ....................................................................................................................... 213

Scale subplots equally ..................................................................................................... 213

Lock contour levels ......................................................................................................... 213

Use color ......................................................................................................................... 213

viii

Table of Contents

Plot settings for contour plots .................................................................................... 214

Axis ................................................................................................................................. 214

Header ............................................................................................................................. 214

Regions ........................................................................................................................... 214

Labels .............................................................................................................................. 214

Contour ........................................................................................................................... 214

Plot settings for sweet spot plots ................................................................................ 215

Axis ................................................................................................................................. 215

Header ............................................................................................................................. 215

Contour ........................................................................................................................... 215

Plot settings for 3D scatter plots ................................................................................ 216

Cube ................................................................................................................................ 216

Axis ................................................................................................................................. 217

Header ............................................................................................................................. 218

Legend ............................................................................................................................ 218

Footer .............................................................................................................................. 218

Symbols........................................................................................................................... 219

Labels .............................................................................................................................. 219

Colors .............................................................................................................................. 219

Zoom and rotate ......................................................................................................... 220

Report generator 221

Introduction................................................................................................................ 221

Starting the report generator ...................................................................................... 221

Report generator window........................................................................................... 222

Command menu bar ................................................................................................... 222

File menu ........................................................................................................................ 222

Edit menu ........................................................................................................................ 224

View menu ...................................................................................................................... 224

Insert menu...................................................................................................................... 224

Format menu ................................................................................................................... 225

Tools menu...................................................................................................................... 225

Help menu ....................................................................................................................... 226

Generate report toolbar .............................................................................................. 226

New ................................................................................................................................. 226

Generate report specific buttons ...................................................................................... 226

Format toolbar ........................................................................................................... 226

Placeholder window................................................................................................... 227

Properties window ..................................................................................................... 228

Adding plots and lists to the report ............................................................................ 228

Help 229

Introduction................................................................................................................ 229

HTML help ................................................................................................................ 229

Registration and activation ........................................................................................ 229

Manage Licenses ....................................................................................................... 229

Umetrics on the Web ................................................................................................. 230

About MODDE .......................................................................................................... 230

ix

User Guide to MODDE

Fit methods ................................................................................................................ 231

Multiple Linear Regression (MLR) ................................................................................. 231

Partial Least Squares (PLS)............................................................................................. 232

Model ......................................................................................................................... 234

Hierarchy......................................................................................................................... 234

Scaling ....................................................................................................................... 235

Scaling X ......................................................................................................................... 235

Scaling Y ......................................................................................................................... 235

Condition number ...................................................................................................... 236

Condition number definition ........................................................................................... 236

Condition number with mixture factors........................................................................... 236

PLS and Cox reference mixture model ........................................................................... 236

MLR (regression) and the Cox model ............................................................................. 236

MLR (regression) and Scheffé model ............................................................................. 237

Missing data ............................................................................................................... 237

Missing data in X ............................................................................................................ 237

Missing data in Y with Multiple Linear Regression ........................................................ 237

Missing data in Y with PLS ............................................................................................ 237

N-value ...................................................................................................................... 237

Residual Standard Deviation (RSD) .......................................................................... 237

ANOVA ..................................................................................................................... 238

Measures of goodness of fit ....................................................................................... 239

Q2.................................................................................................................................... 239

R2 .................................................................................................................................... 239

Degrees of freedom ......................................................................................................... 239

Coefficients ................................................................................................................ 240

Scaled and centered coefficients ..................................................................................... 240

Normalized coefficients .................................................................................................. 240

PLS orthogonal coefficients ............................................................................................ 240

Confidence intervals........................................................................................................ 240

Coding qualitative factors at more than 2 levels ........................................................ 241

Residuals .................................................................................................................... 241

Raw residuals .................................................................................................................. 241

Standardized residuals ..................................................................................................... 241

Deleted studentized residuals .......................................................................................... 241

Predictions ................................................................................................................. 242

PLS plots.................................................................................................................... 242

Plot loadings.................................................................................................................... 242

Plot scores ....................................................................................................................... 242

PLS coefficients ......................................................................................................... 242

Box-Cox plot (only MLR) ......................................................................................... 243

Mixture data in MODDE ........................................................................................... 243

Mixture factors only ........................................................................................................ 243

Process and mixture factors............................................................................................. 247

Optimizer ................................................................................................................... 248

Desirability ...................................................................................................................... 248

Overall desirability .......................................................................................................... 249

Overall Distance to Target .............................................................................................. 249

Starting simplexes ........................................................................................................... 249

Sensitivity Analysis......................................................................................................... 250

x

Table of Contents

Block interaction ............................................................................................................. 250

Recoding the blocking factors ......................................................................................... 251

Inclusions and blocks ...................................................................................................... 251

Blocking screening designs ............................................................................................. 251

Blocking RSM designs .................................................................................................... 252

Blocking D-Optimal designs ........................................................................................... 252

Random versus fixed block factor ................................................................................... 253

Design Space statistics ............................................................................................... 254

Monte Carlo simulations ................................................................................................. 254

DPMO and Cpk ............................................................................................................... 255

Predictions including model error ................................................................................... 256

Designs for process factors ........................................................................................ 257

Screening designs ............................................................................................................ 257

RSM designs ................................................................................................................... 260

Designs for mixture factors........................................................................................ 263

Mixture and process factors ............................................................................................ 263

Mixture factors definition................................................................................................ 263

Mixture constraint ........................................................................................................... 264

Mixture experimental region ........................................................................................... 264

Classical mixture designs ................................................................................................ 265

D-Optimal designs ..................................................................................................... 268

What are D-Optimal designs? ......................................................................................... 268

Candidate set ................................................................................................................... 268

D-Optimal algorithm ....................................................................................................... 269

Implementation of the D-Optimal algorithm in MODDE ............................................... 269

Potential terms................................................................................................................. 269

Design evaluation ............................................................................................................ 271

Inclusions and design augmentation ................................................................................ 271

Irregular region ............................................................................................................... 272

D-Optimal Onion designs .......................................................................................... 274

Screening onion designs .................................................................................................. 274

RSM onion designs ......................................................................................................... 274

Introduction................................................................................................................ 275

Search function .......................................................................................................... 275

Optimizer objectives .................................................................................................. 276

Limit optimization........................................................................................................... 276

Target optimization ......................................................................................................... 277

Focus optimization .......................................................................................................... 277

Define optimizer specifications ................................................................................. 277

Response specification example in the optimizer ............................................................ 278

Optimizer result ......................................................................................................... 279

Appendix D: Design Space 281

Introduction................................................................................................................ 281

Predictive Design Space Estimation .......................................................................... 281

Monte Carlo simulations ................................................................................................. 282

Evaluate the results and make necessary adjustments. .................................................... 283

xi

User Guide to MODDE

Design Space Validation for robustness testing ......................................................... 284

Design Space Validation example ................................................................................... 284

Evaluation ....................................................................................................................... 285

Factor spreadsheet ........................................................................................................... 285

Response spreadsheet ...................................................................................................... 285

Final adjustments ............................................................................................................ 286

Result statistics for k2 ..................................................................................................... 288

References 289

Index 291

xii

How to get started with MODDE

Installation

You can install MODDE under Windows Vista, XP, and 2000.

software.

To install and activate MODDE follow the steps described below:

1. Download the password protected installation file from the Umetrics web

page www.umetrics.com, click Downloads. The password is available in the

delivery letter.

2. Open the file and when prompted enter personal information as well as

product information found in the delivery letter.

3. After completing the installation, MODDE needs to be activated with a

license file. Activation is done either (a) from an internal license server or (b)

from Umetrics. See the delivery letter, sent to the license administrator at

your company, for instructions.

Starting MODDE

Start MODDE by double-clicking its icon.

• To read about the MODDE software look in Help (contains the same

information as the user guide).

• To run tutorial examples, find them at www.umetrics.com (Downloads),

select an example, open the investigation used in the tutorial (.mip-file

included with the installation in the Investigation folder) and follow the

analysis steps.

• To start a new investigation, on the File menu click New.

Experimental cycle

The experimental cycle consists of three phases:

1. The design phase where you define your factors and within which ranges

they should be varied, your responses, objective, design and model.

2. The analysis phase where you explore your data, review the raw data and the

fit, review diagnostics in plots and lists, refine and interpret the model.

1

User Guide to MODDE

3. The prediction phase where you use the model to predict the optimum area

for operability.

Design phase

Once you have clicked New on the File menu the design wizard is then opened. Enter

the name and location of the new investigation in the appropriate fields.

For details on the design wizard, see the Design Wizard chapter.

Defining factors

On the second page of the design wizard, enter factor names, ranges, etc.

For details on defining factors see the Factors chapter.

Defining responses

On the third page of the design wizard, enter response name(s), etc.

For details on defining responses see the Responses chapter.

Defining objective

On the next page of the design wizard, click your objective Screening, RSM, or Split

Objective. Clicking Paste Data disables Next; clicking Finish opens the worksheet

for pasting.

Given your objective, the type of factors (formulation or process) and the number of

factors, MODDE recommends a design, a model, and a number of center points. The

total required number of runs for this design is displayed. Other choices compatible

with your objective type and number of factors are listed with the required number of

runs.

After clicking Finish, the Worksheet is automatically generated for all classical

designs. With D-Optimal designs, clicking Next opens a dialog for the selection and

generation of the D-Optimal design and worksheet.

After making the experiments, fill in the response values and actual factor values in the

worksheet.

For details on the objective pages, see the Objective, model and design chapter. For

details on the worksheet, see the section Worksheet spreadsheet in the Worksheet

chapter.

Analysis phase

After the response values have been entered in the worksheet you can review the raw

data, fit the model, review the fitted model, interpret the model, and refine the model.

To explore the unfitted data use the Worksheet menu. The plots and lists available are:

the curvature diagnostic plot, scatter plot, histogram plot, descriptive statistics plot and

list, correlation plot and matrix, and the replicate plot.

For details on the worksheet menu plots and lists, see the Worksheet Menu section in

the Worksheet chapter.

2

How to get started with MODDE

The condition number is used to evaluate the goodness of the design. As a rule of

thumb the condition number for screening designs should not exceed 3. For RSM

designs it should not exceed 10.

The condition number is listed in the Evaluate table, found on the Analysis menu. The

evaluate table also lists the number of runs and model terms, and the degrees of

freedom of the residuals.

Fit

When you are ready to fit a model to your design you click Fit on the Analysis menu.

MODDE automatically fits using MLR when the condition number is low and there are

no mixture factors. The fit methods available are MLR, PLS and for mixtures several

variants.

For PLS models you can choose to extract more components than the MODDE default.

To extract more components click Next Component on the Analysis menu. Next

Component is unavailable when MLR is used as fit method.

After fitting the model the Summary of Fit plot is displayed summarizing the fit in four

columns:

• Percent of the variation of the response explained by the model, R2. R2

overestimates the goodness of fit.

• Percent of the variation of the response predicted by the model according to

cross validation, Q2, and expressed in the same units as R2. Q2

underestimates the goodness of fit.

• Model Validity: A Measure of the validity of the model. When the Model

Validity column is larger than 0.25, there is no Lack of Fit of the model (the

model error is in the same range as the pure error).

• Reproducibility: The variation of the response under the same conditions

(pure error), often at the center points, compared to the total variation of the

response.

Diagnostics

MODDE has a number of diagnostic plots:

• Residual plots to find outliers, drifts, trends etc.

• Box Cox Plot to select the best transformation of Y.

• ANOVA: ANalysis Of VAriance, in particular review the Lack of Fit. The

estimation of lack of fit is only available when there are replicated points as

it compares the pure error and the model error.

To interpret the influence of terms on the model use the Coefficient and Effect plots

and lists. The interaction plot is particularly useful if your model has strong interaction

terms. To display the interaction plot, click Effects on the Analysis menu, then click

Interaction plot.

3

User Guide to MODDE

When PLS is used for regression, scores and loadings can be plotted. These plots

provide an overview of the data. On the Analysis menu, click PLS Plots to select the

score or loading plot you want to display.

If you discover bad outliers or want to remove or add a term to the model you can

refine your model.

To remove outliers or insignificant model terms use the interactive exclude tool .

Click the button and then click/mark the outlier/term the in a plot. You can also

exclude it in the worksheet, by right-clicking the specific cell and clicking Exclude

value(s). The model is automatically refitted.

Note: When excluding an outlier or model term in a plot, the outlier or model

terms is only excluded for the displayed response.

Remove/Add terms from/to the model that are insignificant/significant for all

responses. Use Edit | Model or the interactive tool with the coefficient plot.

After refining your model you should once more review the fit and diagnostics as

described above.

Note: You can have a different model for each response in the same

investigation.

When you are content with the models (fit, predictivity, lack of fit etc.) you can use the

model to make predictions and find the “best conditions” area. The plots and lists to

use for this are found under the Predictions menu.

Under Predictions you find the Contour plots, Prediction plots and list, Sweet Spot

plot, Optimizer and the Design Space feature.

For more see the Prediction chapter.

4

Introduction to MODDE and

experimental design

General description

MODDE - (MODeling and DEsign) is a Windows program for the generation and

evaluation of statistical experimental designs.

Methods of statistical experimental designs have evolved since the pioneering work of

Fisher in 1926. These methods, further refined by Box, Hunter, Scheffé, Tagushi and

others, provides the users with a powerful methodology for efficient experimentation.

The application icon for MODDE is a pink circle with a gray M inside.

Experimental design is how to conduct and plan experiments in order to extract the

maximum amount of information from the collected data in the presence of noise. The

basic idea is to vary all relevant factors simultaneously, over a set of planned

experiments, and then connect the results by means of a mathematical model. This

model is then used for interpretation, predictions and optimization.

During an investigation one needs answers to the following questions:

• Which factors have a real influence on the responses (results)?

• Which factors have significant interactions (synergies or antagonism)?

• What are the best settings of the factors to achieve optimal conditions for

best performance of a process, a system or a product?

• What are the predicted values of the responses (results) for given settings of

the factors?

An experimental design can be set up to answer all of these questions.

Screening is the first stage of an investigation where the goal is just to identify the

important factors. An important factor is a factor that causes substantial changes

(effects) in the response when it varies.

5

User Guide to MODDE

In the screening stage one uses simple models (linear or linear with interactions), and

experimental designs that allows the identification of the factors with the largest effects

in the fewest possible number of experimental runs.

MODDE supports: Full Factorial, Fractional factorial, L-designs, Plackett Burman,

Rechtschaffner, Onion, and D-optimal designs for screening experiments.

With mixture factors, MODDE supports the classical axial design when the region is a

simplex.

Process factors: MODDE supports up to 32 factors in problems involving process

factors only.

Mixture factors: Up to 20 mixture factors are allowed in problems involving mixture

factors only.

Process and mixture factors: In problems involving both mixture and process

factors, up to 12 factors are supported.

Split objective is available only when there are both process and mixture factors

defined. Up to 12 factors are supported.

For more, see the Selecting model and design section in the Objective, model and

design chapter.

After screening, the goal of an investigation is usually to approximate the response by

a quadratic polynomial (model) in order to:

• Understand in more detail HOW the factors influence the response; get a

map of the system.

• Make predictions, optimize or find a region of operability.

MODDE supports: Three-level full factorial, central composite, (CCC and CCF), Box

Behnken, Rechtschaffner, Doehlert, Onion, and D-optimal designs for RSM

investigations.

With mixture factors, MODDE supports the modified simplex centroid when the

experimental region is a simplex.

For investigations with only qualitative terms no square or cubic terms can be

estimated. Creating RSM-designs for such investigations is therefore impossible.

Process factors: RSM designs are supported for up to 20 process factors

Mixture factors: Up to 15 mixture factors are allowed in problems involving mixture

factors only.

Special Cubic Model is supported for up to 8 mixture factors, and the full cubic for up

to 5 mixture factors.

Process and mixture factors: In problems involving both mixture and process

factors, up to 12 factors are supported.

6

Introduction to MODDE and experimental design

Split objective is available only when there are both process and mixture factors

defined. Up to 12 factors are supported.

For more, see the Selecting model and design section in the Objective, model and

design chapter.

Fit methods

The data collected by the experimental design is used to estimate the coefficients of the

model. The model represents the relationship between the response Y and the factors

X1, X2, etc.

MODDE uses multiple linear regression (MLR) or Partial Least Squares (PLS) to

estimate the coefficients of the terms in the model. MODDE recommends PLS when

the investigation has a high condition number.

With Multiple Linear Regression the coefficients of the model are computed to

minimize the sum of squares of the residuals, i.e. the sum of squared deviations

between the observed and fitted values of each response. The least squares regression

method yields small variances for the coefficients and small prediction errors. It is

important to note that MLR separately fits one response at a time and hence assumes

them to be independent.

PLS deals with many responses simultaneously, taking their covariances into account.

This provides you with an overview of how all the factors affect all the responses.

• PLS contains the multiple regression solution as a special case, i.e. with a

single response or different models, and a given number of PLS dimensions,

the PLS regression coefficients are identical to those obtained by multiple

regression.

• PLS has been extensively described in the literature and only a brief

description is given here. PLS finds the relationship between a matrix Y

(response variables) and a matrix X (model terms).

• The PLS model consists of a simultaneous projection of both the X and Y

spaces on a low dimensional hyper plane with new coordinates T

(summarizing X) and U (summarizing Y), and then relating U to T.

7

User Guide to MODDE

1. To well approximate the X and Y.

2. To maximize the correlation between X and Y in the projected space

(between u and t).

validation (CV), where PRESS (Predictive Residual Sum of Squares) is computed for

each model dimension. MODDE selects automatically the number of PLS dimensions

that give the smallest PRESS.

PRESS is then re expressed as Q2 = (1 - PRESS/SSY), where SSY is the sum of squares

of Y.

Results

Both MLR and PLS computes regression coefficients for each response. Thus Y is

expressed as a function of the X's according to the selected model (i.e. linear, linear

plus interactions, or quadratic).

8

Introduction to MODDE and experimental design

Analysis phase

All results of model fitting, by MLR or PLS are displayed, in the same way,

graphically and in lists.

Review the model fit by examining the following plots and lists:

• Summary of the fit, R2, Q2, Model validity, and Reproducibility for every

response.

• Coefficients and their 95% confidence intervals.

• ANOVA table.

• Effect plots for screening designs.

Assess the model adequacy further by reviewing the following plots:

• Normal probability plot of residuals

• Plot of residuals against fitted values, run order or other factors.

• Box-Cox plot to check for the optimal transformation of the response.

For PLS, summary of the fit by component and PLS score and loading plots are

available.

Use the fitted model to make predictions in the form of:

• Contour and rotatable 3D plots.

• Optimizer to find the “best conditions” for a desired profile of the responses.

This helps in the interpretation of the results and to find a region of

operability.

• Sweet Spot plot to draw a plot highlighting areas were the responses are

within the specified ranges.

• Design Space to estimate the area of operability or robustness.

9

User Guide to MODDE

Convention

Limitations in investigation names

The following characters cannot be used: = \ / : * “ ? < > |.

The length (including path) cannot be larger than 260 characters.

The following characters cannot be used: ~ * ? \ = [ ] and $.

The length cannot be larger than 50 characters.

Case sensitivity

MODDE is case insensitive. Lower or upper case in names will be displayed as

entered, but for all comparisons lower or upper case are considered the same.

In this manual we use the following syntax when referring to a command menu:

• Menu | Menu item. An example: File | New

• On the Menu menu, click Menu item. An example: On the File menu, click

New.

• Click Menu item on the Menu menu. An example: Click New on the File

menu.

designs

1. Box, W.G. Hunter and J.S. Hunter, “Statistics for Experimenters”, John

Wiley & Sons, Inc., New York (1978).

2. Box and N.R. Draper, “Empirical model-building and Response Surfaces”,

John Wiley & Sons, Inc., New York (1987).

3. C.K Bayne and I.B. Rubin, “Practical Experimental Designs and

Optimization Methods for Chemists”, VCH Publishers, Inc., Deerfield

Beach, Florida (1986).

4. Haaland, “Experimental Design in Biotechnology”, Marcel Dekker, Inc.,

New York (1989).

5. J.A. Cornell, “Experiments with Mixtures”, John Wiley & Sons, Inc., New

York (1981).

6. D.C. Montgomery, “Design and Analysis of Experiments, John Wiley &

Sons, Inc., New York (1997).

10

Overview

The symbol for MODDE is a gray cube with a pink M (above). The application icon is

a pink circle with a grey M inside (below).

Investigation

Experimental plans in MODDE are organized into investigations. You can think of an

investigation as a file folder containing all of the information related to a particular

experiment. When you select or open a given investigation you can access, display and

use all of its information. This information is organized in the following components:

factors, responses, constraints, inclusions, candidate set, model, design, worksheet,

analysis and predictions.

Managing investigations

Investigations are binary files saved by MODDE with the extension *.mip. When you

start a new investigation you select its name and destination directory.

You can open, save, save as, and delete investigations.

You can generate the fold over of investigations with fractional factorial designs or

Plackett Burman.

You can double-click a MODDE investigation (a *.mip file), in Microsoft Explorer, to

open that investigation.

11

User Guide to MODDE

MODDE does not save the fitted model. In order to review the results of the analysis

and use make predictions, you need to fit the model by clicking Analysis | Fit or

having Automatic fit turned on (default) in View | General Options tab General

when the investigation is opened. After the model has been fitted, you can use the

Analysis menu to create plots and list to review the model and fit and use the

Prediction menu to create prediction plots and lists.

All investigations from MODDE 3.0 and upwards can be opened in MODDE 9.0 (the

reverse is not true).

Organization

The MODDE window consists of a command menu bar and toolbars.

12

Overview

With the command menu bar you define or edit your factors and responses, specify

your objective and generate your model, design, and worksheet. After you enter the

results of the experimental plan (the response values) in the worksheet, you analyze

your data, display the results graphically and use the prediction menu.

Each component of the investigation i.e. factors, responses, objective, constraints,

inclusions, candidate set, model, design, worksheet, analysis and predictions is

displayed as a plot or list.

A detailed description of the command menu bar follows.

The command menu bar is located just beneath the title bar.

The menu bar consists of the menus File, Edit, View, Design, Worksheet, Analysis,

Prediction, Show, Window, and Help.

File menu

Under the File menu the following is available:

• New: Start a new investigation.

• Open: Open a MODDE investigation.

• Close: Close a MODDE investigation.

• Save: Saves the current investigation.

• Save As: Saves the current investigation under a specified path and name.

• Delete Investigation: Deletes the current investigation.

• Save Plot/List A : Saves the active plot or list.

• Revert: Reverts to the last saved copy of the investigation.

• Send by email: Sends the current Investigation by e-mail.

• Generate HTML report: Automatic report generator in HTML format.

• Complement Design: Select to complement your design by:

1. Fold over: Complements screening designs of resolution III or IV

by adding the fold over.

2. Estimate square terms in a screening design: complements the

design to support a quadratic model for a selection of factors.

3. Complement the design with D-Optimal to support a specified

model.

4. Screening to RSM Rechtschaffner: Complements the

Rechtschaffner screening design to the RSM Rechtschaffner.

5. Complement the Doehlert design.

6. Plackett Burman Super-Saturated to Plackett Burman:

Complements PBSS to the regular PB.

• Protect Investigation: Allows for a password protected investigation and

locking of investigation.

13

User Guide to MODDE

• Exit.

Edit menu

From the Edit menu you can:

• Undo

• Cut/Copy/Paste and Delete

• Select All

• Row insertion, addition

• Sort

• Edit the Model

• Edit the Reference Mixture

• Edit the Generators of fractional factorial designs

View menu

The following is available from the View menu:

• Toolbars: View/Hide Toolbars.

• Dockable windows: Show or hide dockable windows.

• Add to Favorites: Add the current plot or list to the Favorites dockable

window.

• Add to Report: Add the current plot or list to the current report generated by

MODDE.

• Full screen: Maximize the plot area.

• Investigation Options: Change the default plot and list options.

• General Options: Change the default options.

• Customize: Customize the toolbars.

Design menu

Use the Design menu for the following:

• Factors and Responses: Define and modify factors and responses

• Constraints and Inclusions: Define constraints and inclusions

• Objective: Specify and modify objective, model and design

• D-Optimal: Generate and evaluate D-Optimal designs, open the candidate

set for viewing or editing, evaluate onion plots.

• Design wizard: Open the design wizard

14

Overview

Worksheet menu

Use the Worksheet menu to:

• Edit the Worksheet.

• Set Run Order.

• Open the Curvature Diagnostic Plot.

• Create the Scatter plot.

• Open the Histogram plot.

• Open the Descriptive statistics plot and list.

• Open the Correlation plot or matrix.

• Open the Replicate plot.

Analysis menu

Use the Analysis menu to:

• Evaluate the design

• Analyze each response in the Analysis Wizard

• Select Fit Method (MLR, PLS etc)

• Fit model by MLR or PLS

• Extract the Next Component: Add a PLS component

Review the fit

Results displayed as tables, lists, or graphs

• Summary of the fit

• PLS Summary

• PLS Plots

• Coefficients and Effects

• VIP Plot (PLS only)

Investigate diagnostics

• Residuals Plots

• Box-Cox Plot (MLR only)

• ANOVA

Prediction menu

With the fitted model you can click the Prediction menu and:

• Display contour plot from the Contour plot wizard including mixture

contour plots and response surface plots (3D).

• Create prediction plots.

• Make predictions in the Prediction spreadsheet.

15

User Guide to MODDE

• Use the Optimizer.

• Estimate the Design Space.

Show menu

Use the Show menu to display the following: objective, design matrix, design

region, confounding, model, D-Optimal summary, and reference mixture.

Window menu

Use the Windows menu to access the standard window commands.

Toolbars

Click Toolbars from the View menu to display or hide the following:

1. The Standard toolbar consist of command buttons for immediate action and

menu commands.

2. The Spreadsheet toolbar displays all spreadsheets.

3. The Plot toolbar is for zooming in and out on plots, reading plot values and

coordinates, and drawing regression lines.

4. The Model toolbar (model information) summarizes the investigation. The

summary consists of the number of factors and responses, the number of

runs, the Objective, Design and model and the Fit method.

5. The Window toolbar displays buttons for arranging the open windows and

Full Screen.

6. The Status bar displays an explanation to the button that the mouse points to.

These toolbars are described in detail in the View chapter.

All plot and lists in MODDE have a context sensitive menu that appears when you

right-click the plot or list. This menu includes commands such as Copy, Print, Save,

Add to Favorites, Properties etc.

All plots can be customized by double-clicking the plot or right-clicking the plot and

then clicking Plot Settings.

For more on customizing plots and lists, see the Plots and lists chapter.

16

File

Introduction

Use the File menu to create, open, close, save, and delete investigations, save active

plot or list, revert to last saved investigation, send the current investigation by e-mail,

generate a HTML report, complement the design, lock or password protect the

investigation, for print purposes and to close MODDE.

New

To create a new investigation click File | New.

This first page allows you to:

• Enter the name of the new investigation.

• Select the location where to save.

• Select the design type: Traditional Designs or Advanced Designs including

RED-MUP and D-Optimal designs from an imported candidate set or scores

from a SIMCA-P model.

• Select to import a design from file.

• Enable the audit trail by selecting the Enable the Audit trail check box.

17

User Guide to MODDE

Click Next to open the design wizard. The design wizard guides you through the

design phase, from factor and response definition, objective, design and model

selection, up to the generation of the worksheet.

For a detail description of the design wizard see the Design Wizard chapter.

Traditional designs

When you create a new design Traditional Designs is by default selected. The

traditional designs include classical designs such as factorial, Plackett Burman, L-

designs, Rechtschaffner, and also D-Optimal and onion designs. For details, see the

Design appendix.

Advanced designs

When you select Advanced Designs and click Next the Advanced Designs box is

opened with the available designs:

• RED-MUP.

• Onion or D-Optimal designs from imported candidate set.

• Multivariate onion or D-Optimal designs from scores.

18

File

RED-MUP

RED-MUPs are designs available for 96 (8x12), 384 (16x24), and 1536 (32x48) runs.

The designs are built from sub-designs.

To create a RED-MUP:

1. In the first page of the design wizard click Advanced Designs and then

Next.

2. Click RED-MUP and then Next.

3. Define all factors for the two sub-designs and then click Next.

4. Define the responses and then click Next.

5. Select the objective for both the vertical and the horizontal designs:

Screening or RSM.

6. Leave the factors that should be included in the vertical design with fewer

runs to the left.

7. Move the factors that should be included in the horizontal design to the right.

8. In this page you can also select the number of plates used, and if applicable

the plate factor(s) that contain plate information.

9. Select the desired plate size in the Plate-Size box and optionally select the

Plate/Block factor interactions check box.

10. Click Next to select the vertical design then click Next again to select the

horizontal design. MODDE adds center points when the selected design does

not fill up the plate size.

Note: Some special RED-MUP designs, that aim to aim to make better use of

the plate, are available for the 96 well plates (8 x 12).

19

User Guide to MODDE

To create an onion design from an imported candidate set other than from SIMCA-P:

1. Click Onion or D-Optimal designs from imported candidate set on the

Advanced Designs page.

2. Click the Browse button to find the file holding the candidate set. Many file

types are supported.

3. Click Next to open the Import Candidate Set dialog for defining the correct

factor names, experiment names, and data.

4. Click OK to open the factor definition page in the design wizard. Note that

when the candidate set has been imported in this way you cannot modify or

add factors in the Define factors page.

5. If you want to place constraints on the factors, select the Place constraints

on the experimental region check box and click Next to open the Define

constraints... page.

Note: Only regular factors are imported here. If your candidate set contains

qualitative or formulation factors you have to enter the factors and settings in

the Factor Definition and import the candidate set from the D-Optimal page.

The designs available here are Onion and D-Optimal designs. Onion is only available

when there are enough experiments in comparison with the number of factors. For

more on Onion designs, see the D-Optimal Onion designs section in the Design

appendix and the Tutorial.

Multivariate designs

To create a design using the scores from a SIMCA-P project as factors:

1. On the Advanced Designs page click Multivariate onion or D-Optimal

designs from scores.

2. Click the Browse button under Import scores (factors) from a .usp created

in SIMCA-P 9 or higher to select the SIMCA-P project.

3. SIMCA-P opens automatically. Return to MODDE without closing SIMCA-

P.

4. Select the model from the Model box and click Next to import the factors

from SIMCA-P. The scores are then automatically loaded from the SIMCA-

P .usp-file, and the candidate set for the onion design comprised of all

objects (rows) in the workset of the SIMCA-P model is selected as the basis

of the onion design.

later needs to be installed.

When importing the scores of a SIMCA-P project as factors in MODDE, the only

designs available are the D-Optimal and the Onion designs.

available. For the functionality described here the type of SIMCA-P is not

relevant.

For more on Onion designs, see the D-Optimal Onion designs section in the Design

appendix and the Tutorial.

20

File

If you have already done experiments and want to import them into MODDE for

analysis:

1. Click File | New.

2. Select the Import design from file check box.

3. Click Browse and select the file to import.

4. Click Next and specify what is what in the Data Specification dialog.

there are formulation factors in the imported design, you have to manually

alter the factor type (starting with formulation factor you want to end up last)

in the factor definition page.

Open

To open a MODDE investigation, click Open on the File menu. In the Open-dialog

select the directory and you get a list of all the MODDE Investigation Projects (*.mip)

present in that directory. Double-click the desired investigation to open it or mark it

and click Open.

To open investigations created in MODDE version 4 and earlier, switch to Old

MODDE Files (*. ini) in Files of type to view them, mark the .ini and click Open to

convert it to the current format.

To save the current investigation, click Save on the File menu.

To save the current investigation at a different location or with a different name, click

Save As. In the Save As dialog that opens, enter the new name and location of your

investigation. MODDE switches to the "new" investigation.

Delete investigation

To delete the current investigation click Delete Investigation on the File menu. It is

not possible to delete any other investigations than the current from MODDE.

For read-only investigations Delete Investigation is unavailable.

Save plot/list as

Plots can be saved as Enhanced Meta Files (*.emf), Bitmap files (*.bmp), Jpeg files

(*.jpg) or PNG files (*.png). Lists can be saved as Text files (*.txt) or Web Pages

(*.htm, html).

21

User Guide to MODDE

To save a plot, display it, make sure it is active and then click File | Save Plot As. The

Save Format dialog is displayed.

In the dialog check the Keep aspect ratio box to keep the proportions of the plot as on

the screen or according to a predefined plot size.

In the Plot size box you can choose between Custom, 640x480(VGA),

800x600(SVGA), 1024x768, Original size.

The predefined formats are useful primarily when displaying MODDE plots on a small

screen.

To save a list, display it, make sure it is active and then click File | Save List As. The

Save dialog is then displayed.

In the Save as type box, select file type .txt or .htm/html.

Revert

To revert to the investigation as when it was last saved, click Revert on the File menu.

Send by E-Mail

To send an investigation by e-mail click Send by E-Mail on the File menu. Note that

the investigation sent is the current investigation as it was last saved.

MODDE has an automatic report generator. Create a new report by clicking Generate

HTML Report on the File menu or right-click a plot or list and then click Add to

Report.

The report generator can use the MODDE default template or any template previously

saved. All formatting functionality is available for writing the text. Plots and lists can

be added to the report at any time, as placeholders or actual plots and lists.

22

File

A placeholder tells MODDE the desired item to fill from the current investigation

when you click Update Report. If you add plots and lists as placeholders and save the

template, you can generate a report in the desired format, for any investigation, by

selecting the saved template and clicking Update Report.

For details, see the Report Generator chapter.

Complement design

To complement a design is to make a new investigation consisting of the design, or a

part of the design, of the current investigation plus its complement. See also the section

Inclusions vs. complement design in the chapter Constraints and Inclusions.

Use Complement Design when you want to:

• Estimate separately a set of terms (interactions, or main terms and

interactions) that were confounded in a Resolution III or IV fractional

factorial design.

• Complement a screening design to an RSM design supporting the full

quadratic model.

• Complement a screening design to estimate selective curvature effects.

• Add additional experimental runs to improve the quality (i.e. the condition

number or G-efficiency) of an existing set of experiments.

• Use already performed experiments in a Doehlert design to set up a new

Doehlert moving the center of the design or add a factor. For more on the

Doehlert designs see the Design appendix.

• Use already performed experiments in a Super-Saturated Plackett Burman

design to add experiments resulting in a regular Plackett Burman design.

To complement the current design, click Complement Design on the File menu and

the Complement Design Wizard is opened. Click the desired complementing method

and click Next.

23

User Guide to MODDE

You can complement your design using the following complementing methods:

Fold over: With screening fractional factorial designs of resolution III and N (number

of runs) equal to 8 or 16, it is usually recommended to complement by fold over.

Estimate squares of selected factors in factorial designs: If the screening design

indicates the presence of curvature, you may want to estimate the square terms in

selected factors or you may want to upgrade your design to a full RSM in these

selected factors.

D-Optimal: If you want to upgrade the design to support a customized model, or if

your investigation contains mixture factors, select D-Optimal.

Doehlert: When you have performed a Doehlert design and want to move the design

center or add a factor.

Screening to RSM Rechtschaffner: When you have performed a screening

Rechtschaffner design.

Plackett Burman Super-Saturated to Plackett Burman: When you have performed

a PBSS.

Fold over

When you choose to complement your design with fold over MODDE makes a new

investigation consisting of the design of the current investigation plus its fold over

(complement). The fold over design has as many experimental runs as the original

design.

Fold over designs are available for fractional factorial design of resolution III or IV

and Plackett Burman designs.

With the complete design (original + fold over), all main effects are clear from 2

factors interactions. With resolution III and IV designs MODDE automatically adds a

block factor. You may remove the block factor from the model in the menu Edit |

Model.

To fold over your design:

1. Click File | Complement Design.

2. Click Fold over and then click Next.

3. Enter the name and location of the new investigation. It is recommended to

add an additional center point to detect a shift in the mean.

4. Click Finish and the new investigation opens.

To complement your design with Estimate square terms in a screening design, select

the factors to include in the quadratic model. The unselected factors are excluded from

the model and set in the worksheet on their averages.

For this complementing method to work well the original design has to be of resolution

V or the collapsed design in the selected factors has to be a full factorial (as in the case

above). The design is complemented to a CCF by adding the face center runs, or to

CCC when entering a star distance > 1.

24

File

1. Click Estimate square terms... and click Next.

2. Mark the factors for which to estimate the square terms.

3. Optionally change the star distance. Click Next.

4. Enter the name, location of the new investigation and number of

additional center points.

5. The model has been updated with the squares of the selected factors.

D-Optimal

Complementing a design d-optimally is the most flexible way of complementing a

design.

After clicking File | Complement Design:

1. Click D-Optimal and click Next.

2. Click Edit Model and specify the new model. MODDE recommends the

number of additional new runs based on the specified model, to ensure the

proper degrees of freedom.

3. Enter the name and location of the new investigation and click Finish. The

D-Optimal wizard guides you in generating the new investigation. Here the

original design runs in the selected factors are used as inclusions and the

displayed Design Runs in the D-Optimal page includes the inclusions. The

additional new runs are selected D-Optimally to support the selected model.

25

User Guide to MODDE

Mixture factors

Complementing the design d-optimally with mixture factors, after giving the name and

location of the new investigation, the D-Optimal wizard opens. Select the new model.

The displayed number of runs includes the original design runs. Click Next, the wizard

guides you in generating the new investigation.

Complementing a design d-optimally with mixture and process factors, after giving the

name and location of the new investigation, the D-Optimal wizard opens. The

objective is set to Split Objective. Click Settings | Model and select a new model for

both the process and mixture factors, and if you want interactions between them.

The displayed number of runs includes the original design runs as inclusions. Click

Next; the wizard guides you in generating the new investigation.

26

File

Complement Doehlert

Doehlert designs can be complemented by expanding the design region or adding a

factor.

To complement a Doehlert design, click Doehlert in the Complement Design Wizard

and click Next.

• Leaving the default Select new center selected and selecting one of the

experiments of the design as the center of a new Doehlert design.

• Selecting Add factor and typing the name of the new factor and typing the

Center and Range in the respective boxes. The value you type in Center is

the value that will be entered in the design for the already performed

experiments, for the new factor.

27

User Guide to MODDE

Select how to complement, click Next, enter the name, location of the new

investigation and number of additional center points, and then click Finish to generate

the new investigation.

The design is complemented by adding the star points resulting in a 3-level

Rechtschaffner design.

To complement your screening Rechtschaffner design to an RSM Rechtschaffner

design:

1. Click File | Complement Design.

2. Click Screening to RSM Rechtschaffner and then click Next.

3. Enter the name, location of the new investigation and number of additional

center points, and then click Finish to generate the new investigation.

This option is only available for screening Rechtschaffner designs.

The design is complemented with runs adding up to a regular Plackett Burman design.

To complement your PBSS to regular Plackett Burman:

1. Click Plackett Burman Super-Saturated to Plackett Burman in the

Complement Design wizard.

2. Click Next.

3. Enter the name, location of the new investigation and number of additional

center points and click Finish to generate the new investigation.

This option is only available for Plackett Burman Super-Saturated designs.

28

File

Protect investigation

When you click File | Protect Investigation you can select to Encrypt/Password

protect or Lock the investigation.

Enter a password and the investigation is encrypted and password protected. This

investigation can now be opened only with the selected password.

To remove the encryption, click File | Protect Investigation | Remove Encryption

and enter the password.

Lock investigation

Click File | Protect Investigation | Lock to lock the investigation. Locked

investigations are automatically fitted when opened. Any plot or list can be displayed,

but you cannot make any changes in the investigation. The investigation becomes

'Read only' with the exception of the prediction spreadsheet. If you click Permanently,

unlock on Save As, a copy of the investigation can be unlocked by using File | Save

as. When Permanently is selected the investigation cannot be unlocked.

It is possible to also encrypt and password protect the investigation by selecting the

Encrypt / Password Protect investigation check box. The investigation is then

encrypted. This check box is optional; select it only if you want the investigation to be

password protected.

29

User Guide to MODDE

Print Setup

Change the page orientation, printer, and printer settings by clicking Print Setup on

the File menu.

Plots are preferably printed with Orientation Landscape.

The print menu is only valid for an active list or plot.

Print Preview

On File, click Print Preview and the current window can be view as it will be printed.

Print Preview is only available when there is an open plot or list.

Print

Print is only available for the active plot or list. With the plot or list active, use one of

the following manners to print:

• On File menu click Print.

• Right-click the plot or list and click Print.

• Press CTRL+P.

When printing plots, the plot is by default scaled to look exactly as on the screen.

The lists and plots in MODDE can also be printed from another Windows application

after first being copied through the clipboard to that application.

When clicking Print with a plot active, the Print Format dialog opens. For more on

the dialog, see the Save plot/list as section in this chapter.

Exit

Click Exit from the File menu to close the MODDE program.

30

Edit

Introduction

Use the Edit menu to undo, cut, copy, paste, delete, select all, add experiment/insert

rows/add factor/add response, sort, edit model, edit reference mixture, and edit the

generators.

Undo

Click Edit | Undo or press CTRL+Z to undo changes in MODDE. Such changes can

be changing values or text (factor name for instance), cutting, copying, pasting,

deleting, sorting in spreadsheets, or editing the model.

Undo is activated after changes in:

• The spreadsheets Worksheet, Factors, Responses, Constraints, Inclusions,

Prediction, and Optimizer.

• The model terms in the Model Properties dialog (Edit | Model) or by

clicking the Exclude-button and marking model terms to exclude in a plot.

• Plots displaying experiments (observations) by clicking the Exclude-button

and marking model terms to exclude in a plot.

Undo remembers the ten last actions in the worksheet, in the edit model dialog, and in

plots displaying experiments (observations) or model terms.

Undo works on the active plot or spreadsheet.

Note: After editing the values in worksheet the undo feature of plots

displaying experiments stops working as manual changes in the worksheet

empty the undo-memory for such plots.

Cut (CTRL+X), Copy (CTRL+C), Paste (CTRL+V), Delete (pressing the Delete-key

on the keyboard), and Select All (CTRL+A) are standard Windows commands. They

can all be used in all MODDE spreadsheets. Copy and Select All can be used in all

MODDE lists and tables.

31

User Guide to MODDE

The menu item Add Factor, Add Response, Add Experiment, Insert Rows on the

Edit menu is context sensitive and available for all spreadsheets although in slightly

different forms.

When the factor spreadsheet is active Add Factor is available as the menu item, when

the response spreadsheet is active Add Response is available, when the worksheet is

active Add Experiment is available, and when any other spreadsheet is active Insert

Rows is available. The shortcut menu, displayed after right-clicking a spreadsheet, also

includes this command.

When adding a factor or response the respective dialog is opened.

When selecting Add Experiment or Insert Rows the number of rows marked are

inserted shifting all rows after down, except for in the Worksheet where new rows are

always added last.

Sort

Sorting is available for the worksheet, constraints, inclusions, candidate set, and

predictions list.

To sort a list, right-click and click Sort or click Edit | Sort.

In the dialog, select the column to sort the list by from the Select the column to sort

box and click the Add Column button. The column appears in the list with the default

sort type. Click the sort order you want under Sort selected, Ascending or

Descending.

If a column of the spreadsheet is marked when sort is activated it becomes, by default,

the primary column to sort by.

Add more columns to select secondary and tertiary etc., columns to sort by. Specify for

each column the sort order. Use the Remove button to remove a column from the sort

list or drag the item outside the list.

The sorting starts when OK is clicked.

32

Edit

Sorting the candidate set is useful if you want to exclude some rows that correspond to

undesirable runs.

A candidate set imported to create an onion design cannot be sorted.

To sort the candidate set, click Edit | Sort or right-click and click Sort.

33

User Guide to MODDE

In the Model Properties page you can add or delete model terms such as linear,

interaction, square, and cubic terms. Use Edit | Model to add uncontrolled factors.

Uncontrolled factors are by default not included.

Model

Click Edit | Model or the Edit Model button to modify the model. The Model

Properties dialog opens on the Model Terms page and you can edit the model by

adding or deleting terms.

Use the For Response box to specify for which response you want to alter the design,

if not for all.

A quadratic term is represented by factor1*factor1 and a cross term (interaction) by

factor1*factor2. A cubic term is represented by factor1*factor1*factor1 and a three

factor interaction is represented by factor1*factor2*factor3.

34

Edit

Add terms

To add terms in the Model Properties dialog use one of the following methods:

1. Mark the factors to the left and click the relevant buttons Factors,

Interactions, Squares, or Int. & Sq. (interactions and squares)

2. Double-click a factor or mark it and click the left arrow =>; note that it is

added in the New term field. Continue until the new term is fully defined

and click the second arrow => adding the term to the right side.

3. Position the cursor in the New term field and type the abbreviation of the

factors to include using ‘*’ to separate them.

4. To add three factor interactions, mark the three factors, click the left arrow

and then on the right =>. Or type the abbreviations in the New term field.

Remove terms

To remove terms in the Model Properties dialog, mark the term(s) and click the

Remove button in the dialog.

Undo

The Undo button becomes active after making a change in the model. Clicking Undo

only reverses the last change in the Model Properties dialog.

Reset

Click the Reset button to reset the model to the default model.

The Enforce the mixture model hierarchy check box is available in the Model

Properties dialog, and by default selected when there are formulation factors in the

model. This means that a group of terms are treated as a unit, and terms cannot be

removed individually. If the Enforce the mixture model hierarchy check box is

cleared, the terms can be removed individually but the model can only be fitted with

PLS.

35

User Guide to MODDE

Reference mixture

In Model Properties, click the Reference Mixture tab to switch to the reference

mixture page.

Use this dialog to change the default reference mixture of a Cox model. The reference

mixture is used to impose constraints on the coefficients of the Cox mixture model.

The default reference mixture is the centroid of the experimental region. If the region is

a regular simplex with q mixture factors, the centroid is the point with coordinates 1/ q,

1/ q,....1/ q. If the experimental region is irregular, the centroid is the constrained

centroid of the irregular constrained region.

Click the Reset button to restore the reference mixture to the default values.

36

Edit

Generators

Click Generators on the Edit menu to open the Generators dialog.

A generator is a column of signs in the extended design table of the basic factors that is

used to introduce additional factors in the fractional factorial designs.

For example, let us assume that 5 factors are to be investigated in 8 runs. The extended

design table is the table of the full factorial in three factors (basic factors), symbolically

named a, b and c plus the additional columns for all the interactions. Any

interaction column can be used to introduce additional factors. Let us say that to

introduce the 2 additional factors, d, and e, the column of signs of a*b and a*c are

selected. Then d = ab and e = ac are the generators of the fractional factorial design 25-2

(see Box, Hunter and Hunter for further information).

When MODDE generates fractional factorial designs the default generators used are

those published in Box, Hunter and Hunter.

Editing and/or changing the default generators of a design is done in order to estimate

selected interactions in a fractional factorial design of resolution III or IV instead of the

default.

MODDE supports the choice of positive or negative generators.

To edit a generator, click in the generator column of the desired row, and enter a new

generator. The confounding, in the confounding column, is updated.

When you click OK, your design and worksheet are deleted and new ones are

generated.

37

User Guide to MODDE

worksheet

For fractional factorial designs of resolution III, IV, and V it is possible to edit the

model and/or generators before creating the worksheet by clicking Settings | Edit

Model in the page entitled Select the model and design in the Objective page or

Design wizard.

See the chapter Objective, model and design for more.

38

View

Introduction

Using the View menu you can show/hide the toolbars, show/hide the dockable

windows Analysis Advisor, Audit trail, Favorites, Output, and Notes, and execute the

commands: Add to Favorites, Add to Report, make window Full screen, change the

default investigation options, change the general options, and customize toolbars,

commands and options.

Toolbars

On the View menu, click Toolbars to view the available toolbars. Click the name of

the toolbar to show or hide it. All toolbars can be floating or docked beneath the menu

bar.

Clicking a button on a toolbar will perform a certain task. As a guide to what happens

when a button is clicked, a short text will appear when you hold the pointer over a

button. Text will also appear in the Status bar at the bottom of the screen.

You can customize all toolbars according to your wishes. For more, see Customize

later in this chapter.

Standard toolbar

The Standard toolbar consists of a number of command buttons and the response box.

The buttons listed below are available.

39

User Guide to MODDE

The buttons for File | New, Open, Save, Print, Print Preview, Edit | Cut,

Copy, Paste, and Undo are all standard Windows buttons and work as in other

Windows applications.

Click the Objective button to open the design wizard. If none or too few factors

are defined the design wizard opens on the factor page, otherwise it opens on the

objective page where you select the objective of the design.

Click the Worksheet button to open the worksheet for editing or viewing.

Edit model

Click the Edit model button to edit the model or reference mixture when

applicable. Model Terms is the default page opened. To edit the reference mixture,

click the Reference Mixture tab.

The MODDE ANOVA table, the coefficient plot, normal probability of residuals plot,

observed vs. predicted plot, and the Analysis Wizard can be opened by clicking the

appropriate buttons.

Response box

Use the Response box to change responses in the active plot or list.

40

View

The last response check box cannot be cleared. To get single selection when switching

between responses using the response combo box, hold down the CTRL-button for

single selection functionality.

To open or close the favorites window use one of the following methods:

• Click Dockable Windows on the View menu, and then click Favorites.

• Press CTRL+T.

Show or hide the Analysis Advisor window is available by clicking View | Dockable

Spreadsheet toolbar

The Spreadsheet toolbar contains buttons for all MODDE spreadsheets. In the order of

the toolbar: the factor, response, worksheet, prediction, and optimizer spreadsheets.

Plot toolbar

The Plot toolbar holds buttons that enable you to select type of marking to be used

when marking areas in plots, insert labels or text in plots, zoom in and out, read

positions in graphs, do linear regression in scatter plots, get information about

observations (experiments) or variables (model terms or responses), or exclude

experiments and model terms.

The tools are activated when you click them.

41

User Guide to MODDE

Arrow

The arrow button is used to select which type of marking to use.

Click the small arrow to the right of the arrow and click the type of marker from the

menu.

• Free Mark: Allows marking to take any shape.

• Block Mark: Marks in a rectangular shape.

• X Mark: Vertical bar.

• Y Mark: Horizontal bar.

• No Mark: The arrow works as a data reader displaying the number, name,

and value of plotted data points when hovering near the data point symbol.

Text

Click the T-button to insert a text-field in a plot. The field can contain text or a

value and be inserted in all plots but the contour, response surface, sweet spot, and 3D

scatter plots.

Open the plot, click the T-button, click where you want to position the text-field, type

the text or numbers, and then press ENTER or click somewhere else in the plot.

MODDE will continue to open a new text-field each time you click until the T-button

is pressed again. This label can be removed by clicking it again and emptying the cell.

Zoom in

Click the arrow near the Zoom in button , and select the type of zoom from the

drop down menu:

• Scale xy: Magnifies a rectangular region

• Scale x: Expands the x direction

• Scale y: Expands the y direction

• Subplot: Magnifies a subplot in a multiplot.

And then mark the desired region of the plot to zoom.

Zooming in a scatter 3D plot is described in the Zoom and rotate section in the Plots

and lists chapter.

Zoom out

Click the Zoom out button to revert zoom to original scale in the steps taken

when zooming.

Coordinate Reader

The coordinate reader displays the coordinate values of any point of the plot area.

Click the Read coordinate values button and mark the point of interest and the

coordinate reader will display the coordinates at that point.

42

View

Regression line

The regression line and equation can be displayed for any 2D scatter plot in MODDE.

Open a scatter plot, for instance the Observed vs. predicted plot, and click the

Rotate

For rotating a scatter 3D or response surface plot see the Zoom and rotate section in

the Plots and lists chapter.

To interactively exclude model terms or experiments:

1. Open a plot displaying model terms or experiments.

3. In the plot mark the term(s)/experiment(s) you want to exclude from the

model.

MODDE removes the terms/experiments from the model of the currently displayed

response ONLY and automatically refits the model.

43

User Guide to MODDE

Model toolbar

The Model toolbar displays the summary of the current investigation.

1. Factors: The total number of factors (the number of uncontrolled).

2. Responses: The number of responses.

3. Runs: The number of runs included in the design (not counting rows set as

'Excl' in the worksheet).

4. Objective: The objective, Screening, RSM or Split Objective.

5. Design: The selected design and model.

6. Method of Fit: MLR, PLS etc.

Window toolbar

The Window toolbar commands are general Windows commands and work

accordingly. Click the Window toolbar commands Full screen (press the F9 key to get

back to regular), Cascade Windows, Tile Windows horizontally or Tile Windows

vertically to arrange the windows.

Status bar

The Status bar displays the explanation to the command button that the mouse points

to.

Dockable windows

MODDE has five dockable windows: analysis advisor, audit trail, favorites, output,

and notes.

Open the dockable windows by clicking Dockable Windows on the View menu and

then clicking the desired dockable window.

When you click the Auto Hide button the window will hide away. If you then

hover with the mouse over the dockable window name, it slides out and becomes

visible. If you want your window to stay visible after it has slid out, just click the pin

button again .

44

View

Analysis advisor

The Analysis Advisor is automatically activated after fitting an investigation. The

advisor explains the analysis plots and results.

Show or hide the Analysis Advisor window is available by clicking View | Dockable

Audit trail

When turned on, the audit trail logs changes done to the investigation.

To open or close the audit trail, click Dockable Windows on the View menu, and then

click Audit Trail.

For more, see the Audit trail subsection in the Changing the default options using

Investigation Options section.

Favorites

To open or close the favorites window use one of the following methods:

• Click Dockable Windows on the View menu, and then click Favorites.

• Press CTRL+T.

lists, and plots and can be extended and modified as desired.

Execute a command, or open a plot or list by clicking it. When settings must be

selected, a dialog window opens, select the settings and click OK. Plots and lists are

displayed with its selected settings.

Not all plots in MODDE are available to be added to the favorites as plots. Generally

plots that are displayed for the first response by default, and do not require a dialog for

the selection of settings, can be added to the favorites as plots. Other plots requiring the

selection of settings from a dialog can preferably be added to the favorites as

commands. For instance, if the Contour plot wizard is added as a command, selecting it

from the favorites opens the dialog and settings can be selected.

45

User Guide to MODDE

Adding favorites

To add an open plot or list to favorites, right-click it and click Add to Favorites or

select it from the View menu. Note that this adds the plot with the selected settings to

the favorites.

You can also right-click in the Favorites window and select Add Command to

Favorites.

Favorites window

Right-clicking the Favorites window opens the menu below. A description of the

menu items follows.

Adding favorites

To add an open plot or list to favorites, right-click it and click Add to Favorites or

select it from the View menu. Note that this adds the plot with the selected settings to

the favorites.

You can also right-click in the Favorites window and select Add Command to

Favorites.

46

View

To execute all commands in a folder, right click the folder and select Open All Items

in Folder.

For example with the Analysis folder:

Opening all items in the folder displays the coefficient plot and observed vs. predicted

plot for the first response tiled.

Click Treat Folder as Item to treat the folder as an item. The folder is then displayed

as an item:

Click it to open all the items. This gives the same result as Open All Items in Folder

but with a single click.

47

User Guide to MODDE

Rename

All folders, commands, plots, spreadsheets, and lists can be renamed according to your

wishes by right-clicking it and clicking Rename.

Delete

All items in Favorites can be deleted by right-clicking the item and clicking Delete, or

marking it and pressing the DELETE-key on your keyboard.

Add command to favorites

A number of commands can be added to favorites. The commands from the menu and

toolbars are displayed on the left, under Categories, and the items available under that

command are displayed to the right.

For example, if you click Prediction under Categories, all the commands on the

Prediction menu are displayed to the right.

Click a command, for example Prediction Plot Wizard, and click Add. The command

is added to the Favorites window. You may continue adding commands, and when

done, click Close.

48

View

When a command has a submenu, double-click it to view the submenu items. For

example Analysis | Residuals, double-click Residuals and the submenu of four items

it displayed. Select the desired one and click the Add button.

It is convenient to group commands in folders, and automatically execute all the

commands in the folder in sequence. To create a folder in Favorites, right-click and

click New Folder.

The created folder is default named 'New Folder'; change the name as desired, for

example to 'Residuals Plots'.

To move favorites to the Residuals Plots folder, use the drag-and-drop feature.

49

User Guide to MODDE

The Favorites window configuration can be saved as an .xml-file.

Note: When importing a favorites file, the new favorites will replace the

current favorites. If you want to keep you current configuration and switch

back to it later, export to file before importing.

To save the current favorites configuration to file:

1. Right-click the Favorites window.

2. Click Export.

3. Enter the name and location in the Save As dialog,

4. Click Save.

To import favorites from .xml-file:

1. Right-click the Favorites window.

2. Click Import.

3. Browse for the file in the Open dialog.

4. Click Open.

Restoring favorites

To restore Favorites to the MODDE default, click General Options on the View

menu, click the Restore tab and click the Restore button after Restore favorites.

Output

The output window is a log book of the session. All MODDE messages and actions are

recorded in the Logbook.

Open the output window by clicking Dockable windows on the View menu and

clicking Output.

To make this window smaller, pull the top and it will remember its size. Double-click

the window caption to make it floating or make it dock.

Hint: While dragging the window hold down the CTRL key. It won't dock if

you are close to the frame of the main frame window.

Notes

In Notes you can record your own notes concerning the investigation. You can

paste MODDE plots and lists, and embed objects such as Microsoft Excel

spreadsheet, word, etc. All these commands are available by right-clicking the window.

This file can then be saved as .rft (Rich Text Format) and read directly by a word

processor with all plots.

Open the notes window by clicking Dockable windows on the View menu and

clicking Notes.

50

View

Add to Favorites

Plots and lists can be added to the Favorites dockable window. For more, see the

Favorites section earlier in this chapter.

Add to Report

Plots and lists can be added to the HTML report generator. For more, see the Report

Generator chapter.

Full Screen

You can use the Full screen command to maximize the plot area. Full screen can be

toggled on and off using F9 and is available from the Window toolbar as well as from

the View menu. When Full Screen is selected from the menu, the Window toolbar is

automatically opened as a floating toolbar.

51

User Guide to MODDE

Options

All plots and lists in MODDE have a context sensitive menu, most of them with the

menu item Properties. The settings of the property page are inherited from the

Investigation Options.

To change the options of the active plot or list, see the chapter Plots and Lists.

To change the default options for the current investigation click View | Investigation

Options and select the option to change.

Plot labels

Select the plot label to display as default on plots displaying the experiments, for

example residual plots, by clicking None, Experiment Number, Experiment Name,

or Run Order taken from the worksheet.

Number format

Click the number of decimals 2 - 5 or the scientific (E) format in lists by clicking

Auto, .00, .000, .0000, .00000, or Scientific.

When exporting unscaled coefficients to use in other applications, use the scientific

format to get maximum precision in the coefficients.

52

View

Audit trail

When the Audit Trail is turned on each investigation in MODDE has a separate audit

trail. Each audit trail consists of one or more sessions that in turn consist of events. A

new session is started and appended to the audit trail when an investigation is opened,

and ends when the investigation is saved.

In addition to logging events, MODDE logs information about the user, and date and

time of the events.

To view the audit trail, click the Audit Trail tab in the Output / Notes / Audit trail

dockable window. If this tab is not shown, display it by clicking View | Dockable

Windows | Audit Trail.

By default the audit trail is disabled. To turn it on, select the Log events in the Audit

Trail check box in Investigation Options, tab Audit Trail or select Enable the Audit

Trail on the first page of the design wizard when creating a new investigation.

To empty the audit trail, use the Clear Audit Trail button.

Click the Prompt new users to edit the extended user information box to demand

new users to enter more information than just the user name.

Click the Edit button to change the extended user information.

Click the Save button to save the current version of the audit trail separate from the

investigation, in XML format.

Administrators can disable the entire audit trail page in general options and control the

behavior of the audit trail, i.e., always have it on or off and strict audit trail (forced

saving of the audit trail). For instructions on how to disable the audit trail options, see

the knowledge base at www.umetrics.com.

MODDE uses Internet Explorer 5 functionality to display the audit trail.

53

User Guide to MODDE

Specific actions the MODDE audit trail logs are:

* Factors (adding, modifying, deleting), displaying all details about the factor after the

change

* Responses (adding, modifying, deleting), displaying all details about the response

after the change

* Constraints (modifying, deleting)

* Reference Mixture

* Objective

* Generators

* Design

* Model

* Worksheet, every change of every cell

* Registers when a digital signature in the Audit trail is incorrect.

* Clearing of the Audit trail (View | Investigation Options, Clear Audit trail).

* Activation and deactivation of the Audit Trail.

* Changes in the Audit Trail extended user information.

Strict Audit Trail also logs:

* Open and Close of Investigations

* Printing of plots and lists

* Saving of plots and lists to disk

Alpha level

Select the significance level by clicking 1%, 5%, or 10% to be used in the Lack of

fit (LoF) plot. The default is 5%.

54

View

Coefficients

In MODDE you can select the type of coefficients you want to display. The default is

Scaled and centered coefficients.

With multiple linear regression, MLR, the scaled and centered coefficients are the

coefficients of the fitted model, with the factors centered and scaled. The default

scaling in MLR is orthogonal scaling. With PLS these coefficients are for the factors

centered and scaled to unit variance.

PLS orthogonal

The PLS orthogonal coefficients are available only when fitting the model with PLS.

The PLS orthogonal coefficients are the PLS model coefficients re-expressed to

correspond to factors centered and scaled using orthogonal scaling (coded as -1 to 1).

PLS orthogonal coefficients are not available in investigations with formulation factors

only.

With process and mixture factors, the PLS orthogonal coefficients refer to process

factors scaled orthogonally, and mixture factors unscaled (original units).

Note: The PLS orthogonal coefficients are meant for comparison with

MLR only. They are incorrect when the design is not balanced and the mean is

not equal to the mid-range.

Normalized

To make the coefficients comparable when responses (Y's) have different ranges, you

can select to display the coefficients in Normalized form that is, the coefficients are

divided by the standard deviation of their respective response. The normalized mode is

the system default for the Coefficient Overview Plot.

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User Guide to MODDE

Unscaled

The unscaled coefficients are the coefficients corresponding to unscaled, uncentered

data. When exporting unscaled coefficients to use in other applications, be sure to use

the E-format to get maximum precision in the coefficients.

For qualitative factors at p levels (p > 2), MODDE generates p - 1 dummy variables

numbered from 2 to p.

Click Extended format to display coefficients for all the p levels of the qualitative

factor or Regular to display coefficients for p - 1 levels of the qualitative factor.

Blocking

You can select to have the block factor treated as a fixed or random effect and the

predictions computed accordingly.

Select the block factor as Fixed effect when the external variability can be set at will

and the primary objective for blocking is to eliminate that source of variability

Select the block factor as Random effect when the external variability cannot be

controlled and set at will, and the primary objective is to make prediction without

specifying the block level, and taking into account the external variability.

See the Statistical Appendix for more information.

Confidence level

Select the confidence level 90%, 95%, or 99% for computation of the confidence

interval on the model coefficients, effects, and predictions. The system default is 95%.

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View

List presentation

By default lists are displayed using the Regular - shows all orthogonal settings

option, when there are qualitative factors. And the design matrix by default displays

The current Worksheet scaled and centered.

and design matrix

For qualitative factors at p levels (p > 2), MODDE generates p - 1 dummy variables

numbered from 2 to p.

Click Extended – shows all settings to display all the p levels of the qualitative

factor or Regular – shows all orthogonal settings to display only p - 1 levels of the

qualitative factor.

design matrix

When you have changed the factor settings of worksheet from the default suggested by

MODDE you can select to display the design matrix as the current worksheet scaled

and centered, or as the original design generated by MODDE.

The default is to display The current Worksheet scaled and centered. If you want to

display the original design matrix, click The design as generated by MODDE.

R2 in plots

Click R2 or R2 adjusted to display in the Summary plot and PLS Summary plot. The

default is to display R2.

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User Guide to MODDE

Residuals

Select the type of residuals to be used in the residual plots.

Raw residuals

The raw residual is the difference between the observed and the fitted (predicted)

value.

Standardized residuals

The standardized residual is the raw residual divided by the residual standard deviation

(RSD).

The deleted studentized residual is the raw residual ei divided by its standard deviation

(si) where the standard deviation (si) is computed with observation (i) left out of the

analysis, and corrected for leverage. Deleted studentized residuals require at least two

degrees of freedom.

Deleted Studentized residuals are not available for PLS.

Default

With MLR and 2 or more degrees of freedom, deleted studentized residuals are the

MODDE default when plotting residuals.

With PLS and models with less than 2 degrees of freedom, MODDE uses as default the

Standardized residuals.

Select Factor

Select the factor to display as default in the Residuals | vs. Variable plot and Effects |

Main Effect plot.

General Options

The General Options has three pages with settings that are used for all investigations.

• General with general settings such as automatic fit.

• List Options like coloring and grid styles.

• Restore with buttons to restore plot settings, favorites, and ‘don’t show

again’-messages.

Click General Options on the View menu to access the options.

Click the Show Details button to display a short description of the marked option.

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View

General page

The General page is divided into the parts General, Investigation Settings, Program

Limits, and Audit Trail.

General

Under General you can change the following options:

• With Automatic fit = Yes, each investigation opened is automatically fitted.

This is MODDE's default. If you set Automatic Fit = No MODDE will not

fit when you open, nor when you make changes in the worksheet, but will

still fit when you make changes using the interactive exclude tool.

• With Automatically display log = Yes, the Output window is automatically

opened when opening an investigation. This is MODDE's default.

• In Most recent file list you can enter the number of investigations you want

to see in the recent file list under the menu File. MODDE's default is 6.

• When Show expanded design factors in RED-MUP worksheet = No, the

expanded design factors will be hidden. This is MODDE's default. For more

see the section on RED-MUP in the Design appendix.

• In Theme you can change the look of MODDE. The default is Office 2003

Classic Theme. Available are also Office 2000, Office XP Classic Theme,

Windows XP, and Whidbey.

• OpenGL plots = No is the default and recommended for the Contour and

Sweet Spot Plots. In 3D scatter plots, OpenGL is always used.

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User Guide to MODDE

Investigation settings

The available investigation settings are:

• Max number of layers in Onion Design to limit how many layers that will

be possible to make. MODDE's default is 10.

• Replicate tolerance is the number used when MODDE decides whether

experiments can be considered to be replicates or not. MODDE's default is

0.1, that is, 10% of the range for each factor.

• Show units in worksheet = Yes results displaying the specified factor and

response units in parenthesis after the factor resp. response names.

Program limits

Under Program Limits you can set the Maximum candidate set size.

The size of the candidate set in MODDE is by default limited to 512 000 rows when

MODDE creates the candidate set for you. You can change this limit.

The maximum size of the candidate set that you can create and generate a design from

is limited by the RAM in your computer.

Audit trail

Prompt for extended user info, found under Audit Trail, is by default No. If you

want MODDE to prompt the user to enter extended user information, change this

setting to Yes.

List Options

Use this page to change the default colors on lists. Other options available in tab list

options are:

• Default number format

• Print lists in color

• Headers in bold

• Threshold for the correlation matrix

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View

Restore

Use the Restore page to restore Umetrics defaults for Plot Settings, Favorites, and

'don’t show again'-messages.

Customize

Use Customize to customize toolbars and menus as in Office 2003 and later.

Click Customize on the View menu to open the dialog.

With the Customize dialog open you can interactively customize all available toolbars

and menus by dragging an item to a new location.

Customize toolbars

On the Toolbars page you can:

• Select which toolbars to display by clearing or selecting the available

toolbars.

• Create new toolbars by clicking New.

• Rename toolbars you have created

• Delete toolbars you have created.

• Reset MODDE toolbars to their default content and position.

Customize commands

On the Commands page you can customize available menus and create new menus.

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User Guide to MODDE

Customize options

On the Options page you can select:

• To Always show full menus.

• To display Large icons.

• To Show ScreenTips on toolbars.

• To Show shortcut keys in ScreenTips.

• Menu animations among: (System default), Random, Unfold, Slide,

Fade, None.

Customize keyboard

On the Keyboard page you can select to assign and reassign shortcut keys to new and

old commands.

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Design

Introduction

When you create or modify a design, some or all items on the Design menu are used.

The available items are:

• Factors and Responses: Define and modify factors and responses.

• Constraints and Inclusions: Define constraints and inclusions.

• Objective: Specify and modify objective, model and design

• D-Optimal: Generate and evaluate D-optimal designs, open the candidate set

for viewing or editing, view onion plots.

• Design wizard: Open the design wizard.

Factors

Click Factors on the Design menu to open the factor spreadsheet.

To modify one of the factors listed, mark it and press the ENTER key on your

keyboard or right-click the factor and click Edit.

To add a new factor, double-click the last line or right-click the spreadsheet and click

Add Factor.

For details, see the Factors chapter.

Responses

Click Responses on the Design menu to open the response spreadsheet.

To modify one of the responses listed, mark it and press the ENTER key on your

keyboard or right-click the response and click Edit.

To add a new response, double-click the last line or right-click the spreadsheet and

click Add Response.

For details, see the Responses chapter.

Constraints

Click Constraints on the Design menu to open the Constraints dialog.

To add a constraint, use the spreadsheet part or the graphical part of the dialog.

For details, see the Constraints section in the Constraints and inclusions chapter.

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User Guide to MODDE

Inclusions

Click Inclusions on the Design menu to open the inclusions dialog.

In this dialog you can do the following:

• Import runs from a text file or another investigation to inclusions.

• Import the current worksheet.

• Add the current inclusion runs to the current worksheet.

• Open the D-Optimal page in the design wizard.

For details, see the Inclusions section in the Constraints and inclusions chapter.

Objective

Click Objective on the Design menu to open the objective pages.

In the objective pages you define the purpose of the design by selecting Screening,

Response Surface Modeling (RSM), Split Objective, or Paste Data. Click Next to

select which design you want MODDE to create. When selecting Paste Data, clicking

Finish opens the worksheet allowing you to paste the data.

For details, see the Objective, model and design chapter.

D-Optimal

When you have created a D-Optimal design a number of items are available under D-

Optimal on the Design menu. For all D-Optimal designs you can click:

• Generate to regenerate the design.

• Candidate set to view the current candidate set and which design runs that

are included in the current design.

• Evaluate to view the D-Optimal results and select another one of the

generated designs.

• Design Plot to create the D-Optimal design plot.

For Onion designs you can additionally create onion plots by clicking Onion plot and

Onion 3D Scatter. These plots display the current candidate set colored according to

layer and the experiments currently included colored black.

For details, see the D-Optimal chapter.

Design wizard

The design wizard is automatically opened when starting a new investigation from File

| New. It can also be opened after creating an investigation by clicking Design Wizard

on the Design menu or by pressing CTRL+W.

The design wizard includes pages for creating/modifying factors, creating/modifying

responses, defining/modifying a constraint numerically, objective and design selection,

and when applicable the D-Optimal pages with the possibility to define inclusions.

For details, see the Design Wizard chapter.

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Factors

Introduction

Factors are variables that can be varied, or vary, during an experiment. A typical

example of a factor is amount of raw material or temperature.

Open the Factor spreadsheet by clicking Design | Factors or File | New, and then

Next.

In the Factors spreadsheet (window), you define (enter), modify, and delete factors.

MODDE supports quantitative, qualitative, and mixture factors.

Quantitative factors may be used in a transformed metric. When factors are

transformed, the design is made in the transformed units, but the worksheet is

expressed in original units.

When you start a new investigation from File | New, the factor definition page is the

second page of the Design Wizard. Click New or double-click the last row in the

factor definition spreadsheet to open the factor definition dialog.

From outside the design wizard, the factor definition dialog can be opened by clicking

Design | Factors and then:

• Double-clicking the last line of the spreadsheet or

• Right-clicking the spreadsheet and clicking Add Factor.

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User Guide to MODDE

The Factor Definition dialog is divided in an upper part and a lower part. The upper

part displays Factor name, Abbreviation, and Units and is available independently of

what is displayed in the lower part of the dialog. The lower part has two pages:

General, which is the default page when opening the dialog, and Advanced.

Factor name

Enter the Factor name with up to 50 alphanumeric characters.

Abbreviation

The Abbreviation is automatically filled with the first 3 characters of the factor name.

You can change the abbreviation as desired using up to 5 characters.

The abbreviation is used as plot label in plots, in the Model and Confoundings lists

found under the Show menu, in Worksheet | Correlation | Matrix, and in Edit |

Generators.

Units

Enter the unit of the factor (optional). The units are displayed in the factor spreadsheet

and can optionally be displayed in the worksheet, see the General page section in the

View chapter for more.

General page

On the General page of the factor definition dialog you select which type of factor you

are defining in Type of factor, the factor settings in Low and High or Settings, and

how it is used in Use.

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Factors

Process factors are regular factors (i.e. temp, pH, etc.) that are not part of a mixture or

formulation. They are expressed as amounts or levels, and can be varied independently

of each other. Quantitative, quantitative multilevel, and qualitative factors are

process factors.

Mixture factors are expressed as the fraction of the total amount of the formulation.

Their experimental ranges lie between 0 and 1.

Mixture factors can be defined as Formulation or Filler.

For quantitative and formulation factors the Low and High fields should be filled with

the desired values.

Note: MODDE is limited in the precision of the factor values. Factors ranging

over a larger range than that, for instance. low at 0.0001 and high at 10000,

cannot be treated as a factor.

For quantitative multilevel and qualitative factors the levels planned to be used should

be entered. For a qualitative factor each entry in Settings has to be text, optionally

including numbers, while for quantitative multilevel each entry has to be a number.

Note: In the same experiment you can have both mixture factors and regular

process factors defined as quantitative or qualitative. Up to 12 factors are

allowed when both process and formulation factors are defined in the design.

Quantitative (default)

Quantitative factors are continuous factors defined at two levels, Low and High. To

define more than two levels, see Quantitative multilevel.

Up to 32 factors are allowed for screening designs and up to 20 for RSM designs.

Quantitative multilevel

To specify more than two levels for a quantitative factor click Quantitative multilevel

under Type of Factor.

MODDE supports up to 24 levels for quantitative multilevel factors. Constraints are

not allowed with this type of factor, and the available designs are D-Optimal, Mixed

full factorial, and three level designs when applicable.

Up to 32 factors are allowed for screening designs and up to 20 for RSM designs.

Qualitative

To specify a qualitative factor, click Qualitative under Type of Factor.

Qualitative factors are discrete. For a qualitative factor, the levels should not stand in

relation to each other. If the levels are a range although discrete then the factors should

be defined as quantitative multilevel.

MODDE supports up to 24 levels for qualitative factors.

RSM designs cannot be created with only qualitative terms. With one or more

quantitative terms present up to 20 extended qualitative terms are allowed for RSM

designs.

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User Guide to MODDE

Formulation

To specify a mixture factor, click Formulation under Type of Factor.

Define a mixture factor as Formulation, when it is not an inert filler. Define the

experimental range of the mixture formulation factor by entering its Low and High

values.

Up to 20 formulation factors are allowed in screening designs and up to 16 in RSM

designs.

Filler

Specify a mixture factor as filler, by clicking Filler under Type of Factor, when:

• It is always present in the mixture. That is, the sum of the High of the other

mixture factors does not exceed 1.

• It accounts for a large percentage of the mixture.

• There are no restrictions on its range. Rather that factor is added at the end to

bring the mixture total to the desired amount, 1 (100%).

• You are NOT interested in estimating the effect of the filler per se.

For a filler factor, the experimental range Low and High values are grayed out as it

will be calculated as 1 minus the sum of the other mixture factors.

A typical example of a filler factor is the solvent in a synthesis.

When you specify a filler factor, MODDE checks that the above conditions are met,

and generates:

1. A slack variable model i.e. a model with the filler factor left out.

2. Classical or D-Optimal process design.

If the conditions are not met, MODDE issues a message, and changes the filler factor

to formulation.

See the Statistical appendix for more details on mixture factors.

Use

Under Use you can select how the factor will be used in the design. A factor can be

Controlled, Uncontrolled, or Constant.

Controlled (default)

When you can control the settings of the factor, leave the default under Use

(Controlled).

These factors can be regular process factors (i.e. pH, Temp, etc.) defined as

quantitative, quantitative multilevel or qualitative, or mixture factors, defined as

formulation or filler.

A Filler factor can only be defined as Controlled. Uncontrolled and Constant are

unavailable for a filler factor.

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Factors

Uncontrolled

Define a factor as Uncontrolled (under Use) if you cannot control it but want to

measure and record its value. Examples of such factors are ambient temperature or

humidity.

Mixture factors (defined as Formulation or Filler) cannot be uncontrolled and the

option Uncontrolled is therefore unavailable.

Constant

Define a factor as Constant (under Use) when you want the worksheet to display a

setting of a factor that is not changed.

Quantitative, qualitative, and formulation factors can be defined as Constant factors.

Quantitative and qualitative constant factors are displayed in the worksheet and

counted in the model toolbar.

When mixture factors are constant, the mixture total T for the controlled mixture

factors is equal to: T = 1 - Σ[constant mixture factors].

Multilevel quantitative and filler factors cannot be defined as Constant.

Advanced

For quantitative and quantitative multilevel factors the Advanced tab offers the

possibility to transform and change the MLR scaling. For regular quantitative factors it

is also possible to define number of decimals to be used for the factor from this page.

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User Guide to MODDE

Transformation

To transform a factor, click the Advanced tab, and in the Transform box click the

transformation of your choice.

When you transform a factor, the design is created in the transformed units, but the

worksheet is expressed in original units. Hence transformation of a factor will change

the center point and the star point values in the worksheet.

All transformed factors are displayed with a “~” (tilde) near the name in lists and plots.

The following transformations are available:

Transformation Description

None Default

Lin C1 * Y + C2

(C1 * Y + C2)C3

Power

where C3 can be any value from -2 to 2.

When a transformation is selected (except None), the relevant constant fields are

displayed.

The field C3 is only displayed for the power transformation.

When fitting with MLR the factors can be scaled using orthogonal, mid-range, or unit

variance scaling in the Advanced page of the factor definition dialog box.

Orthogonal (default)

The factors are centered and scaled using the mid-range and Low and High values

from the factor definition. This is the system default.

Mid-range

When you select to scale a factor using mid-range it is centered only using the mid-

range of the factor. Mid-range is calculated as (High-Low)/2 where High and Low are

the values defined in the factor definition.

Unit variance

When you select to scale a factor to unit variance the worksheet columns are scaled

and centered to unit variance in the calculations.

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Factors

Mixture factors

When fitting the model with MLR, the mixture factors are not scaled.

You can select to fit the model in pseudo components. This is recommended when the

mixture region is regular.

For investigations containing both process and mixture factors, by default process

factors are orthogonally scaled and the mixture factors are unscaled. The coefficients

displayed as scaled and centered correspond to this default scaling of the variables i.e.

mixture unscaled and process orthogonally scaled. If you select to display the unscaled

coefficients, they correspond to all factors unscaled, including the process factors.

Note: You should select the same scaling for all the factors, the system default

is recommended.

PLS scaling

When fitting the model with PLS, all factors including mixture factors are always

scaled and centered to unit variance.

For mixture factors, when you select pseudo components, the mixture factors are first

transformed to pseudo components and then scaled to unit variance (pseudo

components can be switched on/off).

Number of decimals

In the Advanced page of the factor definition dialog you can select Number of

decimals.

The values for number of decimals are: Free, 0, 1, 2, 3, 4 and represent the number of

digits displayed after the decimal point.

The Number of decimals-value should correspond to the precision with which the

factor can be set in your equipment. It is important that it is not set too low since after

setting this value all values for that factor will be rounded accordingly in the

worksheet. If you do not know the precision of the instrument, leave No. of decimals

'Free'. 'Free' means that no rounding off of the results and values corresponding to this

factor will take place.

For example, the settings of a factor in a CCC design, is its high value (in

orthogonal scaled units) multiplied by the 4th root of the number of runs in the factorial

part of the design. If the precision of this factor is set to 0 all decimal digits are

removed from this factor setting in the worksheet and computation will take place

using the values in the worksheet.

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User Guide to MODDE

When a factor has been defined, the Factors definition spreadsheet provides an

overview of the factor definitions, with one factor in each row. The factor properties

are listed in the form of name, abbreviation, unit, type (quantitative, quantitative

multilevel, qualitative, formulation, or filler), use (controlled, uncontrolled, or

constant), settings (high and low vales displayed except for quantitative multilevel and

qualitative where all levels are displayed), transformation, precision, MLR scaling, and

PLS scaling.

In the factor definition spreadsheet, the fields Name, Abbr, Units, and Settings can be

modified directly. To modify any of the other fields, double-click one of them and the

Factor Definition dialog box opens.

Factors can be added by double-clicking the last row of the factor definition

spreadsheet or right-clicking the spreadsheet and clicking Add Factor.

To copy factors, mark the factors to copy, click Edit | Copy or press CTRL+C, and

click Edit | Paste or press CTRL+V. MODDE copies the factors and adds a digit after

the name when pasting to make it unique.

Use the menu File | Print or right-click the spreadsheet and click Print to output the

factor definition spreadsheet to a printer.

72

Factors

Opening the factor definition spreadsheet

Click Design | Factors to activate the factor definition spreadsheet and display the list

of defined factors.

Adding a factor

To add a factor through the factor definition dialog use one of the following methods:

• Double-click the last line of the factor definition spreadsheet.

• Right-click the spreadsheet and click Add Factor.

• Open View | Design Wizard and click New in the Define factors page.

Quantitative factors can be added by typing on the last (empty) row starting with

entering the factor name, see the example:

Modifying a factor

It is possible to edit the fields Name, Abbr., Units, and Settings directly in the

spreadsheet.

To modify any of the other fields, double-click that factor in the factors spreadsheet.

The Factor Definition dialog opens with the attributes of the factor to modify.

The Factor Definition dialog can also be opened by clicking View | Design

Wizard and clicking Edit in the Define factors page.

When performing the experiments according to your experimental plan, the worksheet,

you also take note of deviances of the factor settings. When you enter the response

values you must also enter the actual value of the factors in the worksheet.

Copying a factor

Factors can be copied and pasted in the factor spreadsheet by clicking Edit | Copy and

then Edit | Paste or pressing CTRL+C and then CTRL+V.

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User Guide to MODDE

Deleting a factor

To delete a factor, mark it in the factor definition spreadsheet and use one of the

following methods:

• Press the DELETE key on the keyboard.

• Right-click and click Delete.

• Click Edit | Delete.

You are warned of the possible consequences. Click Yes/No in the confirmation box.

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Responses

Introduction

A response is the result from an experiment. A typical example of a response is yield.

Open the response definition spreadsheet from Design | Responses or File | New,

Next, Next.

In the response definition spreadsheet, you define (enter), modify, delete, copy, print,

and list responses. MODDE supports only quantitative responses.

Responses may be transformed, and MODDE supports several transformations. For

transformed responses, predictions, contour plots and 3D plots, are back transformed to

original units.

When you start a new investigation from File | New, the response definition page is the

third page of the Design Wizard. Click New or double-click the last line of the

spreadsheet in the Define responses window to open the response definition dialog.

From outside the Design Wizard, the response definition dialog can be opened by:

• Clicking Design | Responses and double-clicking the last line of the

spreadsheet or

• Right-clicking the spreadsheet and clicking Add Response.

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User Guide to MODDE

Response name

Enter the response name with up to 50 alphanumeric characters in the Response name

box.

Abbreviation

The Abbreviation is automatically filled with the first 3 characters of the response

name. You can change the abbreviation as desired using up to 5 characters.

The abbreviation is used as plot label in plots and in Worksheet | Correlation |

Matrix.

Units

Optionally enter the unit of the response in the Units box. The units are displayed in

the response definition spreadsheet and can optionally be displayed in the worksheet,

see the General page subsection in the View chapter for more.

There are two types of responses: Regular and Derived. After defining the response

and exiting the response definition dialog it is not possible to change the type.

Limits

Fill in the Min, Target, and Max fields when that information is available to you.

These values are then automatically used in the Design Space, Sweet Spot, and

Optimizer windows.

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Responses

Regular responses

Regular responses are the standard responses measured and fitted in the current

investigation. Regular responses can be transformed and it is also possible to change

the modifier for PLS scaling.

Transformation

The following transformations are available:

Transformation Description

None Default

Lin C1 * Y + C2

(C1 * Y + C2)C3

Power

where C3 can be any value from -2 to 2.

When a transformation is selected (except None), the constants in the formula are

entered in the fields displayed after selecting a transformation. The C3 field is only

displayed for the power transformation.

Specifying a transformation for a response is done to get the best mathematical fit of

the estimated function.

the Histogram plot and clicking Transform.

MLR scaling

When fitting the model with MLR no scaling of responses is available.

PLS scaling

When fitting the model with PLS it is possible to scale to unit variance with or without

a modifier.

With the default scaling option, the responses are centered and scaled to unit variance

when fitting.

With the default scaling option, the responses are centered and scaled to unit variance

when fitting.

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User Guide to MODDE

Autoscale modifier

In the PLS Scaling box, click Autoscale Modifier to change the modifier. Leaving the

modifier at the default=1 gives the same result as when selecting Unit Variance. Enter

a different value of the modifier and the response will be scaled to unit variance

multiplied by the value of the modifier.

Note: To keep a response out of the analysis set its autoscale modifier to zero

(i.e., enter 0 in the edit field).

Derived responses

A Derived response is a computed response as function of the factors and/or fitted

regular responses. When you add a derived response, you enter its formula. Derived

responses can be edited and deleted.

Derived responses are displayed in the responses spreadsheet. The values of the

derived responses are entered automatically in the worksheet when the model is fitted.

The derived responses are also available for all plots and list under the Worksheet and

Prediction menus and can be used as regular responses under these menus.

Note: Derived response values are only available after fitting (clicking Fit on

the Analysis menu) the model. When responses are included in the formula,

MODDE uses the fitted (predicted by the model) values of the responses in the

computation.

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Responses

To create derived responses open the Response Definition dialog, enter the name,

abbreviation and units of the response.

Under Select type of response, click Derived, and then click the Edit button.

When clicking the Edit button, the Derived Response Wizard opens. The first page

contains information about derived responses. Select the Don’t show this page again

check box if you do not want to see this information again.

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User Guide to MODDE

Clicking Next opens the next page in which you Enter the formula for the derived

response.

When you click Finish, MODDE parses the formula for correctness, and only

computes and displays the derived response in the worksheet, when you fit the model.

The derived response is added to the responses spreadsheet and the worksheet.

To modify a derived response, you must edit its formula in the Response Definition

dialog. You cannot edit the values in the worksheet.

Derived responses can be copied and deleted as regular responses.

Note: Derived responses are deleted when regular factors are deleted, or

changed and when responses that are part of the derived response are deleted.

In MODDE you generate one derived response at a time.

Hence you can only use sets of variables with the operators avg, stdev, and sum that

return one variable.

Examples using sets of variables

Avg(v[1,3,4] + v[6,8,9])

Results in the average of 3 variables, v1+v6, v3+v8, v4+v9.

Avg(v5 + v[1:6]) is an illegal syntax, the two operands are not of the same size.

Sum(v[1,3,4] +v9)

Results in the sum of 3 variables, v1+v9, v3+v9, v4+v9.

Stdev(v[3:5]*v1)

Results in the standard deviation of the 3 variables v3*v1, v4*v1 and v5*v1

avg(v[1:5]*v8/v7)

Results in the average of 5 variables, i.e. the average of variables 1 to 5 each multiplied

by the ratio v8/v7.

Sum(v8/v7 * v[1:5]) is an illegal syntax.

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Responses

MODDE recognizes the following syntax:

• Integer, Variables (factors or responses), List of Integers and Sets of

Variables

• Integer constant and floating points

• Operator ‘:’ denotes a sequence, i.e., from: to, for example 6:8 means 6,7,8

• List of integers, such as 1,3,5:8 is the same as 1,3,5,6,7,8

• Variables (factors or responses) are denoted by vint, where int refers to the

variable number in the worksheet (i.e. v5, v15, for variables 5 and 15)

• A set of variables (matrix) is denoted by v[int1,int2, int3:int4,int6] with

square brackets. Int refers to the variable number in the worksheet. For

example v[1,5,7:10] refers to the set of variables v1, v5, v7, v8, v9, and v10.

Note: To denote a set of variables you have to use the square brackets [ ], and

not regular parenthesis ( )

The operators and functions listed below are recognized and can be used with a single

variable or a set of variables. Operators have the usual precedence, i.e. ^ > * and / > +

and -. Parenthesis can be used to group expressions in the usual way.

Functions

The functions available are Log10, Ln (natural log), and Exp (exponential).

Addition/subtraction (+, −) can be applied to:

• A set of variables with a constant

• A set of variables with a single variable

• A set of variables with another set of variables of the same size (they are

added pair wise).

• A single variable with a constant or a single variable

Power, multiplication, and division (^,*, /) can be applied to:

• A set of variables with a constant

• A set of variables with a single variable.

variables and another set of variables. The first operand can be a constant, a

variable or a set of variables, but the second and following operands must be

a single variable or a constant.

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User Guide to MODDE

Additional operators

The following additional operators apply to variables or sets of variables:

Avg(v[int1:int2]) Average of variables vint1... to vint2

Note: The parser is not case sensitive (t and T mean the same thing).

When you use a qualitative factor in the formula for a derived response, enter the

values (weights), to be used when computing the derived response, for each qualitative

level setting. If no settings are entered, '0' is used as value for all settings of the

qualitative factor.

Linked responses

A Linked response is a response available in one investigation but fitted in another.

Linked responses are no longer available in MODDE.

Investigations containing linked responses are converted in MODDE 9 to instead hold

different models and/or worksheets. MODDE supports as many models in one

investigation as there are responses.

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Responses

When the responses are defined, the response definition spreadsheet provides an

overview of response definitions, with one response in each row. The response

properties are listed in the form of name, abbreviation, unit, transformation, MLR

Scale, PLS Scale, and type of response (regular or derived). A response is selected by

clicking when pointing to it or by using the keyboard arrow keys to move in the

spreadsheet.

The fields Name, Abbr, Min, Target, and Max can be edited directly in the

spreadsheet. To modify any other fields double-click one of them, or mark the response

and press ENTER, to open the Response Definition dialog. Type cannot be modified

after a response has been defined.

Responses can be added by double-clicking the last row of the Responses definition

spreadsheet or by right-clicking the spreadsheet and then clicking Add Response.

To copy responses, mark the responses to copy, click Edit | Copy or press CTRL+C,

and then click Edit | Paste or press CTRL+V. MODDE copies the responses and adds

a digit after the name when pasting to make it unique.

To print the Responses definition spreadsheet, click Print on the File menu or right-

click the spreadsheet and click Print.

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User Guide to MODDE

Opening the responses spreadsheet

On the Design menu, click Responses to open or activate the Responses spreadsheet

(window) displaying the list of the defined responses.

Adding a response

To add responses, double-click the last entry in the Responses spreadsheet window.

Enter the responses name, abbreviation etc, in the Response Definition dialog.

Modifying a response

The fields Name and Abbr. can be edited directly in the Responses spreadsheet.

To modify other fields for regular or derived responses, mark the desired response in

the responses spreadsheet and:

• Double-click it or

• Press ENTER.

The Response Definition dialog opens with the attributes of the response to modify.

Deleting a response

To delete one or more responses, mark the response(s) in the responses spreadsheet

and press the DELETE key on the keyboard or click Edit | Delete.

A dialog is displayed to confirm the deletion.

Regular and derived responses can be copied and pasted by marking them and then

clicking Edit | Copy and Edit | Paste or pressing CTRL+C and CTRL+V.

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Constraints and inclusions

Constraints

A common problem is that experimentation may not be possible in some region of the

experimental space. For example it may not be possible, in an experiment, to have high

temperature and simultaneously low pH, and you want to cut-off the corner High temp,

Low pH. In MODDE this is solved by adding a Constraint using Design | Constraint.

A linear constraint is a function of the factors that specify a part of the experimental

region to be included or excluded.

The resulting experimental region is an irregular polyhedron. The corners of this region

are called the extreme vertices; they constitute part of the candidate set, i.e. a

discrete set of potentially good runs.

D-optimal designs are the only designs available when the experimental region is

constrained to an irregular polyhedron.

Constraints can be defined for quantitative or formulation factors.

Specifying constraints

Enter your constraints in the Constraints spreadsheet. The Constraints window is

opened by clicking Constraints on the Design menu.

In the upper part, the spreadsheet, you define each constraint (one per row) as a

mathematical relation. In the lower part, the graphical view, you can define constraints,

to be added to the upper part, geometrically. Such constraints may include two factors

only and are shown in the upper part after clicking the Add button.

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User Guide to MODDE

Constraints supported

MODDE supports linear constraints, specified as exclusions, for quantitative process

factors or mixture factors Xk of the form

or

A constraint cannot be defined to include both quantitative and formulation factors.

Constraints cannot be defined in quantitative multilevel, qualitative, filler,

uncontrolled, or constant factors.

MODDE supports up to 50 linear constraints.

To define a constraint in the spreadsheet, enter the coefficients Ak of every factor in the

constraint. Select “<“ or “>“ and enter the Limit of the constraint.

For example, in an experiment with three mixture factors:

X1 qualitative 3 levels: A, B, C

X2 qualitative 2 levels: K, L

X3 mixture

X4 mixture

X5 mixture

X6 mixture

A set of constraints may be entered as follows:

The first constraint specifies to exclude experimental runs where the sum of X3, X4,

and X5 is < 0.6

The second constraint specifies to exclude experimental runs where the sum of X4 and

X5 < 0.3

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Constraints and inclusions

The graphical interface in MODDE helps you define the constraints to exclude a region

of the experimental space defined by the intersection of a line with the experimental

region. Only two factor constraints can be defined graphically.

1. In the Factor on the X-axis and Factor on the Y-axis boxes select the name

of the two factors defining the constraint.

2. Define the coordinates of the extreme vertices (intersection of the line with

the experimental region) or pull the end of the line along the side to select the

region to cut off. When pulling, MODDE enters the current extreme vertices

in Low and High of the selected X and Y-axis factors.

3. Under Exclude area click Above line or Below line to exclude the correct

area.

4. Clicking the Add button. MODDE computes the equation of the line and

enters the coefficients Ak of the two factors in the constraints spreadsheet in

the upper part of the constraints window.

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User Guide to MODDE

For example in an experiment with temperature and pH, temperature varies between

120 and 160C and pH between 1 and 5. You may want to exclude the corner

Temperature =160 and pH =1. Define the extreme acceptable conditions, that is the

lowest pH when temperature is 160, for example pH=3, and the highest temperature

when pH =1 for example temperature = 140.

These are the coordinates of the extreme vertices, the intersection of the line that cuts

off the undesirable corner.

Enter these in the Low and High boxes, and the coefficients of the intersecting line are

computed when you click the Add button.

To modify a constraint graphically, mark the row showing the constraint in the

spreadsheet, change the constraint by pulling the end points of the line, or by

modifying the values in Low and/or High. Then click the Update Constraint-button

to update the constraint formula in the constraints spreadsheet.

Note: Click a row in the spreadsheet defining a constraint in two factors and

MODDE displays the graphical constraint.

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Constraints and inclusions

When defining constraints the only designs available are D-Optimal designs. To create

D-Optimal designs a candidate set is created. When there is a constraint present the

resulting candidate set is formed by the extreme vertices of the irregular region,

defined by the linear constraints.

If there in addition are qualitative or quantitative multilevel factors, the final candidate

set is the product of the full factorial in the qualitative or quantitative multilevel factors

times the candidate set resulting from the linear constraints (extreme vertices, center of

edges, etc. of the irregular experimental region).

Qualitative factors and quantitative multilevel do not appear in the constraint

spreadsheet and cannot be used in constraints.

In the case it is needed to constrain a region defined by a qualitative or quantitative

multilevel factor:

1. Select a D-Optimal design and in the Change D-Optimal settings page of

the design wizard, open the candidate set by clicking the Edit button under

Candidate Set.

2. In the candidate set that opens, find the settings that are undesirable and

delete those rows.

3. When finished, click the Generate D-Optimal button and the Design

Wizard D-Optimal page opens up again.

4. Continue creating the design.

combinations you need to create a D-Optimal design, click Design | D-

Optimal | Candidate Set, and then click Edit | Sort.

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User Guide to MODDE

Inclusions

In MODDE designs can be augmented either using Complement Design (see the

section Complement Design in chapter File menu) or Inclusions.

Inclusions are extra runs that will be part of the worksheet. You can include a set of

experimental runs (inclusions), either at the end of the worksheet or to be part of a D-

Optimal design.

The Inclusions spreadsheet can be opened by clicking Design ⏐ Inclusions or by

clicking the import or Edit buttons in the Change D-Optimal settings page in the

Design Wizard.

Using Inclusions to augment a design is preferred when:

• The extra experiments to include are found in another investigation or in a

text-file as complement design can only complement the current

investigation.

• The experiments were not saved in a MODDE investigation or a text file. In

Inclusions such experiments can be entered manually or pasted.

• When adding experiments after the design has already been created. That is,

when the inclusions should not be part of the design generation.

Using Complement Design to augment a design is preferred when:

• The desired design should be a classical design. Use Fold over or Estimate

square terms in a screening design. When using inclusions D-optimal

designs is the only available choice.

• The desired design should include star points. Use Estimate square terms

in a screening design and change the Star distance.

Inclusions can be added to the worksheet after the design and worksheet have been

created.

Inclusions can be specified before or after the worksheet is generated. If the worksheet

already exists when you enter the inclusions, click the Add to Worksheet button to

add the inclusions last in the worksheet. If you enter the inclusions before the

generation of the worksheet, click the Save and Close button, reopen the Inclusions

spreadsheet after creating the worksheet and click the Add to Worksheet button.

If the inclusions are entered before the generation of a D-Optimal design the Include

in design check box on the D-Optimal page of the design wizard has to be cleared to

avoid including the inclusions.

Note: The inclusions are added to the worksheet only when you click the Add

to Worksheet button

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Constraints and inclusions

With D-Optimal designs Inclusions runs can be a part of the design or added at the

end of the worksheet.

If the inclusions are entered before the generation of a D-Optimal design the Include

in design check box on the D-Optimal page of the design wizard is default selected

and the inclusions are used when creating the D-Optimal design.

Note: When generating D-Optimal designs, and the Include in design check

box is selected, the inclusions are a part of the design and included in the

number of runs.

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User Guide to MODDE

Generating inclusions

Click Design | Inclusions to open the Inclusions spreadsheet, or click the Edit button

in the Inclusions area in the D-Optimal page in the design wizard.

In the inclusions spreadsheet you can add experiments by typing or pasting, by

importing from file, and by importing the current worksheet. You can do several

imports.

Factor and response values can be entered directly in the inclusions spreadsheet. Right-

click the spreadsheet and click Insert Rows to insert as many rows as you need or

press the down arrow key on the keyboard. The rows needed when pasting are created

automatically.

Inclusions can be imported from a tab separated text file (*.txt), or another MODDE

investigation with the same factors, by clicking the Import button. Select either a text

file, a MODDE file (*.mip) or a MODDE 4.0 worksheet (*. dat).

When importing, all the factors defined in the MODDE investigation have to be

present in the file, including uncontrolled, filler, and constant factors.

See also the Design generation criteria section in the D-Optimal chapter.

Importing worksheet

Click the Import Worksheet button to import the current worksheet to use as

inclusions.

Modifying inclusions

If the inclusions already exist, clicking Design | Inclusions or the Edit button in the D-

Optimal page in the design wizard, opens the spreadsheet with the inclusions for

editing.

To delete rows, mark them, press the DELETE key or right-click the spreadsheet and

click Delete.

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Objective, model and design

Introduction

The Objective is the purpose for creating the design. MODDE recognizes two

objectives: Screening (first stage of an investigation when little is known) and

Response Surface Modeling (RSM) (optimization with the important factors.). The

Split Objective supports both screening and RSM. Paste Data defaults to the

screening objective with a linear model.

After defining your factors and responses, clicking Design ⏐ Objective opens the

design wizard which guides you through the selection of objective, design, and model

of the investigation.

The following sections describe the definition of the objective and selection of model

and design. See the Design Appendix chapter for details concerning the available

designs.

There are two dialogs associated with the menu item Objective:

• First: the Select Objective dialog to select the purpose.

• Second: the Select Model and Design dialog to select the type of design and

model.

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User Guide to MODDE

Open the Objective dialog by clicking Design | Objective. Select one of four options

Screening, Response Surface Modeling (RSM), Split Objective, or Paste Data.

Screening objective

Select the Screening objective when:

• You are starting an investigation and know little about the effects of the

factors on the response, the behavior of the response in the experimental

region, or the true size of that region.

• The goal is to reduce the number of factors to those with the largest effect on

the response.

This objective is available for all types of factors and factor combinations.

RSM objective

Select the RSM objective when:

• A lot is known about the investigation i.e. important factors, the size of the

region etc.

• The goal is to approximate the response by a mathematical model for the

purpose of prediction, optimization or finding a region of operability.

This objective is not available when all factors are qualitative.

Split Objective

Select the Split Objective when the investigation holds both process and mixture

factors AND you want to specify separate models for each.

If you want to specify one model for both mixture and process factors, select

Screening or RSM as objective.

The split objective is only available when there are both process and mixture factors

available.

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Objective, model and design

Paste Data

Select Paste Data when you have the design and want to paste it instead of MODDE

creating one for you.

After selecting Paste Data and clicking Finish, the MODDE worksheet will expand

dynamically to fit the size of the pasted data. Click Analysis | Evaluate to view the

condition number of the current worksheet and model.

See also the Import design from file section in the File chapter.

After selecting the objective and clicking Next the Select the model and design page

opens. In this page you can clear or select the Show extended list of designs check

box resulting it displaying:

• only the recommended designs or

• all available designs,

for the current objective and number of factors, with the number of runs and the

associated models.

Designs in MODDE

The design is the protocol for varying the factors in each experiment. Thus the design

is a set of experimental runs spanning the experimental region.

See the Design appendix for more details concerning the designs available in

MODDE.

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User Guide to MODDE

Recommended designs

According to the selected objective and number of factors, MODDE recommends the

two most likely designs. Continue with the recommended design or select another one

by pointing and clicking or pressing the UP and DOWN arrow keys on the keyboard.

MODDE recommends, whenever possible, classical designs.

The recommendations are marked First and Second in the Recommendation column.

Note: By clearing the Show extended list of designs check box you can

display all supported designs in MODDE available for the defined factors and

selected objective.

Runs in design

In the Runs column the number of runs in the design is displayed. When there is a '+'

and/or a '-' sign after the number that means that the number of runs can be changed for

that particular design.

Model

MODDE supports polynomial models, such as linear, interaction, and quadratic. Third

order terms such as cubic or three factor interactions may be added to the model in

Design ⏐ Edit Model after the design generation.

The model for each design is listed in the Model column.

Screening models

Linear and Interaction models are appropriate for the screening objective. When the

model you select is:

• Linear MODDE generates the linear model. You may edit the model and

enter selected interactions.

• Interaction MODDE generates the full interaction model, i. e. all the two

factor interactions are included.

RSM models

Quadratic models are used for the RSM objective. For classical mixture designs cubic

designs are also available. When the model you select is:

• Quadratic MODDE generates the full quadratic model holding all two-factor

interactions and all the square terms of all the factors.

• Special cubic or cubic MODDE generates models accordingly. Such models

are only supported with mixture factors. Such models include all two-factor

interactions, all square terms, and some or all cubic terms.

Split models

When selecting the Split Objective, the model for the process factors and the mixture

factors can be specified independently of each other by clicking the Settings button.

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Objective, model and design

The pseudo resolution applies to designs when they are blocked.

The pseudo resolution of the design is the resolution of the design when all the block

effects (blocking factors and all their interactions) are treated as main effects under the

assumption that there are no interactions between blocks and main effects, or blocks

and main effects interactions.

See also the section Blocks in this chapter and the section Orthogonal blocking in the

Statistical appendix.

Design runs

The Design runs box displays the number of runs for the selected design.

When there exists 2 or more fractional factorial designs of the same resolution, with

different number of runs, the number of runs, in the Runs column, is marked with a

“+”. MODDE defaults to the design with smallest number of runs. Use the Design

runs arrow to select the larger design.

For example, with the screening objective for 7 or 8 factors there exist two-resolution

IV design, one with 16 runs and the other with 32. MODDE selects the one with 16

runs. To select the design with 32 runs, click the Design runs arrow.

With D-Optimal designs the number of runs, in the Runs column, is marked with a ‘+’

and ‘-’ indicating that there exists smaller and larger designs.

When augmenting a design D-Optimally, the number of runs includes the number of

inclusions.

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User Guide to MODDE

Center points

The Center points box displays the number of center points. MODDE always

recommends 3 center points. To change the number of center points:

• Type the desired number

• Click the Center points arrows and click a number.

• Mark the Center points box and press the up or down arrow keys on the

keyboard.

Replicates

The Replicates box displays the number of times to replicate the whole design

including center points. The default is '0', meaning that the design is not replicated.

Enter '1' here to replicate the design once.

To change the number of replicates:

• Type the desired number

• Click the Replicates arrows and click a number.

• Mark the Replicates box and press the up or down arrow keys on the

keyboard.

Total runs

After Total runs, the total number of runs included in the worksheet is listed and

includes: runs in the design plus center points and replicates.

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Objective, model and design

Settings

For some designs the Settings-button is active.

Click the Settings button to:

• Edit the generators and/or model for fractional factorial designs of

resolution III, V, and V.

• Change the star distance for a CCC design.

• Specify the model when you have selected the split objective.

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User Guide to MODDE

Before creating a fractional factorial design the model and generators can be changed

to better take into account user knowledge. That is, it is possible to unconfound certain

model terms if desired by changing the generators.

Click the Settings button and click Model to open the Edit Model dialog and add

interactions. Adding interactions makes the confounding pattern clear in Generators.

Click the Settings button and click Generators to change the generators of the design.

Note: The model and generators can be edited outside the design wizard by

clicking Edit | Model and Edit | Generators.

For more details see, the sections Model / reference mixture and Generators in the

Edit chapter.

With CCC designs the star distance can be changed from the default by clicking the

Settings button and clicking Star Distance. The default star distance is calculated as

√√(2K) where K is the number of factors (square root of the square root of 2 to the

power of K).

Note that from 5 factors and upward the factorial part of the design is reduced and the

K used in the calculation of the star distance is that of the full factorial part. This

means that the default star distance value is 2 for both 4 and 5 factors.

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Objective, model and design

When there are both process and mixture factors present the only designs available are

the D-Optimal designs.

Select the split objective to specify separate models for the mixture factors and the

process factors. Click the Settings button, click Model and the Select Model dialog is

opened.

Select the desired models and select the Add interaction between linear process and

mixture factors check box to add interactions between the process and mixture

factors.

Click the Edit model button in the D-Optimal page to edit the models further.

these are part of the quadratic model. Scheffé Models are not supported for

investigations with both process and mixture factors.

Description

Click the Description button, positioned below the Settings button, to display a short

description of the selected design. To hide the text, click the button again.

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User Guide to MODDE

Blocks

MODDE supports Orthogonal Blocking for the 2 levels Factorial, Fractional factorial,

Plackett Burman, CCC, Box Behnken, and D-Optimal designs.

The maximum number of blocks supported by MODDE is 8, with a minimum block

size of 4.

Select the number of blocks to include in your design from the Blocks box.

Orthogonal blocking

The method of dividing experiments into blocks, so that the block effect is

uncorrelated with the main factor effects is called orthogonal blocking.

Orthogonal blocking is a way to deal with extraneous sources of variability that are not

included in the model. For example if one is making 32 experiments and the batches of

raw material are sufficient for 8 experiments, one would like to run the experiments in

blocks of 8 such as the variation between batches of raw material does not affect the

estimate of the main factor effects.

See also the Orthogonal blocking section in the Statistical appendix.

Block interaction

An interaction between a main effect and a block effect is called a block interaction.

When the design supports the interactions between the block effects and the main

effects, the Block interactions check box, in the Select the model and design page is

active. You can select the check box if you want to add the block interactions to your

model.

For details see the Orthogonal blocking section in the Statistical Appendix.

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D-Optimal

D-Optimal designs are computer generated designs, tailor made for a specific

problem. They allow great flexibility in the specifications of your problem. They are

particularly useful when you want to constrain the region and no classical design

exists.

“D-Optimal” means that these designs maximize the information in the selected set of

experimental runs with respect to a stated model.

Given a model, the D-Optimal algorithm selects “N” experimental runs from the

candidate set, as to maximize the information in X.

You can change the number of runs N suggested by the system. The candidate set is

the set of all potentially good runs. The extended design matrix X is created from the

“N” experimental runs expanded with extra columns for the constant, the squares and

cross terms according to the model.

Whenever possible you should use classical designs and these are the default designs

of MODDE. However when classical designs are impossible to apply, D-Optimal

designs are the preferred choice.

MODDE suggests a D-Optimal design when:

1. There is a linear constraint on the factor settings, reducing the experimental

region to an irregular polyhedron. There are no classical designs that can

well investigate an irregular region. A D-Optimal design is then the

preferred choice as it makes efficient use of the entire experimental space.

2. There are formulation factors, with lower and upper bounds, and possibly

additional constraints, making the region an irregular polyhedron.

3. There are qualitative factors, with more than two levels and there is no

mixed level design available. Or the mixed level design suggests too many

runs to be acceptable.

4. The objective is RSM and there are qualitative factors.

5. The number of experimental runs affordable is smaller than the number of

runs of any available classical design.

6. Both process and mixture factors are present.

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User Guide to MODDE

There are two D-Optimal pages in the design wizard: the Change D-Optimal settings

page and the D-Optimal results page.

The first page of the design wizard opens, after selecting a D-Optimal design in the

Select model and design page and clicking Next.

This Change D-Optimal settings page consists of three sections relating to:

1. Design Generation Criteria

2. Design Alternatives

3. Candidate set

The Design Generation Criteria concerns the criteria on which the design is built.

Design runs

Design runs is the number of runs the D-Optimal algorithm will generate, not

including the center points. You can change this number as desired. The smallest

number of runs accepted is the number of terms currently included in the model.

Model terms

The number of terms currently in the model is listed after Model terms. This number

is updated after changes in Edit Model.

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D-Optimal

Click the Edit Model button to edit the model. The edit model dialog opens and you

can edit the model by adding or deleting terms in the specified model. This modifies

the number of model terms.

Note: When the investigation contains only mixture factors, the Edit Model

button is unavailable. The D-Optimal design is always generated from the full

model specified in the design page.

With investigations containing both mixture and process factors, you can only edit the

process factor terms and the interactions between mixture and process factors.

Potential terms

By default MODDE includes a set of potential terms, i.e. additional terms not included

in your model that might be important. The objective is to select a D-Optimal design

rich enough to guard for the potential terms. If you want your design to be just optimal

for your specified model, clear the Use potential terms box.

Inclusions

To use runs available from file as inclusions, click the Import button.

To edit the available inclusions, or paste/type runs to use as inclusions, click the Edit

button.

If you have specified runs as inclusions in the Design | Inclusion window prior to

entering the design wizard, the Include in design check box found under Inclusions, is

by default selected and the inclusions will automatically be part of the D-Optimal

design. Clear this check box if you do not want the inclusions to be part of the D-

Optimal design (but rather manually added at the end of the worksheet).

To add the inclusions after generating the worksheet, open the Inclusions under the

Design menu, and then click Add to worksheet.

Degrees of freedom

Number of Degrees of freedom of the residuals is calculated as:

Number of design runs – Model terms +1 (when you have center points)

The number of degrees of freedom recommended for D-Optimal designs in MODDE is

at least five.

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User Guide to MODDE

The Design alternatives section controls the number of designs generated by the D-

Optimal algorithm.

The performance of a D-Optimal design, depends on the selected number of runs, N,

and the number of terms in the model, p.

MODDE can generate several D-Optimal designs, varying the specified number of

runs N and then evaluate them (G-efficiency, Condition Number, Determinant) as

functions of N.

In the Design Runs Span box, you can select the number of designs to generate with

varying N.

If, for example, you select N ± 3 and 1 repetition, MODDE generate 7 designs ranging

from N-3 to N+3. The default is to generate 25 designs with N ± 2 and 5 repetitions.

Repetitions

In the Repetitions box, select the number of designs you want to generate with the

same number of runs, N. This will give a set of designs for each value of N.

When you have a qualitative factor, or when you have selected to block the design, you

may want the design to have the same number of runs at each level of the qualitative

factor. Thus, the design would be Balanced with respect to the qualitative factor.

If you want a balanced design, select the qualitative factor in the Balance on box. With

a blocked design, by default, the qualitative variable '$Blo' is selected.

If you want MODDE to only select balanced designs, select the Use balanced only

check box.

To be able to get a balanced design, the selected number of design runs must be a

multiple of the number of levels of the qualitative factor. The number of design runs

may be updated, if necessary, to be a multiple of the number of levels of the qualitative

factor.

does not succeed in generating a balanced design, it issues a message. In this

case, to generate a design, you must clear the Use balanced only check box.

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D-Optimal

The Candidate set section concerns the set of design runs to select the D-Optimal

design from.

Generate new is by default selected the first time the D-Optimal page is opened. Click

Generate new when you change the model or the use of potential terms and you want

to generate a new set of candidate runs.

Use the current candidate set is available after importing or creating a candidate set.

Once the candidate set has been generated, the Use the current candidate set option is

by default marked.

Click the Edit button to edit the candidate set. This can be done both with Generate

new and Use the current candidate set selected. A spreadsheet opens with the

candidate set. Make your changes and click the Generate D-Optimal button to return

to the D-Optimal page.

The candidate set can also be opened for editing by clicking Design | D-Optimal |

Candidate set.

You can import a candidate set from many file types.

To import the candidate set:

1. Click the Import button found in the Candidate set section.

2. Find the file holding the candidate set and click Open. Many file types are

supported.

3. The Import Candidate Set window opens allowing you to specify the row

containing the factor names, and optionally the column holding the

experiment names. Here you can exclude and include rows and columns too.

The row defined as Factor Name in the candidate set-file must contain the

factor names and they must be identical to those defined in the MODDE

investigation. Including uncontrolled, filler, and constant factors is optional.

The size of the candidate set in MODDE is by default limited to 512 000 rows when

MODDE creates the candidate set for you.

You can change the limit in General Options on the View menu, tab General, under

Program Limits you find Maximum candidate set size.

The maximum size of the candidate set that you can create and generate a design from

is limited by the RAM in your computer.

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User Guide to MODDE

D-Optimal results

When you click Next on the Change D-Optimal settings page, MODDE generates the

D-Optimal designs and displays them in the D-Optimal results page.

By default, the best design according to G-Efficiency is selected. Use the Auto-select

design by box to instead select the best design according to Determinant or

Condition number. Or select another design manually by marking the design.

Click any column header to sort the list.

To see the D-Optimal results as a plot, select the Display as plot check box.

The columns with the grid pattern represent the currently selected design.

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D-Optimal

Right-click the plot and click Properties to open the D-Optimal Design Plot dialog

allowing:

• Selection of which of the criteria to display, G-efficiency, Determinant, or

Condition number under Show.

• Sorting on Type instead of Design (default) under Sort by.

• Selection of which layers to display when D-Optimal onion designs have

been generated in the Show Layer box.

Click Finish to generate the worksheet. Any already existing design and

worksheet will be deleted.

Click Design | D-Optimal | Generate to regenerate the D-Optimal designs as many

times as needed.

Note: The menu Design | D-Optimal | Generate is not available for onion

designs. To generate a new onion design, select Design | Objective.

After creating a D-Optimal design, the items on Design | D-Optimal are available. The

onion plots are only available when an onion design was generated while Generate is

only available when a regular D-Optimal design has been generated.

Generate

Click Design | D-Optimal | Generate to open the Change D-Optimal Settings page

to re-enter the D-Optimal pages and generate a new set of D-Optimal designs.

See the section D-Optimal pages in the design wizard previously for more.

Candidate set

Click Design | D-Optimal | Candidate Set to open the Candidate set for viewing or

editing.

See the section Candidate set previously for more.

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User Guide to MODDE

Evaluate

Click Design | D-Optimal | Evaluate to open the D-Optimal Results page to view the

other generated designs and their properties. Here you can also select one of the other

designs as your worksheet by marking and clicking Finish.

See the section D-Optimal Results previously for more.

The onion plots are available after creating a D-Optimal onion design. Click Design |

D-Optimal | Onion Plot or Onion 3D Scatter to display onion plots.

See the section D-Optimal onion design for more.

Design plot

Select Design | D-Optimal | Design Plot to display the same information as Evaluate

in a column plot. MODDE displays G-efficiency, Log of the determinant of X'X, and

the condition number of X, for the D-Optimal designs.

When you generate several D-Optimal designs with different N (number of runs), you

can plot any of the D-Optimal criteria (G-efficiency, Condition No, Log of the

determinant of X'X) as a function of N. This plot can also be created from the Design |

D-Optimal | Evaluate and selecting the Display as plot box.

See the Design appendix for more information.

Note: All of the statistics available in the D-Optimal Design Plot are

computed from the runs selected D-optimally and do not include the possible

center points added to the worksheet. With mixture factors, the condition

number refers to the slack variable model with all mixture components scaled

orthogonal.

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D-Optimal

Onion designs are available for process factors only. You can also import a candidate

set from one of the supported file formats or a SIMCA-P file (.usp) to create onion

designs from.

Onion designs are made in a number of layers (shells), with a separate D-Optimal

design for each layer. Typically the number of layers is two or three.

Candidate set

The D-Optimal onion design in MODDE is created from a candidate set. The candidate

set can be created by MODDE, imported from one of the supported file formats, or

imported from SIMCA-P.

When you have defined only process factors and enter the Select model and design

page, you can select to generate an Onion design.

MODDE will then create the same number of candidate sets as layers specified. The

high and low limits for each factor in the candidate set will be based on the percentile

defined for each layer.

E.g. for a factor with Low= -1 and High=1 with the four layers, 0% - 15%, 15% - 30%,

30% - 75% and 75% - 100%, the candidate sets will be generated with the low/high

settings -0.15/0.15, -0.3/0.3, -0.75/0.75 and -1/1. The number of points generated in

each candidate set depends on the number of factors.

If you want to create an onion design using factors found in a file, see the Advanced

designs section in the File chapter.

After importing the candidate set, selecting an Onion design and selecting the intervals

(percentile) for the layers, the candidate set is divided into sub candidate sets for each

layer, based on the experiments distance. The most distant experiment will define

100% and the center will define 0%.

The distance of a specific experiment from the center is calculated as the “geometrical

distance”, i.e. the square root of the sum of squared factor values. The factors are

orthogonally scaled.

To create an onion design using scores from SIMCA-P as design variables (factors),

see the Advanced designs section in the File chapter.

When you select to create an onion design, the candidate set is parted in layers.

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User Guide to MODDE

After selecting an Onion design, and clicking Next, the Layers page is displayed. This

page is organized by layer – from inner (first layer) to outer (last layer).

1. The number of the Layer (starting from inside).

2. The number of Candidate Runs in the layer for imported candidate sets.

3. The span of the layer defined by its % From (Percentile) and % To distance

to the center of the multivariate space. You can change the span of a layer as

long the number of runs in the candidate set remains one and half times

larger than the number of design runs in that layer. Overlapping span

between layers is not allowed. When you change the span of the layers,

MODDE updates the number of candidate set runs in each layer. If the span

of the layers overlap, or the number of runs in the candidate set is not large

enough, the layer is colored in red and a message indicating the problem is

displayed. You must fix the problem before clicking Finish.

4. The number of Design Runs in each layer. You can change the number of

design runs. The number of desired runs must be at least equal to the number

of terms in the model. The recommended number of runs includes 3 degrees

of freedom for the outer layer and 1 degree of freedom for the rest of the

layers.

5. Select the number of D-Optimal designs, in each layer, you want to generate

with the same number of runs. The default number for Repetition is 1.

6. The Model for each layer. You can change the model in each layer. Click the

model you want to change and select another model or mark the layer and

click Edit Model to customize the model. After editing a model, MODDE

writes Model edited in the Comment column. MODDE updates the design

runs according to the new selected model.

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D-Optimal

When you click Finish, MODDE generates several D-Optimal designs in each layer

varying the number of runs by plus and minus 2, and displays the Onion D-Optimal

results.

The table on this page displays, for every layer, the generated designs statistics. By

default, in this table, the designs with the highest G-efficiency are selected.

You can select a different design in a given layer by marking it in the list or using the

Auto-select design by box and selecting a different criterion.

Generate

With Onion D-Optimal designs, you cannot generate a new set of D-Optimal design by

using the menu Design | D-Optimal | Generate.

If you want to generate a new set of Onion D-Optimal designs, click Design |

Objective. The worksheet will be deleted and you can follow the wizard to generate a

new design and worksheet.

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User Guide to MODDE

Candidate set

Click Design | D-Optimal | Candidate set to display the candidate set.

The columns in the spreadsheet are as follows when the candidate set was imported:

1. Design Run number. Corresponds with the experiment number in the

worksheet.

2. The Exp Name (experiment name) when available.

3. The Layer number (the innermost layer = 1).

4. The distance to the center of the multivariate space in Percent.

5. The design variables.

Runs in the candidate set that are not used to generate the D-Optimal design (not

included in the selected percentile ranges), are colored light gray.

When the candidate set is generated by MODDE the additional columns Layer and

Percent are unavailable. The layer belonging is displayed in the onion plots and when

listed (right-click and click Create List) the list is organized according to layer.

Evaluate

Click Design | D-Optimal | Evaluate to display the Onion D-Optimal results page.

You can use the table to select different designs, in selected layers.

See the D-Optimal Results section previously for more.

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D-Optimal

Onion plots

There are two onion plots to visualize the candidate set and the selected D-Optimal

design, the Onion Plot and the Onion 3D scatter.

For the onion scatter plots, the property page has two tabs: Select Factors and Plot

Labels. Use Select Factors to select which factors to display on the X, Y, and Z-axes.

Use Plot Labels to select which labels to display in the plot.

Onion plot

To create the 2D onion plot, click D-Optimal on the Design menu, and then click

Onion Plot.

The onion plot is a 2D scatter plot of the candidate set. The candidate set runs are

colored by layer, and the selected design runs are black.

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User Guide to MODDE

Onion 3D Scatter

To create the 3D Onion plot click D-Optimal on the Design menu, and then click

Onion 3D Scatter.

The Onion 3D scatter plot displays the candidate set colored by layer with the

selected design runs in black.

You can customize the plot using the plot settings. For more, see the Plots and List

chapter.

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Design Wizard

Introduction

The Design Wizard opens when you click File | New, to create a new

investigation, and guides you from the start of the investigation to the generation of the

worksheet. The design wizard can also be opened by clicking Design | Design Wizard.

Exit the wizard at any time by clicking Finish.

The accelerator for the Design Wizard is CTRL+W.

Following is a description of the pages in the Design wizard.

Defining factors

The first page of the design wizard is the Define Factors page. On this page you can

define (enter new factors), modify, and/or delete factors.

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User Guide to MODDE

All functionality available in the Factor spreadsheet described in the Factor chapter

is available in this page of the design wizard. Specific for the design wizard factor

page:

• The New and Edit-button open the Factor Definition dialog.

• The Delete-button deletes the factor(s) currently marked.

• Selecting the Place constraints on the experimental region box and

clicking Next opens the Constraints page of the design wizard. The

Constraints spreadsheet, including graphical constraints, is described in the

chapter Constraints and inclusions.

Note: The graphical constraint using the interface to define the constraint is

not available from the design wizard. If you want to use the graphical

constraint, click Design | Constraints

Clicking Next opens the Define responses page.

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Design Wizard

Defining responses

In the Define responses page you can define (enter new response), modify, or delete

responses.

chapter is available in the design wizard. Specific for the design wizard response page:

• The New and Edit-buttons opens the Response Definition dialog.

• The Delete-button deletes the response(s) currently marked.

Clicking Next opens the Select the objective page.

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User Guide to MODDE

In the Select the objective page you select the objective of your

investigation: Screening, RSM, Split Objective, or Paste Data. Objectives are

described in detail in the Objective chapter, section Selecting objective.

Clicking Next opens the Select the model and design page.

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Design Wizard

The Select the model and design page lists all designs, their resolution, the associated

models and number of runs, compatible with your objective and number of factors. See

the Selecting model and design section in the Objective chapter for details.

The Pseudo resolution applies to designs when they are blocked. See the section

Blocks in the Objective, model and design chapter and the section named

Orthogonal blocking in the Statistical appendix for more on Blocks.

If your design is classical, click Finish to generate the worksheet. If your design is D-

Optimal click Next to open the D-Optimal page of the wizard.

Note: You can sort the Design list on any column by clicking on its header.

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User Guide to MODDE

The Change D-Optimal settings page, the D-Optimal results page that appears after

clicking Next, and the creation of D-Optimal designs are described in detail in the D-

Optimal chapter.

When you click Next, MODDE generates the D-Optimal designs and displays the

results in the evaluation list consisting of:

1. The design number.

2. The number of runs in the design not including the 3 center points.

3. Statistics on the design.

The selected design is highlighted and marked with the worksheet icon.

Note: Sort the list according to any column by clicking its header.

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Worksheet

Introduction

After you have selected the model and design, MODDE generates the worksheet. The

worksheet is a spreadsheet used for storing the data (factors and response values) and

is where you enter the experimental results. The worksheet is by default sorted in

standard order.

Whenever you change the design (by editing the generators or selecting another

design) both the design and the worksheet are deleted and new ones are generated.

MODDE issues a message whenever the worksheet is regenerated.

The data in the worksheet are used when selecting to plot or list from the Worksheet

menu.

Worksheet menu

After the worksheet has been created and you have entered results, there are a number

of plots and lists available under the Worksheet menu.

All responses, regular and derived, are available in the plots and lists of the Worksheet

menu.

To open the worksheet spreadsheet, on Worksheet menu click Worksheet or click the

Worksheet button .

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User Guide to MODDE

Randomizing the run order is done to avoid that the effect of external variability, such

as room temperature or who performs the experiment, coincides with the effect of a

factor. By default the worksheet is Fully randomized.

With screening designs you can randomize To detect curvature. To do that, before

performing any experiments click Worksheet | Set Run Order and in the dialog

displayed, click To detect curvature. To display this dialog every time when you

create a screening worksheet, select the Always display this dialog after generating a

new design check box.

To re-randomize the run order after the worksheet has been created but before entering

results, on the Worksheet menu, click Set Run Order.

The run order can only be randomized for experiments with no results in the

worksheet.

Fully randomized

With RSM designs and Screening designs at more than 2 levels, Fully randomized is

the order in which you should perform the experiments and this is also the only

available order for these cases.

With 2 level screening designs, it is desirable to guard against strong curvature in the

response caused by too wide ranges in the factors. Strong curvature in the response

masks the effect of the factors. In this case you should select To detect curvature.

To detect curvature, one should first perform the following experiments:

1. A center point

2. A point with as many factors at high (+) as possible

3. A point with as many factors at low (–) as possible

After selecting To detect curvature and creating the worksheet you will find the three

points above at run order 1-3 and the rest of the runs randomized.

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Worksheet

Once the first three experiments are performed and the results are entered in the

worksheet, on the Worksheet menu, click Curvature Diagnostic plot to evaluate the

result.

Strong curvature

If the Curvature Diagnostic Plot exhibits strong curvature as is shown above, you

should first re-measure the center point and re-do the plot. If the plot still exhibits

strong curvature, reduce the ranges of the factors by 2 / 3 and restart the project.

No curvature

If the Curvature Diagnostic Plot does not exhibit curvature, as the one below,

continue performing the rest of the experiments.

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User Guide to MODDE

For 2D plots, select the variable to be plotted on the X-axis by marking it and clicking

the arrow ‘=>’. Mark the other variable(s) and click the arrow to Series.

For 3D plots, select the variables to be plotted on X, Y, and Series axes.

Click the Delete button in the dialog to remove factors or responses from the Y-

axis or from Series. To change what to display on the X-axis, mark and click the arrow

to add the new variable.

Click the Color by Variable tab to color by a factor or a response. With the scatter

plot created from the Worksheet menu you can also color by run order and experiment

number.

You can customize the 3D plot using the property page and plot settings. See the Plots

and List chapter.

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Worksheet

Histogram

On the Worksheet menu click Histogram to display the histogram of the currently

selected response.

Select the desired response or add more responses by right-clicking the plot and

clicking Properties, or by making the selection in the Response box.

Transform in Histogram

You can transform a response by right-clicking the Histogram plot and clicking

Transform.

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User Guide to MODDE

Descriptive statistics

Descriptive statistics can be displayed both as plot and in a list for all available

responses.

On the Worksheet menu, click Descriptive Statistics, then click Plot to open a Box

Whisker plot for the selected response.

The Box Whisker plot illustrates how the response values are distributed around the

response mean. The plot uses a box defined by the 25th and 75th percentiles and

whiskers ending at the maximum and minimum values.

Select the desired response or add more responses by:

• Right-clicking and then clicking Properties.

• Selecting in the Response box.

The descriptive statistics list summarizes the descriptive statistics for all responses.

On the Worksheet menu, click Descriptive Statistics, and then click List.

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Worksheet

Correlation

The linear correlation coefficients R between all the terms in the model and all the

responses are displayed in the Correlation Matrix and Correlation Plot.

Process factors are transformed, scaled, and centered as specified in the

factor definition for MLR (default = orthogonal scaling). Responses are transformed as

specified in the response definition.

Formulation factors are always scaled orthogonally.

The value of the correlation coefficient R represents the extent of the linear association

between two terms. The value of R ranges from -1 to 1. When R is near zero there is no

linear relationship between the terms.

Correlation matrix

On the Worksheet menu, click Correlation, and then click Matrix.

Correlation coefficients above the threshold, between a term in the model and the

responses are colored green and those between terms of the model are colored red.

To change the threshold, colors, or number format, right-click and click Properties.

Correlation plot

On the Worksheet menu, click Correlation, and then click Plot.

The default plot displays the 10 largest correlation coefficients.

To change number of correlations to display or limit the number of correlations

according to a threshold:

1. Right-click the plot and click Properties.

2. Make the change, for instance click Show absolute correlations above

threshold and enter a value. With '0' all correlations are displayed

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User Guide to MODDE

Replicate plot

In the replicate plot the values of the response are plotted vs. experimental runs

displaying the variation in the response for replicated experiments.

On the Worksheet menu click Replicate Plot to display the plot.

Select the desired response or add more responses by right-clicking and clicking

Properties, or by making the selection in the Response box.

Note: When the response has been transformed the Replicate plot displays the

back transformed values. To display the plot in the transformed metric, select

the Show transformed values check box in the Options tab in Properties.

Replicated experiments

MODDE checks the rows of all the factors (both included and excluded) in the

worksheet for replicates. Rows in the worksheet with the same factor values plus or

minus a tolerance are considered replicates.

The default Replicate tolerance is 0.1 (10%). You can change the Replicate

tolerance used in General Options on the View menu, tab General.

The replicates are used for the computation of the pure error and displayed on the same

Replicate Index in the Replicate Plot.

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Worksheet

Worksheet spreadsheet

Description of the worksheet

Experiment number: Exp No start with number one and are assigned sequentially.

They cannot be edited.

Experiment name: MODDE assigns a default experiment name, Exp Name, on the

form Nxx, where xx is the experiment number. You may edit the name and enter your

own identification. The Plot Label named Experiment Name displays the text entered

under Exp Name when plotted.

Run order: The Run Order is the order in which the experiments should be

performed. MODDE suggests a randomized run order. Sort the worksheet according to

run order before performing the experiments.

Include or exclude: The fourth column labeled Incl/Excl indicates if the experiment is

included or excluded from the analysis. When the worksheet is generated all

experiments are marked Incl and are included in the analysis. To exclude an

experiment from the analysis select Excl in the worksheet.

Note: Excluded rows are excluded from the analysis for all responses. To

exclude the response value for only one response, right-click the cell and click

Exclude value(s).

Factors: In the Factor columns the factors are listed in original units.

Blocking: When you have selected Blocks in the Select the model and design page,

the column $BlockV displays which block each experiment has been assigned to.

For details on blocking, see the Orthogonal blocking section in the Statistical

appendix.

Responses: In the columns to the far right all responses are found. The response values

are listed in original units.

When responses have missing values, in the analysis, MODDE creates individual

models for all responses excluding only the row with the missing value for the relevant

response.

Missing values in controlled factors are not allowed.

You cannot delete the worksheet; MODDE will automatically delete the worksheet

when you make modifications to the factors.

On the Worksheet menu click Worksheet to display the spreadsheet or click the

worksheet button.

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User Guide to MODDE

To add extra runs to the worksheet:

• Open the worksheet window, then click Edit | Add Experiments.

• Open the worksheet window, right-click and click Add Experiment.

• On the Design menu, click Inclusions. Type values or import the

experimental runs you want added to the worksheet. Then click the Add to

Worksheet button. The inclusions will be added at the end of the worksheet.

The first four columns of the worksheet are automatically filled in when adding

experiments.

To sort a column in the worksheet:

• Right-click the desired column and then click Sort.

• Mark the worksheet, then click Edit | Sort.

Suspicious values in the worksheet are colored in red. Non-transformable values have a

red background. Mark a colored cell to display a message about why it is colored in the

status bar.

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Analysis

Introduction

After entering the response values in the worksheet, analyze the resulting data in the

menu Analysis.

Use the Analysis Wizard to guide you through from raw data analysis to interpretation

and diagnostics.

You can also manually fit the model to the data by using either MLR (Multiple

Linear Regression) or PLS (Projection to Latent Structure) and clicking Fit. To review

the fit, display as lists or plots, the summary of the fit, the coefficients, the effects, and

the analysis of variance (ANOVA). Residual plots and the Box-Cox plot (only for

MLR) are available for diagnostic purposes.

The Analysis menu is organized as follows:

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User Guide to MODDE

Evaluate

Click Evaluate on the Analysis menu to display an evaluation of the current worksheet

and model. The table includes condition number, (number of) worksheet runs, (number

of) model terms, DF (degrees of freedom) residual, DF lack of fit, and DF pure error

individually for each response. These values differ between the responses when they

have different models or excluded values.

Condition number

The Condition Number is the ratio of the largest and the smallest singular values of X

(eigenvalues of X'X) where X is the extended design matrix. This condition number

represents a measure of the sphericity of the design (orthogonality). All factorial

designs, without center points, have a condition number of 1 and the design points are

situated on the surface of a sphere. For more see the Statistical appendix.

With factors orthogonally scaled all classical screening designs have a condition

number =1 without center points and <3 with center points. The condition number of

classical RSM designs varies according to the number of factors but remains <10.

For a definition of the condition number, see the Statistical appendix.

The condition number with mixture data depends on the method of fit and the type of

model. For details see the Statistical appendix.

In addition to the condition number the evaluation table also displays:

• Worksheet runs: the number of runs included in the Worksheet spreadsheet.

• Model terms: the number of terms included in the current model.

• DF residuals: The degrees of freedom of the residuals.

• DF lack of fit: the degrees of freedom of the Lack of Fit

• DF pure error (repl. runs): degrees of freedom of the pure error calculated

using the replicated runs (experiments). If there are no replicated runs the

pure error cannot be calculated.

For details on degrees of freedom see the Statistical appendix.

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Analysis

Analysis Wizard

The Analysis Wizard guides you through the main steps from review of the raw data

and the fit, to the diagnostics and refining of the model.

When opening the Analysis Wizard, the model is automatically fitted using the default

fit method.

In the Analysis Wizard each response is handled separately in a step wise manner

where you start looking at plots, pruning the model etc. for one response, and when

done you step over to the next response.

The following features are available as buttons in the Analysis Wizard:

• Display or hide Min, Target, and Max limits when available in the response

definition.

• Display regression line in the Residual Normal Probability Plot and

Note: All changes done in the Analysis Wizard take effect immediately.

Clicking Close closes the Analysis Wizard but all changes remain.

To open the Analysis Wizard, click Analysis | Analysis Wizard and select a starting

response, or click the button in the Standard toolbar. Clicking the Analysis

Wizard button opens the Analysis Wizard for the first response.

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User Guide to MODDE

The Analysis Wizard includes the following plots with a descriptive text: Replicate

Plot, Histogram Plot, Summary Plot, Coefficient Plot, Residual Normal

Probability Plot, and Observed vs. Predicted Plot.

You can customize the text displayed in the Analysis Wizard by opening the

'AnalysisWizard.zip' file in the program folder and editing the .mht-files.

When fitting the model to the data MODDE uses the default fit method unless you

select a different fit method.

To select fit method, click Select Fit Method on the Analysis menu and click your

choice. Only change the fit method when you have a reason for it. Normally you can

leave the MODDE default Auto as fit method.

To fit the data click Fit on the Analysis menu.

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Analysis

The following fit methods are available: Auto, MLR, PLS, Scheffé MLR, MLR with

Pseudo Components, PLS with Pseudo Components, and Scheffé MLR with

Pseudo Components.

Select Auto to use the default. MODDE defaults to using Multiple Linear

Regression (MLR) as long as the condition number permits. When the condition

number becomes too large, MODDE defaults to using PLS. You may override the

default by selecting PLS.

Note: If your X matrix has a condition number > 3000, MODDE will only fit

the model with PLS and the condition number selecting MLR is displayed as

infinite.

Scheffé MLR

Select Scheffé MLR to fit the mixture data with a Scheffé type model. When you select

this fit method, the model is restored to its default specification. When your

investigation contains both mixture and process factors Scheffé MLR is unavailable as

such models are only available in MODDE for experiments with mixture factors only.

Select MLR, PLS or Scheffé with pseudo components to analyze the mixture data

transformed to pseudo components.

When you select a fit method with pseudo components, MODDE displays all mixture

designs (the design matrix not the worksheet) with the mixture factors transformed to

pseudo components. When the mixture region is a simplex, transforming to pseudo

components gives all mixture factors the range 0 to 1. When the mixture region is not a

simplex, pseudo components stretch the experimental region.

To fit the data click Fit on the Analysis menu.

When fitting with MLR, MODDE will separately but automatically fit all of the

responses. Use the Response box to select the desired response, or right-click, click

Properties, and tab Select Responses.

If some response values are missing, MODDE excludes the row(s) with missing data

for that specific response and keeps it for all others in the calculations.

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User Guide to MODDE

With PLS all responses are fitted simultaneously.

PLS handles missing values in the responses, without excluding the runs from the

analysis when the same model is used for all responses. When the models are not

identical, the fit is done separately for each response and missing is handled as for

MLR.

When fitting the model with PLS, MODDE computes as many PLS components as

significant by cross validation. See statistical appendices for significance rules. To add

more PLS components click Next Component on the Analysis menu.

Once the model is fitted the command menus to display results and perform

diagnostics are available. Specific menus pertaining only to PLS are unavailable when

fitting the model with MLR.

To exclude response(s) from the analysis, set their unit variance modifier to zero, in the

response dialog box. This will give the response(s) zero variance, and hence exclude

them from the analysis.

Note that with PLS the X matrix is always scaled and centered to unit variance. The

centered responses are scaled as you selected in the response definition menu. The

default is unit variance.

For more details on PLS see the Statistical appendix.

Note: The default method of fit with the Cox reference mixture model is PLS.

When the model obeys mixture hierarchy you can if you want fit the model

with MLR. When fitting the model with PLS, the condition number refers to

the X matrix, with unit variance coding.

The advisor opens when you fit the model and guides through the analysis. To turn on

or off the advisor:

• On the View menu, click Dockable Windows, and then click Analysis

Advisor.

If you want to extract more components than significant according to the cross-

validation rules, click Next Component on the Analysis menu. All open plots and lists

are automatically updated.

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Analysis

After fitting the model, review the fit in plots and lists. If the model was fitted with

MLR the PLS Summary plots are unavailable.

To display the summary of fit plot, on the Analysis menu click Summary, then click

Plot.

For every response MODDE displays 4 columns: R2, Q2, Model Validity, and

Reproducibility.

Note: R2 and Q2 provide the best summary of the fit of the model. R2 is an

overestimated and Q2 an underestimated measure of the goodness of fit of the

model

Saturated models

R2 and R2 Adjusted are not available for saturated models, i.e. models with DF

(degrees of freedom) equal to zero (see statistical appendices). However, with PLS Q2

can still be computed for saturated models and is hence displayed in plots and lists.

Statistics

In the plot footer MODDE displays:

N = Number of experimental runs.

DF = N-p (the degrees of freedom of the residuals).

Cond. no. = Condition number of the extended design matrix coded as selected in the

factor definition box: MLR scaling, or for PLS, unit variance.

2

R

The first column in the summary plot is R2 and is the fraction of the variation of the

response explained by the model:

R 2 = SS REG /SS

SSREG = the sum of squares of Y corrected for the mean, explained by the

model.

SS = the total sum of squares of Y corrected for the mean.

R2 overestimates the goodness of fit.

The R2 value is always between 0 and 1. Values close to 1 for both R2 and Q2

indicate very good model with excellent predictive power.

For details see the Statistical appendix.

You may select to plot R2 Adjusted instead of R2 by clicking it in the

Properties page or set it to be default displayed by clicking Investigation

Options on the View menu, tab R2.

R2 Adjusted: The fraction of variation of the response explained by the model

adjusted for degrees of freedom.

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Q2

The second column in the summary plot is Q2 and is the fraction of the variation of the

response predicted by the model according to cross validation and expressed in the

same units as R2.

Q 2 = 1 - PRESS/SS

PRESS = the prediction residual sum of squares.

SS = the total sum of squares of Y corrected for the mean.

Q2 underestimates the goodness of fit.

The Q2 is usually between 0 and 1. Q2 can be negative for very poor models. With PLS

negative Q2 are truncated to zero for computational purposes. Values close to 1 for

both R2 and Q2 indicate a very good model with excellent predictive power.

For details see the Statistical appendix.

Model validity

The third column in the summary plot is the Model Validity and is a measure of the

validity of the model.

When the model validity column is larger than 0.25, there is no lack of fit of the model.

This means that the model error is in the same range as the pure error.

When the model validity is less than 0.25 you have a significant lack of fit and the

model error is significantly larger than the pure error (reproducibility).

A model validity value of 1 represents a perfect model.

Validity = 1 + 0.57647*log(plof)

where plof = p for lack of fit.

Reproducibility

The forth column in the summary plot is the Reproducibility which is the variation of

the response under the same conditions (pure error), often at the center points,

compared to the total variation of the response.

Reproducibility = 1 - (MS(Pure error)/MS(total SS corrected)).

MS = Mean squares, or Variance.

A reproducibility value of 1 represents perfect reproducibility.

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Analysis

To open the Summary List, on the Analysis menu, click Summary, and then click

List.

The list displays for each response: R2, R2 Adjusted, Q2, SDY=Standard Deviation of

the Y (response), RSD=the Residual Standard Deviation, N=number of experiments,

model validity, and reproducibility. For more details on SDY and RSD, see the

Statistical appendix.

To display the PLS Total Summary plot, on the Analysis menu, click PLS

Summary, and then click Summary Plot.

For every fitted response the plot displays R2 and Q2. The definition for R2 and Q2 is

the same as in the Summary of Fit Plot.

You may select to plot R2 Adjusted instead of R2 by selecting it in the Properties

page or setting it as default in View | Investigation Options, tab R2.

The condition number is calculated for the extended design matrix with the factors

scaled to unit variance.

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To display the PLS Summary for 'response' plot, on the Analysis menu click PLS

Summary, then click Response Plot.

This plot displays the R2 and Q2 per PLS component for the selected response. You can

change the selected response using the Response box. You may select to display R2

adjusted instead of R2 in the Property page and in the Investigation Options menu.

To display the PLS Summary List, on the Analysis menu, click PLS Summary, and

then click List.

The PLS summary list displays R2, R2 adjusted and Q2 per PLS component for all the

responses (Total) and for each response.

Saturated models

R2 and R2 Adjusted are not available for saturated models, i.e. models with DF

(degrees of freedom) equal to zero (see statistical appendices). However, with PLS Q2

can still be computed for saturated models and is hence displayed in plots and lists.

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Analysis

Investigating diagnostics

Use the diagnostic plots and lists to find outliers, needed transformations etc.

To display the normal probability plot of residuals, on the Analysis menu, click

Normal Prob. Plot Residuals.

The residuals are plotted on a cumulative normal probability scale.

This plot makes it easy to detect:

• Normality of the residuals. If the residuals are normally distributed, the

points on the probability plot follow close to a straight line

• Outliers. These are points deviating from the normal probability line, and

having large absolute values of studentized residuals i.e. larger than 4

standard deviation indicated by red lines on the plot.

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Residuals

Under Analysis | Residuals three residual plots and one list are available.

To display the Residuals vs. Predicted Y plot, on the Analysis menu, click Residuals,

and then click vs. Predicted Response.

The plot shows the residuals vs. the fitted values. This plot is particularly useful to

detect non-constant variance of the residuals. If the spread of the residuals increases

with the fitted values, you may need to transform your response by taking its logarithm

or its square root.

To display the Residuals vs. Run Order plot, on the Analysis menu, click Residuals,

and then click vs. Run Order.

This plot shows the residuals vs. run order (the order in which you performed the

experiments) and helps you detect any dependency of the residuals on time.

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Analysis

To display the Residuals vs. Variable plot, on the Analysis menu, click Residuals,

and then click vs. Variable.

You may plot residuals vs. any factor or response in the model. Patterns in this plot

may help detect systematic effects left out of the model.

Right-click the plot and click Properties to select which variable to display on the x-

axis.

Residual list

To display the Residuals List, on the Analysis menu, click Residuals, and then click

List.

The number under the response name, is the experiment number.

Observed: The value of the response as listed in the worksheet.

Predicted: The predicted value for that observation.

Observed - Predicted: The residual for that observation.

Confidence Interval: The 95% confidence interval on the predicted value. You can

change the confidence level in the Property page and in Investigation Options.

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Each plot type can display different types of residuals: Raw, Standardized, or Deleted

Studentized.

To change the default type of residual to display, on the View menu, click

Investigation Options, and in tab Residuals click to make your change.

Raw residuals

The raw residual is the difference between the observed and the fitted (predicted)

value.

Standardized residuals

The standardized residual is the raw residual divided by the residual standard deviation

(RSD). With PLS and models with less than 2 degrees of freedom, MODDE uses as

default the standardized residuals.

Deleted studentized residuals

The deleted studentized residual is the raw residual eIi divided by its standard deviation

(si) where the standard deviation (si) is computed with observation (i) left out of the

analysis, and corrected for leverage. Deleted studentized residuals, requires at least two

degrees of freedom.

For MLR models with 2 or more degrees of freedom, deleted studentized residuals are

the default when plotting residuals.

With PLS, deleted studentized residuals are not available.

To open the distance to model in y space plot, on the Analysis menu, click Distance to

Model (Y).

The RSD of an object in the Y space is proportional to the object distance to the hyper

plane of the PLS model in the Y space. MODDE computes the object distance to the

PLS model (DModY) in the Y space and displays them as columns in a plot.

A large DModY value indicates that the experiment may be an outlier.

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Analysis

To open the Box Cox plot, on the Analysis menu click Box Cox Plot.

The Box Cox plot displays the maximum likelihood as a function of the power of the

transformation by plotting values of lambda, λ, vs. the maximum likelihood.

If the response values vary more than a magnitude of ten in the experimental domain, a

transformation is often recommended.

The maximum point on the Box Cox plot gives the value of (lambda, λ) for the

response transformation Yλ that gives the best fit of the model. This is the maximum

likelihood estimator for λ. For more, see the Statistical appendix.

MODDE displays λmax and its 95% confidence interval as λlower and λupper in the footer

and on the plot as 3 vertical lines.

If λ=1 is included in that interval, then no transformation is recommended.

If λ=1 is not included in the interval then Yλmax is the recommended transformation.

You do not have to use the precise value of λmax but a near convenient value.

Common transformations are:

• λmax = -1, use the Power transformation and C3 = -1.

• λmax = 0, use the Logarithmic (10Log) transformation.

• λmax = 0.5, use the Power transformation and C3 = 0.5.

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To display the observed vs. predicted plot, on the Analysis menu, click Observed vs.

Predicted.

The observed vs. predicted plot displays the plot of the observed values vs. the fitted or

predicted values. Plots with the points close to straight line indicate good models.

A regression line can be fitted by clicking the regression button on the Plot toolbar.

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Analysis

To display the lack of fit plot, on the Analysis menu, click Lack of Fit Plot.

The lack of fit plot compares the Lack of Fit (LoF) component to the pure

error component and displays a graph with 3 bars.

• SD-LoF: Shows the variation of the response due to the lack of fit of the

model (i.e. the model error) adjusted for degrees of freedom and in the same

units as Y. This is the square root of MS (mean square) lack of fit.

• SD-pe (Pure error): Shows the variation due to the replicated experiments

(observations) adjusted for degrees of freedom and in the same units as Y.

This is the square root of MS (mean square) pure error.

• SD-pe*sqrt(F(crit)): Shows SD pure error (second bar) multiplied by the

square root of the critical F.

The critical F is the value of the F-distribution over which SD LoF is statistically

significant at the 95% confidence level.

Hence, when the third bar is smaller than the first, the lack of fit is significant at

the 5% level (see statistical appendices).

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The analysis of variance (ANOVA) partitions the total variation of the response (Sum

of Squares, SS, corrected for the mean) into a component due to the regression model

and a component due to the residuals.

ANOVA plot

To display the ANOVA plot, on the Analysis menu, click ANOVA, and then click

Anova Plot.

In the ANOVA plot the regression component is compared with the residual

component and 3 bars are displayed.

• SD Regression: Shows the variation of the response explained by the model,

adjusted for degrees of freedom and in the same units as Y. This is the square

root of MS (mean square) regression.

• RSD: Shows the variation of the response not explained by the model,

adjusted for degrees of freedom and in the same units as Y. This is the

residuals standard deviation.

• RSD*sqrt(F(crit)): Shows RSD (second bar) multiplied by the square root

of the critical F.

The critical F is the value of the F-distribution over which SD regression is statistically

significant at the 95% confidence level.

Hence, when the third bar is smaller than the first, the model is significant at the

5% level. For more see the Statistical appendix.

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Analysis

ANOVA table

To open the ANOVA table, on the Analysis menu, click ANOVA, and then click

Anova Table.

The analysis of variance (ANOVA) table is displayed for the selected response.

If there are replicated observations, the residual sum of squares is further partitioned

into PURE ERROR and LACK OF FIT. A goodness of fit test is performed by

comparing the MS (mean square) lack of fit to the MS (mean square) pure error. See

the Statistical appendix for more information.

Replicated observations

MODDE checks the rows of the factors in the worksheet for replicates. Rows in the

worksheet with the same factor values plus or minus a 10% tolerance interval are

considered replicates and used for the computation of the pure error. The replicate

tolerance can be changed in General Options.

Note: The red coloring of the p-values always refer to the 95% resp. 5%

levels.

At the bottom of plots and tables the following is displayed:

N = Number of Runs.

DF = N-p degrees of freedom of the residuals.

R2, R2 adjusted, Q2 and RSD (residual standard deviation).

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When you are satisfied with the diagnostic part of the evaluation you can start the next

phase: reviewing and interpreting the model. To review and interpret the model, use

the coefficient, effect, and variable importance plots and lists.

There are two coefficient plots and two coefficient lists available in MODDE.

When confoundings are present, the coefficient plots and lists display a bracket # after

the term. Point to the column to view the confounded terms.

Coefficient plot

To create the coefficient plot, on the Analysis menu click Coefficients, and then click

Plot.

• The coefficient plot displays the coefficients, when changing from 0 to high,

for the selected response with the confidence interval as error bars. By

default, the coefficients refer to the data scaled and centered.

• You can select which type of coefficient to display from Properties. Select

Scaled and centered (default), Normalized, Unscaled, or PLS orthogonal

(only available for PLS).

• When you have confounded terms in your investigation these terms are

marked with a bracket #. Hoover over the column in the plot and you will get

information about which term(s) it is confounded with. This information is

available also in the coefficient overview plot.

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Analysis

To create the coefficient overview plot, on the Analysis menu click Coefficients, and

then click Overview Plot.

The overview plot displays the coefficient values for every response as bar graphs side

by side.

To make the coefficients comparable when responses (Y's) have different ranges,

MODDE displays the coefficients in Normalized form that is the coefficients are

divided by the standard deviation of their respective response. The Normalized mode

is the default for the overview plot. You can change it to regular scale and centered

coefficients by right-clicking and then clicking Properties.

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User Guide to MODDE

Coefficient list

To create the coefficient list, on the Analysis menu click Coefficients, and then click

List.

P-values signaling non significant coefficients at the selected confidence interval are

colored in red.

For the selected response(s), this list includes:

Terms: Under the response name the name of the terms included in the model are

listed. To display the list for another response, or more than one response, use the

Response bar or Properties.

Coefficients: Value of the coefficient.

Standard error: Standard error of the coefficient

P Value: Probability to get the displayed value for the coefficient if its true value was

zero.

Confidence interval: The 95% confidence interval on the coefficient value. To select a

different level for the confidence interval open Properties or Investigation Options.

To create the coefficient overview list, on the Analysis menu click Coefficients, and

then click Overview List.

The coefficient overview list displays the scaled and centered coefficients for all the

responses. Non significant coefficients at the selected confidence interval are colored

in red.

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Analysis

In MODDE you can create four effects plots:

1. Effect plot: Displays the effect calculated as twice the MLR coefficient and

sorted descending in absolute value.

2. Effect normal probability plot: Displays the effects on a normal probability

scale.

3. Main effect plot: Displays predicted values of the selected response, when

the factor varies from its low to its high level.

4. Interaction plot: Displays predicted values of the response, when a factor

varies from its low to its high level, plotted for all the combinations of levels

of the other factor(s).

The Effects List displays the effects and their confidence intervals.

Note: When an expanded list of the qualitative levels is desirable, use the

coefficients plots and lists to display or list the coefficients for every level of a

qualitative variable instead of the effects plots and lists. Note that the effects

for linear and interaction models are twice the corresponding coefficients.

To open the effects plot, on the Analysis menu, click Effects, and then click Plot.

For process factors the values of the effects (computed as twice the MLR coefficients)

are plotted sorted (in absolute value) in descending order. The ± 95% confidence

interval is shown as error bars.

For mixture factors this plot displays the adjusted Cox effects (unavailable for Scheffé

models). This effect represents the change in the response values when component k

varies over its range, all other mixture factors kept in the same proportion as in the

reference mixture.

For details on how the mixture effects are calculated, see Statistical appendix, section

Mixture data in MODDE.

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To open the effects normal probability plot, on the Analysis menu, click Effects, and

then click Normal Probability Plot.

The plot displays the effects plotted on a cumulative normal probability scale.

You should only use this plot when you have a saturated model (model with as many

terms as experimental runs). For saturated models MODDE cannot compute standard

errors, p values and confidence intervals. Use the N-Plot to help you determine the

important effects.

This plot, proposed by Daniel's in 1954, is based on the fact that if all estimated effects

were noise, they would have a normal distribution and when plotted on a normal

cumulative plot, would fall on a straight line. Hence effects significantly different from

zero (noise) will fall outside the normal line.

Note that this plot assumes independent effects, and that all estimable effects are

plotted. Hence, it is only relevant for screening designs with saturated models DF = 0.

Also for this plot to be meaningful, one needs models with at least 10 effects. If these

conditions are not met MODDE will warn you that this plot may not be statistically

correct.

Note: The normal probability of effects plot is not available with mixture

factors

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Analysis

To open the main effects plot, on the Analysis menu, click Effects, and then click

Main Effect.

To switch factors, right-click the plot, click Properties, click the Select Factor tab,

and then click the factor.

For process factors the plot displays the predicted values of the selected response,

when the factor varies from its low to its high level, all other factors in the design held

constant at their averages.

If the design has replicated points for the displayed factor where the other factors are

also at their averages, the observed values of these points are displayed with red

symbol.

When you selected to display a mixture factor Xk, this plot displays the predicted

change in the response when Xk varies from its low to its high level, the relative

amounts of all other mixture factors are kept in the same proportion as in the standard

reference mixture.

For details, see the Statistical appendix, section Mixture data in MODDE.

With formulation factors you can adjust according to reference or to range using

Properties.

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Interaction plot

To open the interaction plot, on the Analysis menu, click Effects, and then click

Interaction Plot.

To switch to another interaction and/or switch the factor displayed on the x-axis:

1. Right-click the plot and click Properties.

2. In tab Interaction Effects select the term in the Interaction term box and/or

select the factor in the Factor on X-axis box.

Note: This plot is only available for process factor. No interaction plots are

available for mixture factors.

When you select a 2 factor interaction, the predicted values of the response, when one

factor varies from its low to its high level, are plotted for both levels of the other factor,

all remaining factors in the design being set on their average.

If you have mixture factors in the model, these are all set at the standard reference

mixture.

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Analysis

When you select a 3-factor interaction, the predicted values of the response, when a

factor varies from its low to its high level, are plotted for all the combinations of levels

of the other two factors.

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User Guide to MODDE

Effects list

To open the effects list, on the Analysis menu, click Effects, and then click List.

The values of the effects (twice the coefficients) are listed with their 95% confidence

interval sorted (in absolute value) in descending order.

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Analysis

The VIP values reflect the importance of terms in the model both with respect to Y, i.e.

its correlation to all the responses, and with respect to X (the projection). With

designed data, i.e. close to orthogonal X the VIP values mainly reflect the correlation

of the terms to all the responses.

To open the VIP plot, on the Analysis menu, click Variable Importance (VIP), and

then click Plot.

The VIP plot displays the VIP values as a column plot sorted in descending order.

To open the VIP list, on the Analysis menu, click Variable Importance (VIP), and

then click List.

The VIP list displays the sorted VIP values and the PLS coefficients for all responses

in the investigation.

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User Guide to MODDE

The score and loading plots complement each other. The position of an observation in

a given direction in a score plot is influenced by variables lying in the same direction

in the loading plot.

There are four types of PLS plots available:

• Score Scatter Plot – displays the score vectors t and/or u in a scatter plot.

Use the score plots to reveal groups, trends, outliers, and similarities. The

plot marks represent your experiments.

• Score Column Plot – displays the score vectors t or u in a column plot.

• Loading Scatter Plot – displays the loading vectors p, c, w and/or wc in a

scatter plot. Use the loading plots to investigate the correlation between

terms in your model. The plot marks represent the terms currently in the

model and/or the response-variables. The response variables are displayed

when plotting the c-vectors.

• Loading Column Plot – displays the loading vectors p, c, w or wc in a

column plot.

To open a score plot, on the Analysis menu, click PLS Plots, and then click Score

Scatter Plot or Score Column Plot.

You can create three different score scatter plots:

1. T scores (for ex.: t1 vs. t2): t scores are windows in the X space displaying

the objects as situated on the projection plane or hyper plane.

2. U scores (for ex.: u1 vs. u2): u scores are windows in the Y space, displaying

the objects as situated on the projection plane or hyper plane.

3. T vs. U scores (for ex.: t1 vs. u1): Displays the objects in the projected X (T)

and Y (U) space, and how well the Y space coordinate (u) correlates to the X

space coordinate (t).

Score column plots can only be created for one vector at a time.

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Analysis

T scores: t1 vs. t2, t1

These plots are projections from the X space displaying the objects as situated on the

projection plane or hyper plane.

These plots are projections from the Y space, displaying the objects as situated on the

projection plane or hyper plane.

These plots display the objects in the projected X (T) and Y (U) space, and how well

the Y space coordinate (u) correlates to the X space coordinate (t).

You can add a regression line to the plot by using the Plot toolbar.

To open a loading plot, on the Analysis menu, click PLS Plots, and then click

Loading Scatter Plot or Loading Column Plot.

The loading plots display the correlation between the X variables T(X) and the Y

variables U(Y).

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1. p loadings (for ex.: p1 vs. p2): These plots show the importance of the X

variables in the approximation of the X matrix.

2. w loadings (for ex.: w1 vs. w2): The w's are the weights that combine the X

variables (first dimension) or the residuals of the X variables (subsequent

dimensions) to form the scores t. These weights are selected so as to

maximize the correlation between T and U, thereby indirectly Y. X variables

with large w's (positive or negative) are highly correlated with U (Y).

Variables with large w's are situated far away from the origin (on the positive

or negative side) on the plot.

3. c loadings (for ex.: c1 vs. c2): These plots display the correlation between the

Y variables and the X scores T (X). The c's are the weights that combine the

Y variables with the scores u; so as to maximize their correlation with X. Y

variables with large c's are highly correlated with T (X).

4. wc loadings (for ex.: wc1 vs. wc2): These plots show both the X-weights (w)

and Y-weights (c), and thereby the correlation structure between X and Y.

One sees how the X and Y variables combine in the projections, and how the

X variables relate to Y.

Loading column plots can only be created for one vector at a time.

For details see the Statistical appendix.

The default loading scatter plot is the wc1 vs. wc2 plot. The w's are the weights that

combine the X variables to the scores t, so as to maximize their correlation with Y. X

variables with large w's are highly correlated with U(Y). Variables having large w's are

positioned far away from the zero point in the plot.

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Prediction

Introduction

To make prediction using the model means:

• Using contour plots for interpretation.

• Making predictions in the prediction plots and list.

• Optimizing for selection of “best conditions”.

• Investigating robustness to disturbances using the Design Space.

The prediction menu includes:

• Contour Plot Wizard

• Prediction Plot Wizard

• Response Prediction Plot

• Prediction List

• Scatter Plot

• Sweet Spot Plot

• Optimizer

• Design Space Validation - only briefly described here but more thoroughly

in the Design Space chapter and Appendix D: Design Space.

Note: The Prediction menu applies to all responses, regular and derived.

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The contour plot wizard guides you through the selection and specification of 2D and

4D contour plots for mixture and process factors and 2D Surface plots for process

factors.

To open the contour plot wizard, on the Prediction menu, click Contour Plot Wizard.

Under Inner plot type, the default plot type for the inner axes is selected. If you have

both process and formulation factors in the investigation, click the type of factor to

display on the inner axes: Process or Mixture.

On the outer axes you can vary process factors only.

Selecting responses

You can select to display all responses for the 2D contour plots but with more than 9

the plots become very small. The contours are not overlaid, but displayed next to each

other.

Select which response(s) to display by marking in Available responses and clicking

the => and/or marking in Selected responses and clicking <=.

Using constraints

Select the Use constraints box if you want the available constraints to be displayed in

the plot.

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Prediction

Plot options

To select the resolution of the plot, that is, the grid calculated to create the contour plot,

click Plot Options. Note that you can type a resolution value here or click one of the

predefined resolutions.

You can also select to scale the subplots equally, to lock the contour levels, to produce

the plot with/without color and with/without contour level labels.

For more, see the Customizing contour plots sections in the Plots and lists chapter.

2D contour

The 2D contour plot displays the predicted response values, spanned by two factors, in

a response surface contour plot. For mixture the plot is spanned by three factors.

On the first page of the contour wizard, under Plot type, click Contour.

Under Inner plot type, if you have both process and mixture factors in the model,

click Process or Mixture to indicate which factors you want to display on the inner

axes.

Select which responses to display and click Next.

In the Axes and Constants dialog, select the factors to be plotted on the x and the y

axes. Change the default ranges as desired. When your factors are mixture, select the

three mixture factors to be plotted.

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By default, all constant factors are set at their mid-range values; change these values as

desired. After the plot has been created the constant factors are found to the right in the

plot. When you change the value of the constant factors the contour plots are updated.

To hide the constants, right-click the window, and clear View Constants.

Zooming subplot

To zoom in on a subplot, click Subplot in the Zoom plot menu from the Plot toolbar.

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Prediction

4D contour

The 4D Contour plot displays the predicted response values, spanned by two factors,

in 9 response surface contour plots in a 3x3 grid spanned by another two factors. For

mixture the plots are spanned by three factors.

On the first page of the contour wizard, under Plot type, click 4D Contour.

factors, and with both mixture and process factors, but not with mixture

factors only.

Under Inner plot type, if you have both process and mixture factors in the model,

click Process or Mixture to indicate which factors you want to display on the inner

axes.

Select which response to display and click Next.

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When the model includes both process and mixture factors, the mixture factors can

only be selected as inner factors.

Select two process factors for the axes under Factors at the plot axes, or three mixture

factors

Outer axes factors

Select two process factors for the outer axes. The response contours are plotted for the

low, middle, and high levels of these factors.

You can also select qualitative factors for the outer axes and select for which settings

to display the contour plots.

When there are more than 4 factors in the model, the remaining factors are held

constant

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Prediction

By default all plots are equally scaled, that is, the color coding is the same for all plots.

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Response Surface

The Response Surface plot displays the predicted response values, spanned by two

factors, in a response surface plot. This plot is only available for models with two or

more process factors and can only display one response.

On the first page of the contour wizard, under Plot type, click Surface.

Select the responses to display and click Next.

In the Axes and Constants dialog, select the factors to be plotted on the x and the y

axes. Change the default ranges as desired.

By default, all constant factors are held constant at their mid-range values; change

these values as desired. After the plot has been created the constant factors are found to

the right in the plot. When you change the value of the constant factors the contour

plots are updated.

To hide the constants, right-click the plot and clear View Constants.

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Prediction

The prediction plot wizard guides you through the selection and specification of

prediction plots. In the prediction plots the predictions of the selected responses are

displayed for their low, center, and high levels. The predictions of each subplot are

adjusted for all the other factors.

To open the prediction plot wizard, on the Prediction menu, click Prediction Plot

Wizard.

You can create two types of plots in the prediction plot wizard: the Prediction plot and

the Overlay prediction plot. The prediction plot displays the predicted value for the

low, center, and high values of up to 3 factors and up to 3 responses with confidence

intervals when the Show confidence intervals check box is selected. The overlay

prediction plot displays the predicted value for the low, center, and high values of up to

3 factors and up to 9 responses. No confidence intervals can be displayed for the

overlay plot.

On the first page of the prediction plot wizard you need to select: plot type, factor type,

responses, and whether to display confidence intervals.

Plot type

To select to create a prediction plot, under Plot type click Prediction or Overlay

prediction on the first page of the prediction plot wizard.

Factor type

Under Factors at the X-axes, click the type of factor to vary: Process or Mixture.

You cannot vary simultaneously both process and mixture factors.

Selecting responses

You can select to display up to 3 responses for the prediction plot and 9 for the overlay

prediction plot. Select which response(s) to display by marking in Available responses

and clicking the => and/or marking in Selected responses and clicking <=.

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Select the Show confidence intervals check box to display the 95% (default)

confidence intervals. Change the confidence level in Investigation Options under the

View menu or right-click the plot and click Properties.

After clicking Next on the first page of the Prediction Plot Wizard, the Axes and

Constants dialog box is displayed.

Select the factors to be plotted under Factors at the X-axes. Change the default ranges

as desired.

Select values for the factors when they are kept constant under Constant factors.

When a mixture factor varies, the relative amounts of all other mixture factors are kept

in the same proportion as in the standard reference mixture and no mixture factors are

displayed in the Constant factors box. If no standard reference mixture is specified,

the centroid of the constrained region is used as the default.

Range or reference

You can select to keep the relative amount of the other mixture factors in the same

proportion as their ranges, rather than the reference mixture (default) by clicking

Adjusted to range.

In the Overlay Prediction Plot, the predictions for all the selected responses (max. 9)

are displayed in the same plot for up to 3 factors.

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Prediction

The response prediction plot displays the predicted response values for one factor (the

default factor in Investigation Options) and for all levels present for that factor in the

worksheet.

This plot displays a spline representing the variation of the fitted response when the

selected factor varies over the range defined in the design, adjusted for all remaining

factors. The 95% confidence intervals are displayed.

Right-click the plot and click Properties to:

• Select the response(s) on the Select Responses page. You can also use the

Response box.

• Select which factor to display on the Select Factor page. For mixture factors

you can also select to Adjust proportional to reference mixture or Adjust

proportional to ranges

• Select confidence level on the Confidence Level page.

Factor type

The response prediction plot can be displayed for process and mixture factors although

only one at a time.

Process factor

When the selected factor is a process factor, all other factors are kept constant on their

averages.

Mixture Factor

When the selected factor is a mixture factor, the relative amounts of all other mixture

factors are kept in the same proportion as in the standard reference mixture. If no

standard reference mixture is specified, the centroid of the constrained region is used

as default.

Response prediction plot example

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Prediction list

In the prediction list you can type or paste factor settings to make predictions. The

lower and upper level 95% confidence intervals for these predictions are also

calculated.

To open the prediction list, on the Prediction menu, click Prediction List.

To insert rows, right-click the list and click Insert Rows or press the DOWN arrow

key when on the last row.

If the model has been fitted the predictions are calculated automatically after entering

settings for all factors. If you do not want the predictions to be automatically updated,

right-click the list and clear Auto Update. To make predictions with auto update

cleared, right-click the list and click Update Predictions or press the F5 key.

To change the confidence level of the confidence intervals, right-click the list and click

Properties.

Note: With PLS and an X matrix with large condition number, the standard

error of predictions is computed and displayed instead of the confidence

interval.

Scatter plot

In the prediction scatter plot you can view your factors and predicted responses as 2D

and 3D scatter plots.

Note: The points displayed in the scatter plots are the points in the current

prediction list. The scatter plot is updated with new points when you enter

them in the prediction list.

To create a prediction scatter plot, on the Prediction menu, click Scatter Plot.

For 2D plots, select the variable to be plotted on the X-axis by marking it and clicking

the arrow ‘=>’. Mark the other variable(s) and click the arrow to Series.

For 3D plots, select the variables to be plotted on the X, Y, and Series axes.

Click the Delete button in the dialog to remove factors or responses from the Y-

axis or from Series. To change what to display on the X-axis, use the arrow to add the

new variable.

Click the Color by Variable tab to color by a factor or a response.

You can customize the 3D plot using the property page and plot settings. See the Plot

settings for 3D scatter and Onion 3D plots section in the Plots and Lists chapter.

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Prediction

The Sweet Spot plot highlights the areas were the responses are within the user

specified ranges. The sweet spot plot can be displayed as 2D or 4D for process or

mixture factors.

To open the sweet spot plot, on the Prediction menu, click Sweet Spot Plot.

If the investigation contains both mixture and process factors, select the type of factor

you want on the axes for the 2D and for the inner axes for the 4D.

Plot type

To select to create the 2D sweet spot plot click Sweet Spot and to select the 4D with

up to four factors (5 with mixture) click 4D Sweet Spot. Click Next.

Response Selection

In the Response Selection page, enter the settings for the relevant responses.

Note: If you have entered Min and/or Max values in the response definition,

this page is automatically filled with those values. To update with updated

values from the response definition, click the Get Limits button.

For each response you have to select:

• To Include or Exclude each response under Incl/Excl.

• Which type of values, Value or Percent, you are entering under Min and

Max.

• Type the values that are of interest under Min and Max. MODDE has

entered the smallest and the largest values found in the worksheet. Change

them according to your desired sweet spot. You can also select or clear the

Use Constraints check box and change the resolution in the Resolution box.

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Plot axes

Click Next to open the Axes and Constants page, or for 4D sweet spot, the 4D Axes

page.

Mixture factors can only be selected as inner factors in a 4D plot.

Select two process factors for the axes under Factors at the plot axes, or three mixture

factors

For the 4D, select two process factors for the outer axes. The sweet spot contours are

plotted for the low, middle, and high levels of these factors.

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Prediction

The sweet spot plot uses the color scale from green to blue with:

• Green for the ‘sweet spot’, that is the areas where all responses are within the

selected range.

• Blue for areas where one of the responses is within its selected range.

• White for areas where none of the responses are within their selected ranges.

• Other colors for areas with more than one response within its range but not

all.

The above are the default settings and you can define specific colors in the plot settings

dialog.

The constants are displayed to the right in the sweet spot plot window. Make a change

in the constants and the plot is updated automatically. The constants can be hidden by

right-clicking the plot and clearing View Constants.

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User Guide to MODDE

Optimizer

You can use the optimizer to find an experimental area limited both by factor settings

and response criteria.

To open the optimizer, on the Prediction menu click Optimizer. MODDE opens a

dialog box with 3 spreadsheets.

1. Limit optimization – where the objective is to reach a solution where all

responses are within the specification limits. This is default in MODDE.

2. Target optimization – where the objective is to reach a solution where all

responses are as close to target as possible. For the target optimization it is

necessary that all responses can be optimized close to or to reach the target.

Otherwise you may end up with an unacceptable solution.

3. Focus optimization – where you want to favor one or several responses over

the others using individual weights.

For more information about the optimizer objectives see Appendix C: Optimizer and

the Optimizer section in the Statistical appendix.

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Prediction

In the factor spreadsheet all factors are available with their current roles and their

ranges according to the worksheet.

The Role is set to define whether the factor can vary or not during the optimization. If

the factor can vary within an interval, you should set the role 'Free', if the factor

should not vary you should set the role 'Constant'. By default, all factors included in

the model are 'Free'.

When a factor is 'Free' it is varied during the optimization within its specified range as

defined by Low Limit and High Limit. Default these low and high limits are taken

from the smallest and largest values found for that specific factor in the worksheet.

You can change the range to widen or narrow the search region.

When a factor is 'Constant', it will be held at the selected constant value during the

optimization. The default constant value is the center point. Change this value by

typing another under Value.

The Sensitivity Range is the disturbance added to the factor settings proposed by the

optimizer in the run list. 5% is the default and signifies a disturbance of + 5% of the

factor range for the Monte Carlo simulations. The result is shown in the run list as

DPMO (Defects Per Million Opportunities) outside the accepted response area.

Response spreadsheet

In the response spreadsheet all the responses used in your model are available. Before

starting the optimization you must select the Criteria for your response(s), weights and

limits.

If you have specified Min, Target, and/or Max in the response definition, these

specifications are copied to the Optimizer response section. If no Min, Target, or

Max settings are defined in the response definition, the response will be by default

Predicted.

Note: You can fetch updated limits from the response definition by right-

clicking and clicking Update limits from response definition.

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You can choose:

• Minimize the response. Type the highest value you can accept under Max

and your target value under Target.

• Maximize the response. Type the smallest value you can accept under Min

and your target value under Target.

• Target the response. Type the smallest, largest, resp. desired value under

Min, Max, resp. Target.

• Predicted response. The response will not participate in the optimization but

the prediction will be displayed.

• Excluded response. The response will not be a part of the optimization nor

displayed in the run list.

When you have not entered Min, Target, or Max values and you choose to Minimize

or Maximize, MODDE makes an educated guess of your limits. It is imperative that

the limits are well chosen and reflect the data at hand.

When the difference between the minimum/maximum and target values is too small

the optimizer will not run. When this happens you should increase the range.

Weight

In the column Weight you can enter a number between 0.1 and 1 reflecting the

importance of the response. Default is 1 indicating that all responses are of equal

importance.

The weight will change the optimization objective described in the first section of this

chapter as follows:

• Weight = 1 for all responses results in a limit optimization (default).

• Weight = 0.2 for all responses results in a strict target optimization.

• Individual weights for the responses results in an optimization where the

responses with higher weights are favored in the quest for all responses to

reach inside the limits.

For more information see Appendix C - Optimizer.

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Prediction

Run list

The run list includes the factors, responses, iterations, Log(D), and DPMO. The D in

Log(D) is a normalized distance to the target. See Appendix C: Optimizer for more

information.

After running the optimizer the best proposal, lowest Log(D) is selected. Note that if

alternative solutions with Log(D) close to the best are found, another run than the

marked one may be optimal when looking at practical aspects.

Minimum for Log(D) = -10 (on target). A Log(D) < =0 means that all results are

within specification limits or very close.

DPMO gives additional information about how robust the proposed run will be to

disturbances in the factor settings.

In the run list above, row 6 has a DPMO = 0 meaning that with disturbances + 5% on

the factor settings will give a solution inside the specifications. Row 1 has

approximately the same Log(D) but a DPMO = 5600 indicating that a small

disturbance in the factor settings from this point will result in some hits outside the

specifications. Therefore row 6 is preferable.

After running the optimizer, you can scroll back and forth through the iterations using

the Iteration slider near the Iteration number.

You can specify that the minimum and maximum limits for the responses are absolute.

No suggestion from the optimizer will then be shown that have predicted values for a

response outside the specified limits. Note that this may result in that no suggestion is

displayed.

To use absolute limits, select the Absolute response limits check box above the run

list, or right-click the window and click Properties to open the Optimizer Properties,

in tab Options, select the Use absolute response limits check box.

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User Guide to MODDE

Sensitivity analysis

The Analyze sensitivity check box is by default selected to display complementary

information about the proposed optimal factor settings. The sensitivity is expressed as

DPMO (Defects Per Million Opportunities) outside specifications, based on Monte

Carlo simulations and including prediction error. Note that DPMO is an estimate of the

result after the number of simulation performed; 10 000 simulations will give a fair

estimate.

Most commands available in the optimizer can be reached by right-clicking the

Optimizer window. The two plots Simplex Evaluation and Response Simplex

Evaluation and the Optimizer Properties can only be opened by right-clicking the

Optimizer window and are described here.

The Simplex Evaluation plot displays the Log(D) plotted vs. iterations.

Open the plot by right-clicking the Optimizer window and clicking Plot | Simplex

Evaluation.

The Response Simplex Evaluation plot displays the predicted response value vs.

iterations. The target and specified limit(s) are displayed for each response.

Open the plot by clicking Plot | Response Simplex Evaluation on the context menu.

Select which responses to display in the dialog box that opens.

Optimizer Properties

In the Options tab optimizer settings are specified.

Feature Description Default

Use absolute When selected, only the runs where all responses are predicted Not

response limits inside the specified limits are displayed in the run list. selected.

When selected, the DPMO is calculated for runs where all responses

are predicted inside the specified limits. The Sensitivity Range for

Calculate DPMO the factors specifies the range used in the DPMO calculations. Selected.

This is a sensitivity analysis that indicates if a solution is sensitive or

insensitive to small changes.

Include Model When selected, the sensitivity analysis (DPMO) includes the model

Selected.

Error error in addition to the sensitivity range.

Simulations 10 000

is scaled up to the unit 'dots per million operations'.

Include weight in

When selected, the weight specified in the response spreadsheet is Not

calculation of

included when calculating Log(D). selected.

Log(D)

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Prediction

Optimizer buttons

There are seven optimizer buttons: Generate start runs, run optimizer, generate start

points from selected, contour plot wizard, copy to predictions, sweet spot plot wizard,

and analyze design space.

The Design Space, opened by clicking the Analyze Design Space - button is described

in the Design Space chapter.

If the run list is empty, MODDE automatically generates starting runs when the

optimization starts.

If you want to display and/or modify the starting runs of the simplexes, click the

MODDE generates start runs from the corners and center of the experimental

region, plus the three best runs.

For details on how the start runs are selected see the Statistical appendix, section

Optimizer.

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User Guide to MODDE

Start the optimizer by clicking the Run Optimizer (play) button or right-click

the list and click Run Optimizer.

The optimizer runs to completion and displays the results as:

• Final factor settings.

• Predicted responses values.

• Number of iterations.

• Log(D), i.e., the logarithm of the overall distance to Target. The smaller the

Log(D) the better is the result. At Log(D) = -10 all predicted responses are

on target.

• DPMO, estimated number of hits outside specification on one million

simulations. A smaller DPMO means that the solution is less sensitive to

disturbances.

Restarting the optimizer

After convergence, you can always click the Run Optimizer (play) button to restart

the optimizer. It restarts from the displayed resulting runs of the previous search. If you

do not want to continue with the resulting runs click the Generate new starting points

or Generate starting points around selected button to specify other start runs.

When one of the simplexes is closest to Target, you may want to restart the optimizer

with new starting runs selected from the corners and center of a fractional

factorial around this “best run”.

Mark the run, and click the Generate start points from selected button or right-

click the list and click New Runs from Selected.

In the dialog box displayed the run you marked is the default run to optimize around.

To switch to another run, enter another run in the Center around optimizer run box.

Enter the percent of the factor range in the Factor range box. The percentage entered

here is used to calculate the new high and low limits for the start runs.

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Prediction

After convergence of the optimizer you can create contour plots using the results.

Mark the best run and click the Contour Plot Wizard button to open the

Contour Wizard Setup dialog box. You can also open the wizard by right-clicking

the list, clicking Plot and selecting Contour Plot Wizard.

In the Contour Wizard Setup dialog:

• Center around the optimum found by the optimizer is by default marked,

and the run to use in the center is the one you marked. If you want to select

another run enter the new run number.

• Selecting Factor definitions results in displaying same factor settings as

when you enter the contour plot wizard from the Prediction menu.

• Selecting Optimizer factor setup results in displaying the current factor

settings in the Optimizer.

Center around the optimum found by the optimizer

With Center around the optimum... selected, clicking OK opens the contour plot

wizard dialog box.

If you create a 2D contour plot the first two factors (for process factors; first three

factors for mixture factors) are varied around their optimum settings (20% range) and

the other factors are set constant to their optimal values.

If you create a 4D contour plot the first two factors (for process factors; first three

factors for mixture factors) are varied around their optimum settings (20% range), the

3rd and 4th are set at their low, high, and center values using the 20% optimum range,

and other factors are set constant to their optimal values.

The resulting plot displays the area outside the factor range shaded.

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User Guide to MODDE

In the created contour plot the predicted parts that are outside the original factor

settings are displayed shaded when the plot is extrapolated.

The selected run is displayed in the plot as lines from the axes with arrows pointing

toward the position of the selected run.

To get predicted response values with confidence intervals for the resulting factor

settings, click the Copy to Predictions button or right-click and click Copy to

Predictions.

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When you choose to create the sweet spot plot from the optimizer, MODDE uses the

range of the responses as specified in the response spreadsheet fields Min, Target, and

Max.

To create the sweet spot plot click the Sweet Spot Plot Wizard button . You can

also open the sweet spot plot by right-clicking, clicking Plot and then clicking Sweet

Spot Plot. In the dialog that opens you can select to create the 2D sweet spot plot by

clicking Sweet Spot or 4D by clicking 4D Sweet Spot.

The selected run is displayed in the plot as lines from the axes with arrows pointing

toward the position of the selected run.

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User Guide to MODDE

Limitations with a sweet spot plot presentation are the number of dimensions and the

lack of probability estimate in the predicted surface. With Design Space (DS)

estimation we can show how the factor settings can be varied around a selected

setpoint (optimum) and still fulfill the response criteria.

The estimation of a safe DS region is performed using Monte Carlo simulations on the

factor settings. MODDE performs a search to identify the largest possible range for

each factor that can be used and still meet all response requirements. The default limit

is less than 10 000 (1%) hits outside the limits for each response. The results are

displayed in the Predictive Design Space Estimate window.

The Predictive Design Space Estimate window is opened by clicking the Analyze

Design Space Validation is a way to test if the system investigated is robust against

disturbances in the investigated region. The test is done with Monte Carlo simulations,

meaning that a number of random disturbances on the factors will give a distribution of

predictions. The function is described in Appendix D: Design Space.

To open the Design Space Validation window, click Prediction | Design Space

Validation. The window has two parts, a factor spreadsheet and a response

spreadsheet.

For more see the Design Space chapter next.

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Design Space

Introduction

The calculation of the design space is a search function that expands the possible factor

ranges from a setpoint (optimum) to the largest possible range where all response

predictions are still within the specifications.

Predictions in the design space are done with Monte Carlo simulations. The resulting

distribution of predictions simulates a real situation with a random combination of

factor setting disturbances within a given range.

There are two Design Space features in MODDE:

• Predictive Design Space Estimation for optimization.

• Design Space Validation for robustness testing.

DS is used as an abbreviation for Design Space in this user guide.

Limitations with a sweet spot plot presentation are the number of dimensions and the

lack of probability estimate in the predicted surface. With Design Space (DS)

estimation we can show how the factor settings can be varied around a selected

setpoint (optimum) and still fulfill the response criteria.

The estimation of a safe DS region is performed using Monte Carlo simulations on the

factor settings. MODDE performs a search to identify the largest possible range for

each factor that can be used and still meet all response requirements. The default limit

is less than 10 000 (1%) hits outside the limits for each response. The results are

displayed in the Predictive Design Space Estimate window.

The Predictive Design Space Estimate window is opened by clicking the Analyze

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User Guide to MODDE

Design Space validation is a way to test if the investigated system is robust against

disturbances in the investigated region.

The aim of robustness testing is to evaluate if a process, or a system, performs

satisfactory even when some influential factors are allowed to vary. In other words, we

want to investigate the system’s sensitivity (or preferably lack of sensitivity) to

changes in certain critical factors. The advantages of a robust process or system

include simpler process control, a known range of applicability and an ensured quality

of the product or process.

A robustness test is usually carried out before the release of an almost finished product,

or analytical system, as a test to ensure quality. Umetrics recommends the use of DoE

for robustness testing and such a design is usually centered on the factor combination,

which is currently used for running the analytical system, or the process. We call this

the setpoint. The setpoint may have been found through a screening design, an

optimization design, or some other identification principle, such as written quality

documentation. The aim of robustness testing is, therefore, to explore robustness close

to the chosen setpoint.

In this case we use Monte Carlo simulations on the regression model and simulate

random disturbances within the investigated range of operation for all factors. The

regression model originates from a low resolution design supporting linear models

since we assume that small disturbances have mainly linear effects. Fractional factorial

resolution III and Placket Burman designs are recommended.

The Design Space window is parted in two. The upper part displays the factor section

and the lower part the response section. The window displayed below was created from

the Optimizer.

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Design Space

Factor spreadsheet

In the factor spreadsheet the following functionality is available for each factor:

Item Description Setting

center, and high values from the factor

definition.

Low,

Optimum, The acceptable factor range For Predictive DS Estimate: by default

High. the Optimum is the value for the selected

run in the run list. The Low and High

values are the 95%* confidence with

normal distribution.

range of variation for the specific factor

is used, with respect to the settings for For DS Validation: by default 'Locked'.

Role other factors and response For Predictive DS Estimate: by default

specifications. 'Free'.

‘Locked’ means that the range settings

of the factor are locked.

‘Uniform’, ‘Normal’, ‘Triangular’ or

‘Target’.

‘Uniform’ means that all factor settings

within the specified range have the same

probability to appear. For quantitative factors, by default

‘Normal’ means that the simulations are 'Normal'.

Distribution

normally distributed within the factor For formulation factors, by default

range. 'Triangular'.

‘Triangular’ means that the distribution

has the shape of a triangle; a good way

to get a skewed distribution for a factor.

‘Target’ means that the factor will be set

to a fixed value, the "Optimum" value.

Estimated acceptable range is the

Estimated Min estimated minimum factor value for Calculated.

which the predictions still fall inside the

specifications.

Estimated acceptable range is the

Estimated Max estimated maximum factor value for Calculated.

which the predictions still fall inside the

specifications.

The yellow lines are the factor settings of the selected optimal run in the optimizer.

The red lines are the Low and High factor settings of the experimental region.

Estimated The black T bar represents the region of acceptable variability valid for that factor

acceptable when all other factors are locked at the optimum. Valid means that all predictions of

range the responses are within the specifications. No model error is considered in this

search.

The blue region represents the 95%* part of random factor variability with normal

distribution where all predictions are within the specifications.

*95% is the default. In the Design Space Properties you can change to 99%.

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User Guide to MODDE

Response spreadsheet

In the response spreadsheet the following functionality is available for each response:

Item Description Default

The optimization range

Max specified in the Optimizer.

'Minimize’, ‘Maximize’,

‘Target’, and ‘Predicted’ as

specified in the optimizer.

Criterion What the algorithm is aiming for. When the search does not

reach inside the limits for a

response, the Criterion is set

to 'Not Met'

the SixSigma statistics and is estimated in this Estimated by MODDE when

Cpk

simulation. Cpk =1 means that approximately 0.13%* selected.

of the predictions will fall outside the specifications.

many predictions will be outside the specification per

DPMO Estimated by MODDE.

one million predictions in the selected DS with the

selected distribution.

The yellow line represents Target value for the responses as specified in the

Predicted Optimizer.

response The red lines are the specification limits for each response as specified in Optimizer.

profile The faded green region represents the probability of a prediction for a random

distribution of factor settings in the given ranges (low-optimum-high), the DS.

* See table in the DPMO and Cpk section in Appendix A: Statistical notes.

There are four design space buttons: Run the Monte Carlo simulations, present the

frequency histogram over the responses, show the individual response DS estimation,

and properties.

• Resample reruns the Design Space calculations.

• Create Histogram opens the response histogram plot.

• Individual response analysis displays a detailed DS estimate for the

individual responses. This window displays an overview of the acceptable

factor ranges which makes it easier to understand which the limiting

responses are. In the window below the response Soot has the smallest

acceptable interval and will therefore be the most limiting response, affecting

the complete region of operability for each

factor.

• Properties opens the Design Space Properties dialog. For more see the

Design Space Properties sub section.

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Design Space

Parameters section

In the Parameters section the settings used in the design space estimation are

displayed and can be adjusted.

Option Description Default

Acceptable range Number of simulations done in each step of the search for the

20 000

simulations acceptable range for the factors.

Response profile Number of simulations for the final predictions of the response

100 000

simulations profile.

DPMO target The first response that exceeds this target will stop the expansion 1 000

of the accepted factor range.

Not

Use total DPMO target for all responses. When this check box is not selected the

selected.

DPMO target is for each response.

Include model error Selected.

distribution.

Space.

Automatic update As this calculation includes many computational operations you Selected.

may want to inactivate it and do the calculations when all settings

have been adjusted instead of after each adjustment.

Defines the Low and High values in such a way that 95%, in the

Limits at 95 or 99 %

default case, of the Monte Carlo simulations are inside the limits.

confidence for 95%

Selecting 99% widens the included area by lowering the Low limit

normal distribution

and increasing the High limit in the factor spreadsheet.

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User Guide to MODDE

Show section

In the Show section what to display and how can be adjusted.

Option Description Default

available fields are: By default all the columns but

Factor

fields Factors (factor names), Low, Optimum, High, St.Dev, Possible Min and Possible

Role, Distribution, Possible Min, Possible Max and Max are displayed.

Estimated acceptable range.

Columns shown in the response part of the DS. The By default Responses, Min,

Response available fields are: Responses (response names), Min, Target, Max, Criterion,

fields Target, Max, Criterion, Cpk, DPMO, Average, St.Dev, DPMO, and Predicted

%Outside, Median, 1st Quartile, 3rd Quartile, and response profile are

Predicted response profile. displayed.

Displays the range of colors of the distribution bars.

range responses.

Factor histogram

When double-clicking the estimated acceptable range for the factors, the Factor

Histogram opens. This histogram displays the distribution of the factor settings used

for the simulation.

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Design Space

Response histogram

The result of the Monte Carlo simulations can be presented as frequency histograms

by:

• Double-clicking Predicted response profile.

• Right-clicking the Design Space window and clicking Response

Histogram.

All statistics can be shown in a specific list, opened by right-clicking the Design Space

window and clicking Design Space Statistics.

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User Guide to MODDE

After displaying the Design Space final adjustments can be made to find a safe region

of variability for all factors where all results are within specifications (DS). In some

publications the selected region inside DS where we have selected to operate the

process is called “Control Space”.

Reasons for final adjustments can be practical and/or economical. A limitation in one

factor will result in a wider range for another factor. Different type of distributions can

also be selected for different factors.

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Show

Introduction

On the Show menu the following items are available: Objective list, Design Matrix,

Design Region plot, Confoundings list, D-Optimal Summary table, Model list, and

Reference Mixture list.

Objective

To open the Objective list, on the Show menu click Objective. The Objective list

displays the selections made in the Objective pages of the design wizard

Maximum Runs: the maximum number of runs that MODDE can include in a design

created by MODDE.

Objective: the selected objective.

Process Model: the type of model created for the process factors.

Mixture Model: the type of model created for the mixture factors.

Design: the selected design.

Runs in Design: the selected number of runs in the design created by MODDE. If you

have added runs after creating the design they will not be included here.

Center points: the number of center points selected.

Replicates: the number of times the entire design has been replicated.

N = Actual Runs: the number of runs created by MODDE.

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Design matrix

To display the Design Matrix, on the Show menu, click Design Matrix.

The Design Matrix displays the experimental plan in coded unit for quantitative

factors, as in the worksheet for qualitative factors and in pseudo components for

formulation factors.

If you have qualitative factors at more than two levels, you can select to display the

design with the qualitative factors extended.

To display the design matrix with the qualitative factors extended:

1. Right-click the matrix and click Properties.

2. Click Extended – shows all settings and click OK.

3. Optionally switch back by clicking Regular – shows all orthogonal

settings.

By default the Design Matrix is derived from the worksheet, and reflects any changes

(excluded runs, changed values, additional runs etc.,) done to the factor part of the

worksheet after it’s generation.

To display the original design matrix generated by MODDE:

1. Right-click the matrix and click Properties.

2. Click The design as generated by MODDE and click OK.

3. Optionally switch back by clicking The current Worksheet scaled and

centered.

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Show

Design region

Open the Design Region plot to get an overview of your experimental plan.

To open the Design Region plot, on the Show menu, click Design Region.

Use the Response box or right-click the plot and click Properties to switch to another

response.

The Design Region plot:

• Is displayed as one or more cubes.

• Can be displayed for classical designs with up to 5 process factors.

• Displays the response values at the star points on the face of the cubes for

CCC designs.

• Displays the points in the design region plot color coded according to the

response values entered in the worksheet. The response range is parted

equally resulting in three groups named High, Medium, and Low.

• Displays points where the factor settings are not at the original value, at the

closes intersection for low, center, and high factor settings. In this plot, the

replicate tolerance is therefore NOT used to identify replicates.

• Displays a black point, Conflicting colors when the response values to be

displayed have been assigned to different color groups (High, Medium, and

Low).

Hint: When you want to view 3 factors in 3D, use the Scatter Plot found under

the Worksheet and Prediction menus.

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The Design Region plot is not available for mixture designs. Enter any values and use

the Prediction | Contour Plot Wizard, with the Use constraints check box selected

when applicable, to investigate the design region. Or use the Worksheet | Scatter

Plot.

Confoundings

Open the Confoundings list to see which terms that are mathematically identical in the

current design. For instance, in the example below the term M*TH is included in the

model, but the effect of this term is confounded with the effect of H*S. This means that

using this design there is no way of telling whether the coefficient displayed for M*TH

reflects M*TH, H*S, or a mixture of both.

To list the confoundings click Confoundings on the Show menu.

For factorial designs resolution III or IV, the Confoundings list displays the

confounding pattern for the complete interaction model.

In the Term column, the background of the terms included in the model is colored.

In the coefficient plots and lists, confounded terms are marked with a bracket #-sign.

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Show

Summary D-Optimal

To displays a list summarizing the generation of a D-Optimal design click D-Optimal

Summary on the Show menu.

Under Candidate set the properties of the used candidate set are listed in the form of

Extreme Vertices, Edge points, Centroid of high dim. Surfaces, and Total Runs.

Under D-Optimal the properties of the selected design are listed in the form of

Objective, Model Type, Potential Terms, Number of Inclusions, Constraints,

Design Runs, Selected Design Number, G-Efficiency, log(Det. of X' X), Norm.

log(Det. of X' X), and Condition number.

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Model

On the Show menu click Model to display the selected model.

If you have qualitative factors at more than two levels and want to display the model

with the qualitative factors extended:

1. Right-click the Model list.

2. Click Properties.

3. Click Extended – Show all settings.

Reference mixture

To display the reference mixture used in the analysis of the design click Reference

Mixture on the Show menu.

To change the reference mixture, click Model / Reference Mixture on the Edit menu

and click the Reference Mixture tab.

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Plots and lists

Introduction

You can customize the plots in MODDE using the Plot Settings page. You can change

the properties of plots and lists from the property page accessed by right-clicking the

plot or list and clicking Properties.

Most plots can be transformed into lists by right-clicking the plot and selecting Create

List.

Properties page

Opening property page by right-clicking

To open the property page of a plot or list, right-click the plot or list and click

Properties.

With Properties open, click the desired option from the context menu and the plot or

list is updated when you click OK or Apply. The default of most properties available

from the Properties page can be changed in Investigation Options available from the

View menu.

If you, after fitting the model, make changes to the responses (add, delete or

transform), the worksheet (include, exclude runs or values), the model (add or remove

terms), or change fit method, MODDE refits the model and all open plots or lists are

updated.

Save plots and lists by:

• With the plot or list active, on the File menu, click Save Plot/List As.

• Right-click the plot or list and click Save Plot/List As.

For details, see the section Save plot/list as in the File chapter.

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When there are many responses in your investigation you can select to display a

multiple plot with all or selected responses. Click the desired responses or All

Responses in the Response box.

Note: When displaying multiple plots, opening the Properties page displays

the properties for the first displayed response.

Plot settings

Use Plot Settings to customize the most common attributes of the axes, of the plot area

and of the header and footer.

There are two different types of plot settings dialogs in MODDE:

• Plot settings for 3D scatter plot and contour, response surface, and sweet spot

plot where all options are in the same dialog.

• Plot settings for other plots are divided in Axis, Header and Footer, and

Plot Area pages.

Open Plot Settings by double-clicking the plot or right-click and click Plot Settings,

then when applicable click Axis, Header and Footer, or Plot Area.

After customization, most features can be saved as default plot settings in two ways:

• Click the Save Settings button in the Plot Settings dialog.

• Right-click the plot and click Save as Default Plot Settings.

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Plots and lists

Axis

To change the settings of the plot axes, right-click the plot, click Plot Settings, and

then click Axis. This dialog is also opened if you double-click one of the axes.

All of the properties apply to the selected axis: X, Y, or Y2 (the second Y-axis).

In this dialog you can change general settings, such as scale, gridlines, titles, and fonts

by clicking the appropriate tab.

Scale

To change the scale, enter the Minimum and Maximum data values and the value to

Increment by. You can specify the spacing of the minor tick marks and the number of

Decimal places to display on the tick label.

Click the Recalculate Scale button to restore the Minimum and Maximum values.

You can change the tick label from the Normal (default) number to Scientific notation

or Time. The value in Rotation controls the orientation of the label in degrees.

Miscellaneous

By default the axes are in normal scale. You can change them to Logarithmic scale or

Values in reverse order by selecting the corresponding check box. The axes are

default displayed. To hide an axis, clear the Show axis check box.

The Always recalculate scales check box is by default selected. If you do not want

MODDE to recalculate the scale you should clear the check box.

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Gridlines

In the Gridlines tab, select the Show gridlines check box to display the grid lines of

the selected axis. The grid lines are placed on the tick marks. Select the Pattern,

Color, and Width of the gridline.

Title

In the Title tab, select to show or hide the axis title, change the text and its orientation.

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Font

In the Font tab, select the font for both the axis titles and the tick mark labels.

For how to customize the axes of the 3D scatter plots, see the section later in this

chapter.

You can customize or remove/add the headers and footers of the plot.

To access the header and footer titles and fonts, right-click the plot, click Plot Settings,

and then click Header and Footer to open the Format Header/Footer page, click the

Title or Font tab as desired.

In this page you can also select to not display the time stamp by clicking Time stamp

under Titles, and then clearing the Is visible check box. Make this the default by

clicking the Save Settings button if desired.

For how to customize the header and footer of the 3D scatter plots, see the section later

in this chapter.

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User Guide to MODDE

Plot Area

To change the settings of the interior of the plot, right-click the plot, click Plot

Settings, and then click Plot Area. This dialog is also opened if you double-click the

plot area.

In this dialog you can change symbol style, line style, data labels, and font by clicking

the appropriate tab.

Symbol style

Select the shape, color and size of all the symbols in a series.

Line style

Click the Line Style tab to change the properties of lines in line plots.

Data labels

Click the Data Labels tab to change the attributes of all the labels on data points inside

the plot area. Color, alignment, or orientation (Rotation) applies to all the labels in a

given series.

Font

Click the Font tab to select the font for all the data labels.

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Background

Click Background, found under Series to the left in the dialog, to change the borders

of the window, plot, and chart areas.

Legend

Click Legend, found under Background to the left in the dialog, and select or clear the

Show Legend check box to show or hide the legend. Here you can also change text

placement, color, background and border styles of the legend.

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User Guide to MODDE

Column style

When you have a column plot you can change the pattern, color, column width, and

overlap for each or all series in the Format Plot Area dialog.

For how to customize the plot area of the 3D scatter plots, see the section later in this

chapter.

After customizing the plots you can save the settings of some attributes, such as fonts,

gridlines symbol type etc.:

• Click the Save Settings button in the Plot Settings dialog.

• Right-click the plot and click Save as default Plot Settings.

You can always restore Umetrics default Plot settings in View | General Options |

Restore.

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Plots and lists

Right-click the contour plot and click Properties to open the property page.

In tab Contour Plot Options you can select the Resolution, select to Scale subplots

equally, select to Lock contour levels, select to Use color in the plot, and select to

Show contour level labels.

Resolution

Resolution is the precision used when creating the contour plot. Selecting a higher

resolution requires more calculations and is therefore more time consuming.

To select the resolution of the plot, click one of the predefined resolutions or type a

resolution value here.

In tab Contour Plot Options in the property page of the Contour Plot you can select

the Scale subplots equally (subplots share contour levels) check box.

When the Scale subplots equally box is selected the colors of all contour subplots

represent the same values.

The plot has subplots when you display the 4D contour or you have selected to display

more than one response in the 2D contour plot.

You can select the Lock contour levels check box to keep the current contour level

colors and limits.

Use color

By clearing the Use color check box you can choose to display the contour and surface

plots without colors.

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Clear the Show contour levels labels check box to display the contour plots without

the level labels.

To change the fonts on the labels, headers and footers, or the attributes of the axes,

double-click the plot or right-click the plot and then click Plot Settings.

Axis

Click Axis to change settings of the axes. For more, see the Plot settings for 3D

scatter and Onion 3D plots section later in this chapter.

Header

Click Header or Footer to customize the positioning and coloring. For more, see the

Plot settings for 3D scatter and Onion 3D plots section later in this chapter.

Regions

Use the Region style page to customize how the area outside the factor setup is

visualized. By default, this area is shaded white.

Labels

Click Labels to:

• Clear the Show label check box to hide the plot labels.

• Select the position of the plot labels in the Anchor box.

• Select the Connect with attach point check box when the label is separated

from the line (using Offset) and you want a line between the label and the

point.

• Customize the Text and Background color and Transparency of the plot

label.

• Select the Is visible check box under Border to display a border around each

label. Enter custom values in the Margin and Width fields.

• Click the Font tab to customize the font.

Contour

In Contour Level Colors in the Plot Settings page you can customize levels and

colors according to the below.

The default plot displays a number of contour levels. To display fewer or more contour

levels, type a new value in the Number of Levels box. In Individual level colors the

new number of levels will be displayed.

Note: To for instance display the contour levels for 10, 20, 30 …100 you need

to type Min=0 and Max=110 in Color level range, and in the Number of

Levels box type 10.

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Plots and lists

After Color range on the contour levels the color buttons, defining the color scale

used in the plot, are positioned.

To change from the default colors, click the respective buttons, and click the color to

use.

To change the color of one of the available levels under Individual level colors, mark

the level and click the Color button, and then click the new color.

To remove one of the available levels, mark it and click the Remove button.

You can also add levels by typing a value in the field under the Add button, and then

clicking the Add button.

Click the Contour Line Style tab to customize the contour line color, width, and

pattern.

To change the fonts on the labels, headers and footers, or the attributes of the axes,

double-click the labels or the axes, or right-click and click Plot Settings.

The Plot Settings dialog for the Sweet Spot Plot is very similar to the one for the

contour plots and 3D plots.

Axis

Click Axis to change settings of the axes. For more, see the Plot settings for 3D

scatter and Onion 3D plots section later in this chapter.

Header

Click Header or Footer to customize the positioning and coloring. For more, see the

Plot settings for 3D scatter and Onion 3D plots section later in this chapter.

Contour

In Contour Level Colors in the Plot Settings page you can customize the colors

according to the below.

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User Guide to MODDE

The default plot displays up to 5 colors in the legend. These levels are by default

colored from blue to green where green represents the sweet spot.

To change the color of one of the available levels:

1. Under Individual level colors, mark the level and click the color button.

2. Then click the new color.

To change the range used, click the respective color buttons and click the new color.

The plot settings described here are available for all 3D scatter plots created by

MODDE, both regular and Onion. In the plot settings dialog you can customize: the

cube the plot is displayed in, the axes, the header, footer, legend, plot symbols and plot

labels. Open plot settings by right-clicking the plot and selecting Plot Settings.

Cube

Click Cube to:

• Clear the Color cube sides check box to make the cube sides transparent.

When the Color cube sides check box is selected the sides are colored in the

color specified in Side color.

• Customize the Side color.

• Select/clear the Show gridlines and Gridlines on minor ticks check boxes

to show/hide the gridlines.

• Change the Line width, Pattern, and Line color to specify the properties of

the gridlines.

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Plots and lists

Axis

Click Axis to change settings of the axes. For each axis you can select:

• To display the annotation of the axis.

• The minimum and maximum values of the axis and the step size.

• To autoscale the axis.

• The axis title.

In the Axis General tab you can:

• Customize the axes color and size.

• Customize the annotations color and distance from the axis.

• Select/clear the Show axis arrows check box to display arrows/regular axes.

• Select the axis arrow color.

• Select the level of Transparency for the axes and annotation respectively.

• Adjust autoscaling properties.

In the Ticks tab you can:

• Customize the tick's direction and size for normal and minor ticks.

• Clear the Show ticks and Show minor ticks check boxes to hide the ticks.

In the Font tab you can select the font and size of the annotation and titles of the axes.

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User Guide to MODDE

Header

Click Header to:

• Select/clear the Is visible check box under Header to show/hide the header.

• Select the position of the header in the Anchor box.

• Customize the Border and text color of the header.

• Customize the Background color of the header.

• Select/clear the Is visible check box under Border to show/hide the border.

• Customize the Margin and Width of the border.

In the Font tab you can select the font and size of the header.

Legend

Click Legend to:

• Select/clear the Show legend check box to show/hide the legend.

• Select the position of the legend in the Anchor box.

• Select the orientation of the legend in the Orientation box.

• Select the text adjustment of the legend in the Text adjust box.

• Customize Border and Text color and Background color of the legend.

• Select/clear the Is visible check box under Border to show/hide the border.

• Customize the Margin and Width of the border.

Footer

Click Footer to:

• Select/clear the Is visible check box under Footer to show/hide the footer.

• Select the position of the footer in the Anchor box.

• Customize the Border and text color of the footer.

• Customize the Background color of the footer.

• Select/clear the Is visible check box under Border to show/hide the border.

• Customize the Margin and Width of the border.

In the Font tab you can select the font and size of the footer.

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Plots and lists

Symbols

Click Symbols and the individual series to change the properties of the symbols. When

you mark the individual series you change the properties of that series only. When you

mark Symbols you change the properties of all series. In these pages you can

• Select the Shape of the symbol.

• Customize the Color of the symbol.

• Select the Size of the symbols.

• Select the Draw style of the symbol, where the choices are Fill, Wireframe,

and Point. Fill is the default.

• Select the Line style when the Draw style is Wireframe.

Labels

Click Labels to:

• Select/clear the Show label check box to show/hide the plot labels.

• Select the position of the plot labels in the Anchor box.

• Select the Connect with point check box when the labels are separated from

their position (using Offset) and you want a line between the label and the

point.

• Customize the Offset in X, Y, and Z space of the plot labels.

• Customize the Text color of the plot label.

Colors

Click Colors to:

• Change the Highlight Style displayed when hovering over a point. For more

about the content on this page, see the Symbols topic above.

• Change Marking Color for the marked points.

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User Guide to MODDE

Turn the 3D scatter plot or response surface plot by holding down the left mouse-

button and moving the mouse in the direction you want to turn the plot.

Zoom in or out in the plot by using the mouse wheel. To zoom in a regular plot, see the

Plot toolbar section in the View chapter.

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Report generator

Introduction

MODDE has an automatic report generator. You start the report by clicking File |

Generate HTML Report. A dialog opens where you can select the MODDE default

template, or any other report as a template.

In the report generator, basic formatting functionality is available for writing text.

Plots, lists, and model results of MODDE can be added to the report at any time. These

items are added to the report as placeholders.

A placeholder stands in the place of contents which MODDE will provide, let it be a

plot, list or any text or number.

The placeholders enable you to use the same report, as a template, in different

investigations. You can then edit the text, and just click the Update Report button to

update all MODDE results from the current investigation.

To open the report generator, click File | Generate HTML Report or press CTRL+R.

The following window opens and you can select any template or report you want to

open.

If you have saved a report with the same name as the investigation, MODDE default

suggests opening that report.

When your investigation has not been fitted MODDE will ask to fit the investigation so

it can automatically fill all the placeholders. You can prevent this question if you select

under View | General Options, to automatically fit investigations when opened.

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User Guide to MODDE

The Generate Report window contains:

• A command menu bar.

• A standard toolbar, named Generate Report, with commonly used

commands.

• A format report toolbar with commonly used formatting commands.

• A main window showing the report template.

• A placeholder window with a list of built-in placeholders.

• A Report Generator FAQ window with a short introduction how to use the

report generator.

• A Properties window where plot size and placeholder properties can be

edited.

The command menu consists of the File, Edit, View, Insert, Format, Tools, and Help

menus.

File menu

On the File menu you find the general Windows commands New, Open, Save As,

Print Preview, Print and Exit. Additionally you find Continue Edit Report With,

Templates, and View in Browser.

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Report generator

Click New to create a new report from the selected template or report.

Click Open to open a report saved in HTML format.

Click Save As to save the report in HTML format. The report is saved with

placeholders and can be used as templates.

Click Print to print the report. Click Print Preview to preview the report.

Click Exit to close the report.

You can continue to work with your report in the editor of your choice by clicking

Continue Edit Report With on the File menu, and then selecting the editor. The

applications listed here are the applications that have registered that they can edit

HTML text with Windows.

Continue Edit Report With is also available as a button on the Generate Report

toolbar.

Templates

You can save templates, restore templates and add or remove custom templates by

clicking Templates on the File menu.

Click:

• Save as Default Template when you have changed/created a template

according to your wishes and want to use it as the default template next time

you generate a report.

• Restore Default Templates if you have made changes to the default

templates and want to remove those changes.

• Save as Custom Template when you have changed/created a template

according to your wishes and want to save it to be able to use it again.

Custom templates will be listed in the “Select template or open existing”

dialog and when you click Insert | Template.

• Add / Remove Custom Templates when you want to add an already created

template or remove one of your custom templates.

View in browser

To view the current report in your default internet browser, on the File menu click

View in Browser. This works with Internet Explorer and Mozilla Firefox.

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User Guide to MODDE

Edit menu

On the Edit menu you find the standard commands Undo (CTRL+Z), Redo, Copy

(CTRL+C), Paste (CTRL+V), Paste Unformatted (CTRL+SHIFT+V), Clear (press

the Delete key), Select All (CTRL+A), and Find (CTRL+F).

View menu

On the View menu you can select to hide or show the following:

• Generate Report toolbar opened/closed by clicking View | Toolbar |

Generate Report. For more, see the Generate report toolbar section later

in this chapter.

• Format toolbar opened/closed by clicking View | Toolbar | Format. For

more, see the Format toolbar section later in this chapter.

• Status bar which displays an explanation when you point to a button. To

show/hide it, click View | Status Bar.

• Placeholders window which displays the placeholders that can be added to

the report. For more see the Placeholders window section.

• Properties window. The properties of plots and images can be customized in

the Properties window. To display the window click Properties. For more

see the Properties window section.

• Click Customize to customize toolbars and menus as in Office 2003 and

later. Find a short introduction in the Customize section in the View chapter.

Insert menu

Use the Insert menu to insert a Hyperlink, Image, File, or Template in the current

report. Here you also can toggle the Grab Plot or List mode explained below.

Hyperlink

To insert a hyperlink, select text in the report and then click View | Hyperlink, also

available by right-clicking the report and clicking Insert Hyperlink. In the dialog that

opens, enter the address of your hyperlink the URL field.

Image

Click View | Image to insert a picture in the report. Also available by right-clicking the

report and clicking Insert Image.

Click the Browse button to find your file.

File

Select View | File to insert a Web page file (*.htm, *.html), a Text file (*.txt), or a

picture file (*.jpg, *.png, *.gif, *.bmp.)

Template

Clicking View | Template opens a dialog where you can select a custom template to

insert in the report. Templates must first have been added using File | Templates |

Save as Custom Template.

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Report generator

Click Insert | Grab Plot or List to toggle the Grab Plot or list mode. When selected,

you can insert a plot or list from the MODDE window into your report. When you

display a plot or list, a hand appears in the MODDE window. Click it and the plot or

list is inserted at the insertion point into your report.

When done click the menu again to deactivate the Grab mode.

Format menu

On the Format menu you can customize Font and Styles and Formatting.

Tools menu

On the Tools menu, find the commands Update Report, Update Placeholder, Show

All Placeholders, Show Placeholder, Remove All Placeholders, and Remove

Placeholder.

Update Report

Click Update Report to update all placeholders with the plots and lists of the current

investigation.

Update Placeholder

Click Update Placeholder to update the marked placeholder.

Click Show All Placeholders to show the underlying placeholders.

Show Placeholder

Click Show Placeholder to show the underlying placeholder of marked plot, list, or

item.

Click Remove All Placeholders when you do not want any items, plots, or lists to be

updated.

Remove Placeholder

Click Remove Placeholder when you do not want a certain item, plot, or list to be

updated. Remove Placeholder is also available as a button on the Generate Report

toolbar.

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User Guide to MODDE

Help menu

To access the FAQ of the report generator, click Welcome Page and FAQ on the

Help menu.

The Generate Report toolbar by default includes the standard command buttons New,

Open, Save, Cut, Copy, Paste, and Undo, and additionally the specific command

buttons Update Placeholders, Remove all Placeholders, Grab Plot or List, and

Continue Edit With. The standard command buttons work according to Windows

standard except for the New command.

New

Click the arrow next to the New button and the following commands are displayed.

• Click New on the menu displays the generate report dialog from which you

can select which report/template to use or to open an existing

report/template.

• Click New Blank Report to start a new report with no text.

• Click New From Default Template if you have created a template that you

have saved as default template. Save a report as a default template by

clicking Templates on the File menu and then clicking Save as Default

Template. Umetrics’ default template is used if no other template has been

specified.

The Generate Report toolbar additionally includes Update Placeholders, Remove all

Placeholders, Grab Plot or List, and Continue Edit With.

For more on the Placeholder buttons see the Tools menu section.

For more on the Grab Plot or List button see the Insert menu section.

For more on the Continue Edit With button see the File menu section.

Format toolbar

The Format toolbar is the standard toolbar for formatting text with three additional

For more, see the Insert menu and File menu sections in this chapter.

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Report generator

Placeholder window

Open the Placeholder dockable window by clicking View | Placeholders.

To insert a placeholder in the report, mark the placeholder and click Insert. To update

the inserted placeholder, click the placeholder then on the Tools menu click Update

Placeholder. You can also click the Update Report button on the Generate report

toolbar to update all placeholders in the report.

Click Show Placeholders to show the underlying placeholders.

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Properties window

Open the Properties dockable window by clicking View | Properties.

In the Properties window you can change the default plot size and to save a plot as

.png, .bmp, or .jpg.

Properties for placeholders are displayed when you click the placeholder. You can

change the properties of the placeholder in the Data field in the properties window.

Click the Data field to view a description on how you can change the properties of the

current placeholder.

To add a plot or list to the report, click the desired position in the report, and then

right-click the plot or list in MODDE and click Add to Report.

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Help

Introduction

MODDE’s help is based on this user guide. The user guide documents are transferred

in to a compiled HTML file. To read the Help file Internet Explorer version 4.0 or

higher must be installed but does not need to be your default browser.

HTML help

The HTML help file is installed to include interactive help and stand alone where the

program is installed.

Open the help by:

• Clicking Contents and Index from the Help menu.

• Clicking MODDE Help from the Program menu.

• Pressing F1 opens the context sensitive help.

Use the Contents, Index, or Search tabs to find what you are looking for.

Additionally, the Analysis Advisor is available to guide you through the analysis. For

more on the Analysis Advisor see that section in the View chapter.

To register and activate, follow the instructions delivered with the delivery letter.

If you choose to register later, click Register on the Help menu and follow the

instructions.

Manage Licenses

If your company has a license server that handles you licenses, follow the instructions

delivered with the delivery letter.

If you choose to activate later, click Manage Licenses on the Help menu and then

follow the instructions delivered with the delivery letter.

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If you have an Internet connection, you can visit the web page of MKS Umetrics

(www.umetrics.com) to get the latest news and other information by clicking Umetrics

on the Web from the Help menu.

About MODDE

To find the version number of MODDE, on the Help menu, click About MODDE.

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Appendix A: Statistical notes

Fit methods

MODDE supports Multiple Linear Regression (MLR) and PLS (Projection to Latent

Structures) for fitting the model to the data.

Multiple linear regression is extensively described in the literature, and this chapter

will only identify the numerical algorithms used to compute the regression results, the

measures of goodness of fit and diagnostics used by MODDE. For additional

information on MLR, see Draper and Smith “Applied Regression Analysis”, Second

Edition, Wiley, New York.

MODDE uses the singular value decomposition (SVD) to solve the system of

equations:

Y = XB+E

where

Y is an n*m matrix of responses.

X (the extended design matrix) is an n*p matrix, with p the number of terms in the

model including the constant.

B is the matrix of regression coefficients.

E is the matrix of residuals.

See Golub and Van Loan (1983) for a description of the SVD and its use to obtain the

regression results.

In case of missing data in a row, this row is excluded for the relevant response only

before the MLR fitting.

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User Guide to MODDE

When several responses have been measured, it is useful to fit a model simultaneously

representing the variation of all the responses to the variation of the factors. PLS deals

with many responses simultaneously, taking their covariance's into account. This

provides an overview of the relationship between the responses and of how all the

factors affect all the responses. This multivariate method of estimating the models for

all the responses simultaneously is called PLS.

PLS contains the multiple regression solution as a special case, i.e. with one

response and a certain number of PLS dimensions, the PLS regression coefficients are

identical to those obtained by multiple regression.

Note: When the models for the responses are different, PLS fits each response

separately.

PLS has been extensively described in the literature and only a brief description is

given here.

PLS finds the relationship between a matrix Y (response variables) and a matrix X

(predictor or factor variables) expressed as:

Y = XB+E

The matrix Y refers to the characteristics of interest (responses). The matrix X refers to

the predictor variables and to their square or/and cross terms if these have been added

to the model.

PLS creates new variables (ta) called X-scores as weighted combinations of the original

X-variables: ta = Xwa, where wa is the combinations weights. These X-scores are few,

often just two or three, and orthogonal (independent). The X-scores are then used to

model the responses.

With several responses, the Y-variables are similarly combined to a few Y-scores (ua)

using weights ca, ua = Yca. The PLS estimations are done in such a way that it

maximizes the correlation, in each model dimension, between ta and ua, One PLS

component (number a) consists of one vector of X-scores (ta), and one of Y-scores (ua),

together with the X and Y-weights (wa and ca).

Hence the PLS model consists of a simultaneous projection of both the X and Y spaces

on a low dimensional hyper plane with new coordinates T (summarizing X) and U

(summarizing Y), and then relating U to T. This analysis has the following two

objectives:

• To well approximate the X and Y spaces by the hyper-planes

• To maximize the correlation between X and Y (u and t).

Mathematically the PLS model can be expressed as:

X = TP' + E

Y = TC' + E

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Appendix A: Statistical notes

Geometrically, we can see the matrices X and Y as n points in two spaces, (see figure),

the X-space with p axes, and the Y-space with m axes, p and m being the number of

columns in X (terms in the model) and in Y (responses).

X3 Y3

t1

u2

t2

u1

X2 Y

2

X1 Y1

t1

u

1

cross validation (CV), where PRESS (see below) is computed for each model

dimension. One selects the number of PLS dimensions that give the smallest PRESS.

The predictive power of an MLR or a PLS model is given by Q2, which is based on the

Prediction Residual Sum of Squares, PRESS. This is a measure of how well the model

will predict the responses for new experimental conditions. The computations are

repeated several times with, each time, different observations kept out of the

calculation of the model. PRESS is then computed as the squared difference between

observed Y and predicted Y when the observations (rows in the tables X and Y) were

kept out from the model estimation. Q2 is computed as:

Q2 = (SS - PRESS)/SS

Here SS = sum of squares of Y corrected for the mean. A Q2 larger than zero indicates

that the component is significant (predictive). An overall Q2 is computed for all PLS

components, for all the responses and for each individual response, and represent the

percent variation of Y that is predictive. Large Q2, 0.7 or larger, indicates that the

model has good predictive ability and will have small prediction errors. Q2 is the

predictive measure corresponding to the measure of fit, R2, (the percent variation of the

response explained by the model).

R2 = (SS - SS resid )/ SS

Q2 gives a lower estimate to how well the model predicts the outcome of new

experiments, while R2 gives an upper estimate.

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User Guide to MODDE

A PLS component is cross-validated if:

Rule 1: PRESS for all Y's together < 1.2

or

Rule 2: PRESS for at least M1/2 Y's < 1.2

and

Rule 3: SS explained for all Y' s together > 1%

or

Rule 4: SS explained for all separate Y's > 2%

MODDE computes a minimum of two PLS components (if they exist), even if not

significant.

Because PLS contains multiple regression as a special case, you can with PLS derive

the same solution as when you fit the Cox model with Multiple Regression. When you

extract as many PLS components as available you get the same solution as MLR.

With MODDE you do the following:

• First fit the model. MODDE extracts only the significant PLS components.

This is the PLS solution.

• Then click Next Component menu and continue extracting PLS components

until no correlation between X and Y remains. This is the MLR solution.

Model

You may edit the model and add or delete terms for individual responses. You may add

up to third order terms (cubic terms, or 3 factors interaction).

If your design is singular with respect to your model, MODDE will fit the model with

PLS, and MLR will not be available.

Hierarchy

MODDE enforces hierarchy of the model terms. You cannot delete the constant term.

You can only delete a linear term if no higher order term containing the factor is still in

the model.

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Appendix A: Statistical notes

Scaling

Scaling X

When fitting the model with multiple linear regression, the design matrix X is scaled

and centered as specified in the factor definition box: MLR scaling. If the choice is not

orthogonal, the condition number will differ from the one displayed when clicking

Analysis | Evaluate.

When fitting the model with PLS the X matrix is always scaled to unit variance.

If warranted, the scaled X matrix is extended with squares and / or cross terms

according to the selected model.

The choices of scaling are:

(x denotes the original factor value and z the scaled one)

Orthogonal scaling:

zi = (xi - M)/R

Where M = Mid-range, R = Range/2.

Mid-range scaling:

zi = (xi - M)

Unit variance scaling:

zi = (xi - M)/s

Where m = average, s = standard deviation computed from the worksheet.

Note that Orthogonal and Mid-range scaling are only available with MLR.

MODDE default scaling for MLR is the orthogonal scaling.

Scaling Y

The matrix of responses Y, when fitting the model with PLS, is by default scaled to

unit variance. You can modify the unit variance scaling weight by using the PLS

scaling box in the factor definition. With MLR the Y's are not scaled.

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User Guide to MODDE

Condition number

The condition number of the orthogonally scaled and centered extended design matrix

using the SVD (Singular value decomposition) is computed when clicking Evaluate on

the Analysis menu. The X matrix is taken from the worksheet. The calculation depends

on fit method (MLR, PLS) and which factors are involved.

The condition number is the ratio of the largest and the smallest singular values of X

(eigenvalues of X'X). This condition number represents a measure of the sphericity of

the design (orthogonality). All factorial designs, without center points have a condition

number of 1 and the design points are situated on the surface of a sphere.

The condition number is calculated for the extended design matrix (X). The extended

design matrix is created as follows:

1. The factor values, taken from the worksheet, are centered and scaled

according to the factor definition box, MLR scaling. With PLS the condition

number is calculated with factors scaled to unit variance.

2. The design matrix is then extended according to the selected model and the

condition number is computed.

If you select Mid-range scaling, and your factors have different ranges, the

condition number of the worksheet becomes very large. This is only a numerical

artifact, but due to the fact that MODDE uses the SVD with MLR, the model

should be fitted with PLS.

number will be different than the one computed in Analysis | Evaluate. In

particular if you select Mid-range scaling and your factors have different

ranges, the condition number of the worksheet becomes very large. When

fitting the model with PLS, the condition number refers to the X matrix, with

unit variance coding.

The condition number with mixture data depends on the method of fit and the type of

model.

When the method of fit is PLS (Cox model) the data are scaled and centered. The

condition number is computed from the worksheet, with the slack variable model

(mixture factor with the largest variance removed) and all mixture factors scaled

orthogonal.

The condition number displayed is the condition number of the Cox model (with the

Cox constraints), derived from the worksheet, with all mixture factors unscaled and

uncentered.

236

Appendix A: Statistical notes

The condition number of the Scheffé model, derived from the worksheet, with all

mixture factors unscaled and uncentered.

Note: With formulation factors and fitting with PLS, the condition number is

computed by excluding the factor with the largest range, and scaling the

remaining ones orthogonal. When fitting with MLR the condition number is

computed without centering and scaling the factors.

Missing data

Missing data in X

Missing data in X are not allowed, and will disable the fit. This does not apply to

uncontrolled X-variables. For MLR experiments with missing in an uncontrolled factor

results in excluding that row in the calculations while PLS can handle this.

When fitting with MLR, each row with missing data in Y is excluded for that specific

response. Hence N, displayed on plots and lists is the number of observations

(experiments) without missing data.

With PLS, missing data are handled differently when the model for all responses is the

same. When all Y values are missing in a row, that row is excluded from the analysis.

When there are some “present” Y-data in a row, the row is NOT excluded, but

included in the projection estimation in PLS. This leads, however, to minor differences

in the displayed N and DF at the bottom of plots and lists.

When the responses have different models, missing is handled as for MLR, see above.

N-value

The N-value used in ANOVA, and for the computation of R2 adjusted, is the actual

number of non-missing observations (experiments) for each response-column. This N-

value and DF = N-p are displayed at the bottom of the ANOVA plots and lists, and on

all residual plots, including observed vs. predicted Y.

For PLS with the same model for all responses, the residual standard deviation RSD,

displayed in the summary table and at the bottom of all plots and lists including

ANOVA, is computed using the total number of observations (experiments) without

excluding the missing values.

For MLR and PLS with different models, RSD is calculated using the actual number of

non-missing experiments for each response.

This is the RSD used in the computation of confidence interval, for coefficients and

predictions.

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User Guide to MODDE

ANOVA

The analysis of variance (ANOVA) partitions the total variation of a selected response

SS (Sum of Squares corrected for the mean) into a part due to the regression model and

a part due to the residuals.

SS = SSregr + SSresid

If there are replicated observations (experiments), the residual sum of squares is further

partitioned into pure error SSpe and Lack of fit SSlof.

SSresid = SSpe + SSlof

DFresid = (n - p)

SSpe = ∑ ( eki - ek )2

DFpe = ∑ ( nk - 1 )2

DFlof = n - p - ∑ ( nk - 1 )2

1. where the ∑ loops over ki resp k.

2. n = number of experimental runs (excluding missing values)

3. nk = number of replicates in the kth set

4. p = number of terms in the model, including the constant

5. ek = average of the nk residuals in the kth set of replicates

6. j = jth residual in the kth set of replicates

A goodness of fit test is performed by comparing the MS (mean square) of lack of fit to

the MS of pure error:

Two ANOVA plots are displayed:

1. The regression goodness of fit test

2. The LoF goodness of fit test

MODDE checks the rows of the worksheet for replicates. Rows in the worksheet are

considered replicates if they match all factor values plus or minus a tolerance which is

by default 10% but can be altered in View | General Options.

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Appendix A: Statistical notes

MODDE computes and displays the following:

Q2

Q2 = (SS - PRESS)/SS

with

(Yi − Y$i )2

PRESS = ∑ 2

i (1 − hi )

where hi is the ith diagonal element of the hat matrix:

X(X'X)-1X'

R2

R2 = (SS - SSresid)/SS

R2 adj = (MS - MSresid)/MS

MS = SS / (n - 1)

MSresid = SSresid / (n - p)

RSD = Residual Standard Deviation = √MSEresid

Degrees of freedom

MODDE always computes the real degrees of freedom RDF of the residuals:

RDF = n - p - ∑( ni - 1 )

where the ∑ loops over i

n = number of experimental runs

ni = number of replicates in the ith set

p = number of terms in the model, including the constant

Saturated models

When RDF = 0 the model is saturated, and MODDE does not compute or display R2,

R2 Adjusted or Q2 when fitting the model with MLR. With PLS, only Q2 is computed

and displayed.

Singular models

Singular models (condition number > 3000) are only fitted with PLS.

If p > n - ∑( n i - 1 ) , the degrees of freedom of the residuals are computed as:

DFresid =∑ (n i - 1), with replicates in the design

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User Guide to MODDE

Coefficients

Scaled and centered coefficients

The regression coefficients computed and displayed by MODDE refer to the centered

and scaled data. You may also select to display the “unscaled and uncentered”

coefficients.

Normalized coefficients

In the overview plot, to make the coefficients comparable between responses, the

“centered and scaled” coefficients are normalized with respect to the variation of Y.

That is, they are divided by the standard deviation of their respective Y's.

The “centered and scaled” coefficients of PLS refer to factor values scaled to unit

variance.

The PLS orthogonal coefficients re-express the coefficients to correspond to factors

centered and orthogonally scaled, i.e. using the Mid-range and Low and High values

from the factor definition.

For matrices with condition number < 3000, MLR and PLS compute confidence

intervals on coefficients as:

-1

√((X’X) ) * RSD * t(α/2, DFresid)

For matrices with condition number > 3000, PLS does not compute confidence

intervals on the coefficients.

Confidence intervals

Confidence intervals of coefficients and predictions are computed using the total

number of observations, regardless of missing values for PLS models with identical

models for all responses. For MLR and PLS with different model for the responses, the

total number of observations is the number of non-missing values per response. This

total number of observations is displayed as N at the bottom of all other plots and lists.

The approximation for PLS with identical models is possible because the confidence

intervals computed with the regression formulas are somewhat too large because the

PLS solution is a shrunk estimator with smaller prediction errors than those of

regression. Hence a small number of missing elements in Y does not make the PLS

confidence intervals larger than those computed with the regression formulas and the

total number of observations.

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Appendix A: Statistical notes

If a term in the model comprises a qualitative factor, C, at k levels, there will be k-1

expanded terms associated with that term. For example, if the levels of the qualitative

factor C are (a, b, c, d) the three expanded terms C(j) are as follows:

C C(2) C(3) C(4)

a -1 -1 -1

b 1 0 0

c 0 1 0

d 0 0 1

The coefficients of these expanded terms are given as the coefficients for level 2 (b), 3

(c), and 4 (d) of C, while the coefficient for level 1 (a) is computed as the negative sum

of the three others. MODDE displays all the four coefficients in the coefficient table

but notes that they are associated with only three degrees of freedom.

Residuals

Raw residuals

The raw residual is the difference between the observed and the fitted (predicted) value

ei = Y i – Ŷ i

The raw residuals are displayed in the residual lists.

Standardized residuals

The standardized residual is the raw residual divided by the residual standard deviation

ei / s (s = RSD)

These are MODDE default for PLS Residual plots.

With MLR, for models with 2 (required) or more degrees of freedom, deleted

studentized residuals are MODDE default when plotting residuals.

Deleted studentized residuals are not available with PLS.

The deleted studentized residual is the raw residual ei divided by its “deleted” standard

deviation (si) which is the residual standard deviation (si) computed with observation

(i) left out of the analysis, and corrected for leverage, i.e.:

ei = ei /(si √(1 - hi))

where

si = is an estimate of the residual standard deviation with observation i left out of the

model

hi is the ith diagonal element of the hat matrix: X(X'X)-1X'

For more information see Belsley, Kuh, and Welsch (1980).

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User Guide to MODDE

Predictions

For X matrices with condition number < 3000, both MLR and PLS computes a

confidence interval for the average predicted y:

Yi + √hi * RSD * t(α / 2, DFresid)

hi is the ith diagonal element of the hat matrix: X(X'X)-1X'

For X matrices with condition number > 3000 and for all Cox mixture models, PLS

computes only the standard error of the average predicted Y:

SE(Y) = √[(1 / N) + t'0 * (T'T)-1* t'0] * RSD

PLS plots

Both scores and loading plots are available:

Plot loadings

WC plots (PLS)

Plots of the X- and Y-weights (w and c) of one PLS dimension against another, say,

no.'s 1 and 2, show how the X-variables influence the Y-variables, and the

correlation structure between X's and Y's. In particular one better understands how the

responses vary their relation to each other and which ones provide similar information.

Plot scores

TT, UU, and TU plots (PLS)

The tt and uu plots, of the X- and Y-scores of, say, dimensions 1 and 2 (i.e. t1 vs. t2, and

u1 vs. u2), can be interpreted as windows into the X- and Y-spaces, respectively,

showing how the design points (experimental conditions, X) and responses profile (Y)

are situated with respect to each other. These plots show the possible presence of

outliers, groups, and other patterns in the data.

The tu plots (t1 vs. u1, t2 vs. u2, etc.) show the relation between X and Y, and display the

degree of fit (good fit corresponds to small scatter around the straight line), indications

of curvature, and outliers.

PLS coefficients

PLS computes regression coefficients (Bm) for each response Ym expressed as a

function of the X's according to the assumed model (i.e. linear, linear plus interactions

or quadratic,). These coefficients are (columns of B) computed as:

B = W(P'W)-1 C'

W and C are (p*A) and (m*A) matrices whose columns are the vectors wa and ca.

p = number of terms in the model

m = number of responses

A = Number of PLS components

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Appendix A: Statistical notes

A useful family of transformation on the necessarily positive Y's is given by the power

transformation:

For not equal to zero Z = Yλ

For equal to zero Z = lnY

MODDE computes Lmax, for values of between -2 and 2, and plots it against the values

of λ with a 95% confidence interval.

Lmax (λ) = ½ ln(SSresid / n) + (λ - 1)* ∑ lnY

SSresid is the Residual Sum of Squares after fitting the model Z = X * β + e for the

selected value of λ.

The value of λ that maximizes Lmax(λ) is the maximum likelihood estimator of λ.

The Box-Cox plot displays the values of lambda, λ, vs. the maximum likelihood.

The system uses your data to compute the best mathematical transformation of the

response to achieve:

• A simple and parsimonious model

• An approximately constant model error variance

• An approximately normal model error distribution.

If the response values vary more than a magnitude of ten in the experimental domain, a

transformation is often recommended.

The maximum point on the Box-Cox plot gives the value of (lambda, λ) for the

response transformation Y that gives the best fit of the model. This is the maximum

likelihood estimator for λ.

For more information see Draper and Smith “Applied Regression Analysis, Second

Edition” Wiley, New York or Box and Draper Response Surface Modeling.

The Box-Cox plot is not available for PLS.

Mixture factors only

Model forms

When the investigation includes mixture factors only there are three model types

available: Slack variable model, Cox reference model, and Scheffé model.

Slack variable model

When you define a mixture factor as filler, MODDE generates the slack variable model

by omitting the filler factor from the model. The model is generated according to the

selected objective and is treated as a non-mixture model. You may select MLR or

PLS to fit the model as with ordinary process factors. With MLR the factors will be

orthogonally scaled.

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User Guide to MODDE

When all mixture factors are formulation factors, MODDE generates, by default, the

Cox reference model, and i.e. the complete polynomial model linear or quadratic.

MODDE supports also a special cubic and a full cubic model (see section Objective,

model and design).

Scheffé model

You may select to fit a Scheffé model, by selecting Scheffé MLR as fit method on the

Analysis | Select Fit Method menu. MODDE expresses the mixture model in the

Scheffé form. The full cubic model is not supported as a Scheffé model.

In MODDE, the default fit method with mixture factors is PLS, and the model form is

the Cox reference mixture model. All factors, including mixture factors are scaled to

unit variance, by default, prior to fitting. This is also done with mixture factors that

have been transformed to pseudo components.

Cox reference model

The Cox reference model can be fitted by MLR (when obeying mixture hierarchy) and

in all cases by PLS.

The coefficients in the Cox model are meaningful and easy to interpret. They represent

the change in the response when going from a standard reference mixture (with

coordinates sk) to the vertex k of the simplex. In other words when component xk

changes by Δk, the change in the response is proportional to bk. Terms of second or

higher degree are interpreted as with regular process variable models. The presence of

square terms, though they are not independent, facilitates the interpretation of quadratic

behavior, or departure from non-linear blending. The constant term is the value of the

response at the standard reference mixture.

• Changing the Standard Reference Mixture.

Click Model / Reference Mixture on the Edit menu to change the

coordinates sk of the standard reference mixture. By default MODDE selects

as reference mixture the centroid of the constrained region.

• Mixture Hierarchy with the Cox reference model.

By default all Cox reference models, linear and quadratic, obey “mixture

hierarchy”. That is the group of terms constrained by:

Σbksk = 0

Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q

(ckj = 1 when j ≠ k and ckj = 2 when k = j.)

are treated as a unit, and terms cannot be removed individually.

If you want to remove terms individually, as with regular process models, clear the

Enforce the mixture model hierarchy check box in the Edit | Model / Reference

Mixture dialog. When the mixture hierarchy is not enforced (this includes cubic

models), the Cox reference model can only be fitted by PLS. The coefficients are the

regular PLS coefficients computed from the projection and not re-expressed relative to

a stated standard reference mixture. Note that in all cases model hierarchy is enforced a

term cannot be removed, if a higher order term containing that factor is still in the

model.

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Appendix A: Statistical notes

In the ANOVA table, the degrees of freedom for regression are the real degrees of

freedom, taking into account the mixture constraint. These are the same as for the

equivalent slack variable model.

Screening plots

When the objective is to find the component effects on the response, the coefficients of

the Cox reference linear model are directly proportional to the Cox effects. The Cox

effect is the change in the response when component k varies from 0 to 1 along the

Cox axis. That is the axis joining the reference point to the kth vertex.

Effect plot

The effect plot displays the adjusted Cox effects. The adjusted effect of component k

is:

k = rk*tk

rk = Uk - Lk

tk = bk/(T-sk)

where:

rk is the range of factor k

tk is the total Cox effect

T is the mixture total. In most cases T=1.

bk is the unscaled uncentered coefficient

sk is the value of the factor at the reference mixture

The Effect Plot is only available for screening designs using the Cox model.

Main effect plot

For a selected mixture factor Xk, this plot displays the predicted change in the response

when Xk varies from its low to its high level, adjusted for all other mixture factors, that

is, by default, the relative amounts of all other mixture factors are kept in the same

proportion as in the standard reference mixture (MODDE does not check if the other

mixture factors are kept within their ranges).

For example, if the Main effect of the mixture factor X1 is being displayed, when X1

takes the value x1, the other mixture factors are assigned the values: xj = (T - x1)* (sj /

T - s1).

Sk are the coordinates of the standard reference mixture. The standard reference

mixture is the one used in the model.

You can change this default and select to have all other mixture factors kept in the

same proportion as their ranges (this ensures no extrapolation).

Interaction Plot

Interaction plot is not available when you only have mixture factors.

In MODDE you can fit Cox reference mixture models (linear or quadratic) with MLR,

only when they obey mixture hierarchy. When fitting the model with MLR the mixture

factors are not scaled and are only transformed to pseudo components when the region

is regular. The model is fitted by imposing the following constraints on the

coefficients:

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User Guide to MODDE

Linear models

Σbksk = 0 (1)

Quadratic models

Σbksk = 0 (1)

Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)

Here ckj = 1 when j ≠ k and ckj = 2 when k = j.

and sk are the coordinates of the standard reference mixture.

With PLS the standard reference mixture is not stated a priori as with multiple linear

regression, and no constraints on the coefficients are explicitly imposed. PLS fits the

mixture models, and deals with all collinearities by projecting on a lower dimensional

subspace. The PLS coefficients can be interpreted as in the Cox model, relative to a

reference mixture resulting from the projection, but not explicitly stated.

Expressing PLS coefficients relative to an explicit standard reference

mixture

With linear and quadratic models obeying hierarchy, it is easy to re-express the PLS

coefficients relative to a stated reference mixture with coordinates sk. (sk expressed in

pseudo component, if pseudo component transformation was used)

On the fitted PLS model one imposes the following constraints, on the uncentered,

unscaled coefficients (See Cox).

Linear models

Σbksk = 0 (1)

Quadratic models

Σbksk = 0 (1)

Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)

Here ckj = 1 when j ≠ k and ckj = 2 when k = j.

The scaled and centered coefficients are recomputed afterwards.

Note: In MODDE, with linear and quadratic models obeying the mixture

hierarchy, (i.e. terms constrained by (1) or (2) can only be removed as a

group, and not individually), by default the PLS coefficients are always

expressed relative to a stated standard reference mixture.

With models containing terms of the third order (cubic), or disobeying mixture

hierarchy, no constraints are imposed on the PLS coefficients. The coefficients are in

this case, the regular PLS coefficients and the reference mixture is implicit and results

from the projection.

With the linear or quadratic Cox reference model, one can re-express the unscaled

coefficients as those of a Scheffé model. The following relationship holds:

Linear

Scheffé‚ bk = Cox (PLS) b0 + bk

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Appendix A: Statistical notes

Quadratic

Scheffé‚ bk = Cox (PLS) b0 + bk + bkk

Scheffé‚ bkj = Cox (PLS) bkj - bkk - bjj

Scheffé models

The Scheffé models are only fitted with MLR and only the main effect plot is

available.

Scheffé models are only available for investigation with all mixture factors.

ANOVA

As described by Snee in “Test Statistics for Mixture Models” (Technometrics, Nov.

1974), the degrees of freedom in the ANOVA table are computed in the same way as

with the slack variable model.

Prediction plot

This plot is available for all objectives and all model forms. As with process

factors, this plot displays a spline representing the variation of the fitted function, when

the selected mixture factor varies over its range, adjusted for the other factors. As with

the main effect plot, this means that the relative amounts of all other mixture factors

are kept in the same proportion as in the standard reference mixture. If no standard

reference mixture is specified, the centroid of the constrained region is used as default.

Mixture contour plot

Trilinear contour plots are available with mixture factors but no response surface plots.

When you have both process and mixture factors, you can select to treat them as one

model, or to specify separate models for the mixture factors, and the process factors.

With both mixture and process factors, the only model form available is the Cox

reference mixture model.

When the model obeys mixture hierarchy, the PLS coefficients are expressed relative

to a stated standard reference mixture. The following constraints are imposed on the

coefficients:

Σbksk = 0

Σbksk = 0 (1)

Σckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)

Here ckj = 1 when j ≠ k and ckj = 2 when k = j.

If γ (gamma) are the coefficients of the interactions between the process and mixture

factors:

Σγksk = 0

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User Guide to MODDE

Note: When the model contains terms of order 3, or contains qualitative and

formulation factors, the PLS coefficients are not adjusted relative to a stated

standard mixture.

MODDE plots

All MODDE plots are available when you have both mixture and process factors. For

both the Main Effect and prediction plots, when you select to vary a process factor, all

of the mixture factors are set to the values of the standard reference mixture. When you

select to vary a mixture factor, process factors are set on their average and the other

mixture factors are kept in the same proportion as in the standard reference mixture or

their ranges.

Optimizer

The Optimizer uses a Nelder Mead simplex method with the fitted response functions,

to optimize an overall desirability function combining the individual desirability of

each response.

For details on how to use the Optimizer, see the Appendix C: Optimizer chapter.

Desirability

For every response y, the desirability function is computed as follows:

f(g(y)) = 100*(e^(λ*g(y)) - 1)

where g(y) = 100*((y -P)/(T - P))

T, L and P are defined as follows:

T = User desired Target

L = User defined worst acceptable response value(s)

P = Worst response value computed from the starting simplex. P is never closer to the

Target than the L(s).

When the response is to be maximized, L is the smallest acceptable value, when the

response is to be minimized L is the largest acceptable value. When the response is to

be on Target, the user gives the smallest and largest acceptable values.

When the response is to be minimized, we must have T < L and when the response is

to be maximized we must have T > L.

For responses to be on target the user must supply lower and upper limits such as

L(lower) < T < L(upper)

L is generated internally when not supplied by the user.

λ is a scaling parameter computed as follows:

⎡ 100 ⎤

ln ⎢

(100 − Limit ) ⎥⎦

λ=− ⎣ ( L − P)

100

(T − P)

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Appendix A: Statistical notes

response by the user. The weight w is a number between 0.1 and 1 (default value). W

effects the shape of the desirability function f(g(y)). For more information about the

effects see Appendix C: Optimizer.

This definition of λ makes f(g(y)) = - (Limit) when y = L and gives the exponential

function f(g(y)) the theoretical range: 0 to -100 (this latter limit can only be reached

asymptotically when y gets close to Target).

When the user wants the response to be on target, L(upper) is used in the calculation of

λ when

y > T and L(lower) is used in the calculation when y < T.

Overall desirability

The overall desirability f(ds) is a weighted average of the individual desirability

function. The weights, denoted w, are the user entered weights between 0.1 and 1,

reflecting the relative importance of the responses.

The “Overall distance to Target”, D, is computed as follows:

⎡ ⎛ yi − T ⎞ ⎤

2

⎢ ∑ wi ⎜ ⎟ ⎥

⎢ ⎝ T − L⎠ ⎥

D = log 10

⎢ M ⎥

⎢ ⎥

⎣ ⎦

M = number of responses.

D = -10 when all responses have reached T.

D is not used in the optimization but is displayed as Log(D) in the run list.

Starting simplexes

The optimizer starts 8 simplexes from 8 starting runs selected as follows:

• The first four are from the corners of a 23-1 design in the factors with the

largest coefficients for the first response.

• The fifth is the overall center point.

• The last three are the 3 “best” runs from the worksheet considering only the

first response and the predicted values.

Duplicated start points will not be shown.

The user can modify these runs or add own.

Each simplex is generated from the starting run by adding an additional run for each

factor with an offset of 20% of the distance from the center to the maximum value, the

other factors being kept at the same values. A check is made that all runs are within the

defined experimental region.

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User Guide to MODDE

Sensitivity Analysis

Sensitivity Analysis is an estimate of how sensitive the proposed factor settings are to

small disturbances. The sensitivity analysis is done with Monte Carlo simulations

(MC) and displayed as DPMO (Defects Per Million Opportunities outside

specifications). Normally distributed random disturbances of + 5% of the range of each

factor are applied and result in an estimate of the total number of DPMO for all active

responses. The user can modify the sensitivity range and the number of MC’s.

DPMO=0 means that the proposed factor settings represent a robust point of operations

for factor disturbances of + 5%.

Orthogonal blocking

When you cannot perform all of the experiments in a homogeneous way, randomizing

the run order of the experiments may not be sufficient to deal with the extraneous

sources of high variability. You may want to run the experiments in homogeneous

groups, i.e., blocks, in such a way that the external source of variability does not

influence the effects of the factors.

For example, suppose you are running a full factorial with 5 factors and 32 runs, and

the batch size of raw material allow you to perform only 8 runs per batch. You may

want to run your experiment in 4 blocks, each composed of 8 runs using homogeneous

material.

The method of dividing 32 runs in 4 blocks of 8 runs, each such as the difference

between the blocks (the raw material) does not affect the estimate of the factors, is

called Orthogonal Blocking.

MODDE supports orthogonal blocking for the 2 level factorial, fractional factorials,

Plackett Burman, CCC, and Box Behnken designs.

MODDE can also block D-Optimal designs. These designs are more flexible with

respect to the number of blocks and the block size, but the blocks in D-Optimal design

are not usually orthogonal to the main factors. The only restriction with D-Optimal

designs is that the number of runs must be a multiple of the block size.

Note: Blocking introduces extra factors in the design, hence reduces the

degree of freedom of the residuals, and the resolution of the design. You

should only block when the extraneous source of variability is high and

cannot be dealt with by randomizing the run order.

Block interaction

An interaction between a main effect and a block effect is called a block interaction.

When the design supports the interactions between the block effects and the main

effects, the Block interactions check box, in the Select model and design dialog in

the design wizard is active. You can select the check box if you want to add the block

interactions to your model.

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Appendix A: Statistical notes

When blocking factors are generated, the blocks are assigned according to the

combination of signs of the blocking factors.

For example to generate 4 blocks, the following scheme of signs of the blocking

factors is used:

$B1 $B2

– – Block 1

+ – Block 2

– + Block 3

+ + Block 4

When you select Show | Design Matrix, the design matrix is displayed in coded units

including the blocking factors.

When the worksheet is generated, the blocking factors are recoded and the model is

reparameterized. Rather than keeping the d blocking factors, such as 2d = k (the

number of blocks), MODDE generates one qualitative variable called $BlockV, with k

levels called B1, B2 ...Bk.

Adding inclusions to a blocked design is not supported, unless the inclusions belong to

one of the blocks present.

Full and fractional factorial designs

The block size and the number of blocks of the 2 level factorial designs are always

powers of 2.

The maximum number of blocks supported by MODDE is 8, with a minimum block

size of 4.

The designs are blocked by introducing blocking factors called $B. There is one

blocking factor for 2 blocks, two for 4 blocks and three for 8 blocks. The block effects

consist of the effects of the blocking factors and all their interactions.

Hence with 8 blocks, there are 7 block effects using 7 degrees of freedom. (It is

equivalent to having added 7 extra factors to your design).

MODDE selects the generators of these blocking factors to achieve the highest

possible pseudo-resolution of the design.

The pseudo-resolution of the design is the resolution of the design when all the block

effects (blocking factors and all their interactions) are treated as main effects under the

assumption that there are no interactions between blocks and main effects, or blocks

and main effects interactions.

These designs can only be split into two blocks by introducing one block variable, and

using its signs to split the design.

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User Guide to MODDE

RSM designs are orthogonally blocked when they fulfill the following two conditions:

1. Each block must be a first order orthogonal block.

2. The fraction of the total sum of squares of each variable contributed by every

block must equal the fraction of the total observations (experiments) allotted

to the block.

The Central Composite Circumscribed designs can be split into two blocks, the cube

portion and the star portion, and satisfying the two above conditions when α (the

distance of the star points to the center) is equal to

α = [k (1+ps ) / (1 + pc) ]1/2

k = number of factors

ps = nso/ns proportion of center points in the star portion

pc = nco/nc proportion of center points in the cube portion

ns = number of star points runs

nc = number of runs from the cube portion

This is the value of α implemented in MODDE when you select blocking a CCC

design.

Smaller blocks

The cube portion of the Central Composite Circumscribed design (CCC) can be split

into further blocks if (a) the factorial or the fractional factorial part of the design can be

split into orthogonal blocks of pseudo resolution 5 and (b) each one of these blocks

have the same number of center points.

These designs can be orthogonally blocked, as specified by Box and Behnken (1960)

and Box and Draper (1987).

These designs can not be blocked.

MODDE can block D-Optimal designs, but usually the blocks are not orthogonal to the

main factors.

The following restrictions apply to blocking D-optimal designs:

1. The blocks must be of equal size.

2. You cannot have interactions between the block factor and the other factors

in the model.

3. The selected number of runs of the design must be a multiple of the number

of blocks.

MODDE blocks the D-Optimal design by generating a qualitative factor, $BlockV,

with as many levels as the selected number of blocks. By default, it then selects only

balanced designs with respect to the blocking factor.

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Appendix A: Statistical notes

It is not always possible to generate a balanced D-Optimal design with respect to the

blocking factor. In this case you may want to change the model, the number of blocks,

or generate an unbalanced design.

You can select to have the block factor treated as fixed or random effect and the

predictions computed accordingly.

Select the block factor as Fixed when the external variability can be set at will (it is

controlled) and the primary objective for blocking is to eliminate that source of

variability.

A fixed block can be modeled as a controlled qualitative factor with a limited number

of levels. All predictions of the responses and contour plots will be made for a selected

block level.

The block is a fixed effect, for example, if you are making 32 experiments, and each 8

runs are done on one of four different machines. There is no other machine than the

four available, not now, nor in the future.

You may want to have 4 blocks to eliminate the variability introduced by the machines,

but all predictions of the response(s) are made for one of the specific machines.

Select the block factor as Random effect when the external variability cannot be

controlled and set at will, and the primary objective is to make predictions without

specifying the block level, and taking into account the external variability.

Since the block level of future experiments is unknown, all predictions of the responses

for random block effects are made without specifying the block level. The confidence

intervals for the responses are increased to account for the uncontrolled external block

variability.

For example, the block is a random effect if you are making 32 experiments, and each

block of 8 runs are made with a different batch of raw material.

Your primary objective is to make predictions for the next unknown batch of raw

material.

When you treat the block factor as Random effect it is often desirable to investigate

the consistency of the factor effects by including in the model all the interactions of the

block factor with the main factors, if possible.

In MODDE the model is always fitted as a fixed effect model, that is with the block

factor treated as a controlled qualitative variable, even when the blocks are specified as

random.

If the random block interaction effects with the main factors are large and significant,

the effect of the main factors varies from block to block, and the confidence intervals

on the prediction will be large due to this uncontrolled variability.

If the random block interaction effects are small and insignificant, the effects of the

main factors are consistent from block to block and the uncertainty of the predictions is

greatly reduced.

To have a realistic size of the confidence intervals, trim the model and remove all

insignificant block interactions effects.

If the block factor is specified as fixed effect, the interactions of the main factors with

the block factor are of less interest.

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User Guide to MODDE

The prediction of the responses, when the block effect is specified as random, are

computed without specifying the block level.

MODDE uses the average block level to predict the response but the confidence

interval is increased to take into account the variability of the response due to the

different blocks, plus the variability of the response due to uncertainty on the

coefficients of the model including all the terms with the block factor.

The calculation of the design space is a search function that expands the possible factor

ranges from a setpoint (optimum) to the largest possible range where all response

predictions are still within the specifications.

Predictions in the design space are done with Monte Carlo simulations. The resulting

distribution of predictions simulates a real situation with a random combination of

factor setting disturbances within a given range.

For more, see also the Appendix D: Design Space and Design Space chapters.

The random factor settings used for predictions can have three different distributions,

'Uniform', 'Normal', and 'Triangular'. The default is that the randomization follows a

normal distribution. In the Distribution box 'Target' is also available.

Uniform

Normal

Triangular

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Appendix A: Statistical notes

The low and high factor settings are the distribution boundaries. For a normal

distribution 95% of the distribution is found within the boundaries, by default. The

automatic search procedure expands the distribution for each factor until one or more

response limits are exceeded according to the specified DPMO target. The automated

search procedure is symmetrical around the setpoint but random for the factors.

DPMO is short for Defects Per Million Opportunities outside specifications and is used

as stop criteria in the design space estimation.

In the Design Space Properties dialog you can select to estimate using individual

DPMO as targets or total DPMO as target. The total DPMO is not necessarily the sum

of the individual DPMOs as the same point may be found outside the limits for more

than one response. So while each point outside is only counted once in the total DPMO

it may be counted several times if summarizing the individual DPMO.

DPMO = Ho * (1 000 000 / Ns)

where Ho = Hits outside specifications, Ns = Number of simulations.

Cpk, Capability index, originates from the SixSigma statistics and is another way of

expressing model robustness.

where

USL = Upper Specification Limit.

LSL = Lower Specification Limit.

μ = predicted average.

σ = estimated standard deviation for predictions.

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User Guide to MODDE

Cpk DPMO %Outside

0.4 115070 11.51

1 1350 0.13

1.3 48 0.0048

1.4 13 0.0013

2 0.0010 9.86588E-08

For more information about Cpk (Process Capability Index) search in Wikipedia.

Predictions from the Monte Carlo simulations by default include the model error. You

can select to not include the model error in the property page.

MLR models: Y = f(x) + e; DF = degrees of freedom.

1. Compute all Y predictions and confidence intervals for the random

simulations in X.

2. Generate a random t distribution on the confidence intervals in 1. based on

DF and e.

3. Add 1 and 2.

The above is true for PLS models too but PLS models with condition number > 3000

and non hierarchical mixture models display the standard error of prediction instead of

confidence intervals.

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Appendix B: Designs

Screening designs

Screening designs are used in the early stages of an investigation to find which factors

are important and if it is necessary to modify their ranges.

All screening designs support linear models and some support interaction models.

The designs you can select with interaction models, i.e. all interactions, are the full

factorial, the fractional factorial, Rechtschaffner, and D-Optimal designs of resolution

V. Fractional factorials of resolution V are supported for up to 12 factors.

MODDE supports the following screening designs:

Full factorial designs can be created at 2 or more levels.

These designs comprise all the possible combinations of the factor levels. For p factors

at 2 levels you need N =2p runs. Full factorial designs are orthogonal (balanced)

designs. Hence, the estimated effect of a factor is independent of the effects of all other

factors.

Full factorials with factors with different number of levels are called Full Factorial

Mixed.

Fractional factorial designs are 2 level designs with resolution III, IV, V or more.

These designs are balanced subsets (fractions) of the full factorials. The resolution of

the design depends on the size of the subset, i.e. the number of runs selected. The

possible resolutions are:

• Resolution III designs where main effects are confounded with 2 factor

interactions.

• Resolution IV designs where two factor interactions are confounded with

each other.

• Resolution V designs where main effects and all two-factor interactions are

clear of each other (unconfounded). MODDE supports resolution V designs.

With both resolution III and IV designs, you can only select the linear model. You may

edit the model and enter selected interactions. In that case, you may have to edit the

generators of the design.

With resolution V designs, MODDE generates the interaction model.

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User Guide to MODDE

The default generators used by MODDE for fractional factorial designs are those

recommended by Box, Hunter and Hunter (page 410). You may edit and change the

generators in the Generator dialog available on the Edit menu. When you update the

confounding, MODDE will warn you if some of the effects in your model are

confounded with each other, i.e. if your model is singular.

Plackett Burman designs are fractional factorial designs of resolution III, generated

with 4, 8, 12, 16, 20, 24, and 28 and more runs. Plackett Burman designs support only

linear models; i.e. you cannot estimate any two-factor interactions.

Plackett Burman Super-Saturated designs, PBSS, are fractional factorial designs of

resolution II, generated with 4, 6, 8, 10, 12, 14, 16, and 18 runs. A super-saturated

design is a Resolution II design with fewer runs than factors. Main effects are

confounded with main effects. It is assumed that only very few of the factors

investigated are active.

Three levels fractional factorial designs are fractional factorial designs from the

Graeco-Latin square family. The available designs are:

• L9: design with up to 4 factors at three levels.

• L27: design with up to 13 factors at three levels.

• L36: design with up to 13 factors at three levels.

• L18 is called mixed as it has one factor at 2 levels and up to 7 factors at three

levels.

With these 3 levels designs MODDE (objective = screening) lets you select only the

linear model, because these designs do not support interactions. In Edit | Model you

may edit the model and include square terms.

D-Optimal designs

D-Optimal designs are computer generated designs that maximize the determinant of

the X'X matrix, X being the extended design matrix.

D-Optimal designs are available for all objectives.

For more see the D-Optimal designs section later in this chapter and see also the D-

Optimal chapter.

Onion designs

Like regular D-Optimal designs, D-Optimal Onion designs can be used both in

screening and in RSM with quadratic models. The Onion designs comprise layers of

designs, usually D-Optimal, where the outermost layer determines which type of model

(screening or RSM) that the Onion design supports. For more see the D-Optimal

onion designs section later.

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Appendix B: Designs

Rechtschaffner designs

Rechtschaffner designs are orthogonal, saturated fractions of resolution V of the 2n and

3n factorial designs. They allow the estimation of all main effects and all first order

interactions without confounding. They are saturated designs, with no degrees of

freedom remaining for the estimation of residuals and diagnostics.

The 2n Rechtschaffner designs are well suited when the objective is screening, with 6

or more factors, and little knowledge about the importance of each individual first

order interaction. In this case it is of interest to estimate all first order interactions,

unconfounded, and then eliminate the insignificant (small) ones, hence recovering

some degrees of freedom for diagnostics and residual analysis.

The required number of runs N for the 2n Rechtschaffner designs with k factors is:

N =1 + k + k(k - 1)/2

It is recommended to add 3 to 4 center points to these designs.

RED-MUP designs

The RED-MUP designs are custom designs developed for the use with 96 well plates

(see figure) and larger (384, 1536, etc.). These are widely used platforms for

experimentation in biochemistry, microbiology, pharmaceutical development, etc.,

with some special properties (buildable and extendable to other factor intervals). The

RED-MUP designs consist of two sub-designs corresponding to the vertical and

horizontal directions of the plates, i.e., 8 and 12, respectively, for 96-well plates. The

total design is made by multiplying the two sub-designs together. Hence, this total

design supports a model with all interactions between the factors in the sub-designs,

plus from each sub-design, the main effects, and when these sub-design so support,

interactions, and quadratic effects.

Below, we use n1 and n2 for the number of rows and columns in the plate, i.e., 8 and

12 in a 96 hole plate. A 96-well plate can handle from 5 full “RSM factors” up to 18

factors for a stretched screening situation.

The layout of a 96 well plate has 8 rows and 12 columns. Hence, the vertical direction

has n1=8, and the horizontal direction has n2=12.

If both sub-designs support only main effects, using for example Plackett Burman sub-

designs, up to n1+n2-2 factors can be investigated, i.e., up to 18 factors in a 96 well

plate. Such a sparse design without center points is not recommended. More reliable

designs with center points in the larger sub-design would allow n1-3 + n2-5 = n1+n2-8

factors, i.e., 12 factors for a 96 well plate.

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User Guide to MODDE

When specifying the RED-MUP design, it is important to distribute the factors over the

two sub-designs (vertical and horizontal) so that (a) the actual experimental protocol

remains simple and doable, (b) the sub-designs and final design make

chemical/biological/engineering sense, and (c) a-priori interesting interactions and

higher order terms can be estimated. Note that all the interactions between each of the

factors in the vertical design and each of the factors in the horizontal designs can

always be estimated. Hence, factor pairs for which interactions are expected should be

split into the two sub-designs. Then their interaction can always be estimated,

regardless of choice of sub-design.

Special designs

When selecting to create a RED-MUP design, there are special designs for the 96 well

plates (8 x 12) which aim to make better use of the plate.

RSM designs

RSM designs are used in later stages of an investigation to develop more elaborate

models (quadratic) in the few important factors, usually not more than 5 or 6.

MODDE supports the following RSM designs:

Full factorial design at three levels is the full factorial design, with every factor varied

at three levels

The two central composite designs available in MODDE are the Central Composite

design Circumscribed (CCC) and Face Centered (CCF).

MODDE supports CCC and CCF designs for up to 12 factors.

These designs are composed of:

• A full or fractional factorial design.

• Star points.

• Replicated center points.

MODDE also supports a reduced CCC and CCF for four factors, with the fractional

part of the design reduced from 16 to 12 runs.

Note that with the CCC designs you may edit the model and include cubic terms, if you

wish.

Box Behnken designs are three level designs. All the design points are located at the

center of the edges of the cube or hypercube, and are all situated on the surface of a

sphere.

D-Optimal designs

D-Optimal designs are computer generated designs that maximize the determinant of

the X'X matrix, X being the extended design matrix.

D-Optimal designs are available for all objectives.

For more see the D-Optimal designs section later in this chapter and see also the D-

Optimal chapter.

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Appendix B: Designs

Onion designs

Like regular D-Optimal designs, D-Optimal Onion designs can be used both in

screening and in RSM with quadratic models. The Onion designs comprise layers of

designs, usually D-Optimal, where the outermost layer determines which type of model

(screening or RSM) that the Onion design supports. For more see the D-Optimal

onion designs section later.

Rechtschaffner designs

Rechtschaffner designs are orthogonal, saturated fractions of resolution V of the 2n and

3n factorial designs. They allow the estimation of all main effects and all first order

interactions without confounding. They are saturated designs, with no degrees of

freedom remaining for the estimation of residuals and diagnostics.

The 3n Rechtschaffner designs are well suited for the RSM objective with 6 or more

factors as they require fewer runs than the classical CCC or CCF non saturated designs.

The intent with these designs is to estimate quadratic terms but performing fewer runs

than with CCC or CCF. Eliminating insignificant terms, after performing the

experiments, results in recovering some degrees of freedom.

The required number of runs N for the 3n Rechtschaffner designs with k factors is:

N = 1 + 2k + k(k - 1)/2

It is recommended to add 3 to 4 center points to these designs.

RED-MUP designs

The RED-MUP designs are custom designs developed for the use with 96 well plates

(see figure below) and larger (384, 1536, etc.). These are widely used platforms for

experimentation in biochemistry, microbiology, pharmaceutical development, etc.,

with some special properties (buildable and extendable to other factor intervals). The

RED-MUP designs consist of two sub-designs corresponding to the vertical and

horizontal directions of the plates, i.e., 8 and 12, respectively, for 96-well plates. The

total design is made by multiplying the two sub-designs together. Hence, this total

design supports a model with all interactions between the factors in the sub-designs,

plus from each sub-design, the main effects, and when these sub-design so support,

interactions, and quadratic effects.

The RED-MUP designs are well suited for the RSM objective with up to 5 or 6 factors.

The intent with these designs is to get a precise model that can be used for optimization

and for detailed understanding.

The maximum number of “RSM factors” depends on the sizes of the sub-designs. An 8

run sub-design, e.g., a Doehlert design with 2 center points, supports 2 “RSM factors”

(1 constant, 2 linear, two quadratic, and one interaction terms), and a 12 run sub-

design, e.g., a three level Rechtschaffner design with 2 center points, supports 3 “RSM

factors” (1 constant, 3 linear, 3 quadratic, and 3 interaction terms) for a total of 5

“RSM factors” for a 96-well plate.

Mixed objective

Since the RED-MUP designs are constructed from two sub-designs, one of these can

be an RSM design and the other a screening design. In such a case the objective is said

to be mixed.

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User Guide to MODDE

Special designs

When selecting to create a RED-MUP design, there are special designs for the 96 well

plates (8 x 12) which aim to fill up the plate.

Doehlert designs

The Doehlert designs are quadratic RSM designs with some special properties

(buildable and extendable to other factor intervals). They allow the estimation of all

main effects, all first order interactions, and all quadratic effects without confounding.

They are saturated designs with similar properties to the CCF and CCC designs.

Geometrically they are polyhedrons based on hyper-triangles (simplexes), with a

hexagon in the simplest two-factor case.

Doehlert design in 2 factors with 6 runs + center points, can be extended to a new

design by adding 3 experiments. Usually also one or two new center points are added

in the new design (i.e., in the figure the right-most point in the old design).

The Doehlert designs are well suited for the RSM objective with up to 5 or 6 factors

(respectively 33 and 45 runs with 3 center points). The intent with these RSM designs

is to get a precise model that can be used for optimization and for detailed

understanding.

The required number of runs N, except for replicated center points, for the quadratic

Doehlert designs with k factors is:

N = 1 + k + k2

It is recommended to add 3 to 4 center points to these designs.

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Appendix B: Designs

In a mixture experiment the responses of interest depend only on the relative

proportions of the components (called mixture factors) that make up the mixture or

formulation. Hence, the sum of all the mixture factors is a constant T, usually equal to

1 when no mixture factors are kept constant.

Mixture factors are expressed as the fraction of the total amount of the formulation.

Their experimental ranges lie between 0 and 1.

Regular factors (i.e., temp, pH, etc.) that are not part of the mixture or formulation are

referred to as process factors. These are expressed as amounts or levels, and can be

either quantitative (measured on a continuous scale) or qualitative (have only

discrete values).

MODDE supports both mixture and process factors in the same experiment.

A mixture factor can be a formulation factor or a filler factor. Only one mixture factor

can be defined as filler.

Formulation factor

Formulation factors are the usual mixture factors used in formulations with specifically

defined experimental ranges. Most mixture experiments have only formulation factors.

Filler factor

The presence of filler is typical of certain types of simple mixture experiments. For

example in a synthesis the solvent is typical filler, as is water in a juice punch. A filler

is a mixture component, usually of little interest, making up a large percentage of the

mixture, and added at the end of a formulation to bring the mixture total to the desired

amount.

It is recommended to define a mixture factor as filler when all three conditions below

are fulfilled:

• The factor is always present in the mixture.

• The factor accounts for a large percentage of the mixture and there is no

restriction on its range. It is added at the end to bring up the mixture total to

the desired amount (usually 1 when no mixture factors are kept constant).

• You are not interested in the effect of the filler per se.

When you specify a filler factor, MODDE checks that these conditions are met and

defaults to a slack variable model, with the filler factor omitted from the model.

Use

All mixture factors are controlled or constant. The Uncontrolled option is unavailable

for both formulation and filler factors.

Formulation factors can be defined as Constant when you want to keep them constant

in the experiment.

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User Guide to MODDE

When mixture factors are constant, the mixture total T = 1 - Sum (constant mixture

factors). When no formulation factors are defined as constant, the mixture total has to

be equal to 1. MODDE issues an error message and stops whenever the mixture total is

not equal to T or 1.

Scaling

Mixture factors are always unscaled when you fit the model with MLR. When you fit

the model with PLS, all mixture factors are scaled to unit variance.

Note: When the mixture region is regular, mixture factors are first

transformed to pseudo components, and then scaled with PLS models.

Mixture constraint

In a mixture experiment the mixture total (i.e. the sum of all the mixture factors in the

experiment) is equal to a constant T. The mixture Total T is generally equal to 1 when

no mixture factor is kept constant. This mixture constraint implies that the mixture

factors are not independent, and this collinearity has implications on the mixture

experimental region, the mixture designs, and the mixture model formulation.

When all mixture factors vary from 0 to T (the mixture total), the shape of the

experimental region is a Simplex. With constraints on their ranges, the experimental

region is usually an irregular polyhedron inside the simplex. In some constrained cases,

as for example, with lower bounds constraints only, the experimental region is a small

simplex inside the original simplex. See Crosier (1984).

MODDE checks for consistent bounds, and computes:

RU = ∑Ui - T

RL = T - ∑Li

Li and Ui are the lower and upper bound of the ith mixture factors.

From RL, RU and Ri (the range of every formulation factor) MODDE determines if the

experimental region is a Simplex (the L simplex oriented as the original one, or the U

simplex with opposite orientation) or an irregular polyhedron.

When the mixture region is the L or U simplex, MODDE defaults to transforming the

mixture factors to pseudo component to make all their ranges vary between 0 and 1.

This is very similar to orthogonal scaling of process factor, to make their ranges vary

between -1 and +1.

With a regular mixture region, MODDE uses classical mixture designs.

The design is expressed in pseudo components and the worksheet is of course always

displayed in original units.

The analysis is performed on the mixture factors transformed to pseudo

component, as the coefficients of the Cox model can then be directly interpreted as the

mixture factors effects.

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Note: You can select to have the analysis done on the mixture factors

expressed in original unit under the Analysis menu.

When the mixture region is the L simplex, the L pseudo component transformation is

defined as:

Pi =(Xi - Li)/(RL)

The transformed mixture factors Pi vary from 0 to 1.

When the mixture region is the U simplex, the U pseudo component transformation is

defined as:

Pi =(Ui - Xi)/(RU)

The transformed mixture factors Pi vary from 0 to 1, but in this case the new simplex in

the P's has an opposite orientation to the original simplex in X, that implies that effects

in P are reversed from those in X.

When all factors are mixture factors and the shape of the region is a simplex, the

designs available in MODDE are the following classical mixture designs (all classical

mixture designs are displayed in pseudo components in the design matrix, and by

default the analysis is done with the formulation factors transformed to pseudo

components).

Screening designs

MODDE provides three variants of the axial design. Axial designs locate all the

experimental points on the axis of the simplex and are recommended for screening, see

Snee (references).

Standard Axial (AXN)

The standard axial design includes the following 2*q +m runs (q = number of mixture

factors, m centroid points as specified by user).

1. All the q vertex points. The coordinates of the ith Vertex point is

xi = (0, 0, 0..1, 0, 0..).

2. All q interior points of the simplex. The coordinates of the ith Interior point is

xi = (1/2q, 1/2q, 1/2q,..(q+1)/2q, 1/2q, 1/2q..).

3. The overall centroid of the simplex with coordinates

x = (1/q, 1/q,....., 1/q..) replicated (m-1) times.

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The extended axial design includes the following 3*q +m runs (q = number of mixture

factors, m specified by user).

1. All the q vertex points. The coordinates of the ith Vertex point is xi = (0, 0,

0..1, 0, 0..).

2. All q interior points of the simplex. The coordinates of the ith Interior point is

xi = (1/2q, 1/2q, 1/2q,..(q+1)/2q, 1/2q, 1/2q..).

3. All the q End points. The coordinates of the ith End point is

xi = (1/(q-1), 1/(q-1), 1/(q-1), 0, 1/(q-1), 1/(q-1)..).

4. The overall centroid of the simplex with coordinates

x = (1/q, 1/q,....., 1/q..) replicated (m-1) times.

Reduced Axial (AXR)

The reduced axial design includes the following (q+m) (specified by user) points:

1. All the q vertex points.

2. A subset or none (specified by user) selected from the q interior points.

3. The overall centroid replicated as desired.

RSM

MODDE provides 2 variants of the quadratic model designs, one special cubic and one

cubic. The simplex centroid design has all the experimental points on the vertices, and

on the center of the faces of consecutive dimensions.

Modified simplex centroid (SimM)

The modified simplex centroid design supports a quadratic model and includes the

following:

1. The q vertex points. The coordinates of the ith Vertex point is

xi = (0, 0, 0..1, 0, 0..).

2. The (q (q-1))/2 Edge centers. The coordinates of the ijth edge point is xij = (0,

0, 1/2, 1/2 0, 0..).

3. The q Interior check points. The coordinates of the ith interior point is xi =

(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).

4. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as

desired.

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Appendix B: Designs

The modified simplex centroid face center design supports a quadratic model and

includes the following:

1. The q vertex points. The coordinates of the ith Vertex point is

xi = (0, 0, 0..1, 0, 0..).

2. The (q (q-1))/2 Edge centers. The coordinates of the ijth edge point is xij = (0,

0, 1/2, 1/2 0, 0..).

3. The q Face centers of dimension (q-1). The coordinates of the ith face center

is: (1/q-1, 1/q-1,..,0, 1/q-1..1/q-1).

4. The q Interior check points. The coordinates of the ith interior point is xi =

(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).

5. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as

desired.

Simplex centroid Special Cubic (SimSC)

The simplex centroid special cubic design supports a special cubic model and includes

the following:

1. The q vertex points. The coordinates of the ith Vertex point is

xi = (0, 0, 0..1, 0, 0..).

2. The (q (q-1)) 1/3, 2/3 Edge points. The coordinates of the ijth edge point is

xij = (0, 0, 1/3, 2/3, 0, 0..), xji = (0, 0, 2/3, 1/3, 0, 0..).

3. The q(q-1)(q-2)/6 Face centers of dimension 2. The coordinates of the ith

face center is (0, 0, 0, 1/3, 1/3, 1/3..0, 0, ).

4. The q Interior check points. The coordinates of the ith interior point is xi =

(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).

5. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as

desired.

Simplex Centroid Cubic (SimC)

The simplex centroid cubic design supports a cubic model and includes the following:

1. The q vertex points. The coordinates of the ith Vertex point is

xi = (0, 0, 0..1, 0, 0..).

2. The (q (q-1)) 1/3, 2/3 Edge points. The coordinates of the ijth edge point is

xij = (0, 0, 1/3, 2/3, 0, 0..), xji = (0, 0, 2/3, 1/3, 0, 0..).

3. The q(q-1)/2 Edge centers. The coordinates of the ith edge center is xi = (0, 0,

0, 1/2, 1/2, 0...0).

4. The q(q-1)(q-2)/6 Face centers of dimension 2. The coordinates of the ith

face center is (0, 0, 0, 1/3, 1/3, 1/3..0, 0, ).

5. The q Interior check points. The coordinates of the ith interior point is xi =

(1/2q, 1/2q, (q+1)/2q, 1/2q, 1/2q..).

6. The overall centroid with coordinates x = (1/q, 1/q,...1/q), replicated as

desired.

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User Guide to MODDE

D-Optimal designs

What are D-Optimal designs?

D-Optimal designs are computer generated designs, tailor made for a specific

problem. They allow great flexibility in the specifications of your problem. They are

particularly useful when you want to constrain the region and no classical design

exists.

“D-Optimal” means that these designs maximize the information in the selected set of

experimental runs with respect to a stated model.

For a specified regression model Y = X*β + ε where:

Y is a (N x 1) vector of observed responses,

X is a (N x p) extended design matrix, i.e. the n experimental runs extended with

additional columns to correspond to the p terms of the model (i.e., the added columns

are for the constant term, interaction terms, square terms, etc..)

β (beta) is a (p x 1) vector of unknown coefficients to be determined by fitting the

model to the observed responses.

ε (epsilon) is a (N x 1) vector of residuals (the differences between the observed and

predicted values of the response y). They are assumed to be independent of each other,

normally distributed and with constant variance σ2

The D-Optimal design maximizes the determinant of the X'X matrix, which is an

overall measure of the information in X. Geometrically; this corresponds to

maximizing the volume of X in a p dimensional space.

Candidate set

D-Optimal designs are constructed by selecting N runs from a candidate set. This

candidate set is the discrete set of “all potential good runs”.

MODDE generates the candidate set as follows:

I) For a regular process region, the candidate set consists of one or more of the

following sets of points (depending on your model and the number of factors):

• The full factorial for up to 10 factors, reduced factorial for up to 32 factors.

• Centers of edges between hyper-cube corners

• Centers of the faces of the hyper-cube.

• Overall centroid

II) For constrained regions of mixture or/and process factors, the candidate set consists

of one or more of the following set of points:

• The extreme vertices of the constrained region

• The centers of the edges. If these exceed 200, the center of the 200 longest

edges

• The centers of the various high dimensional faces

• The overall centroid.

MODDE has implemented an algorithm to compute the extreme vertices, center of

edges, center of faces etc. as described by Piepel (1988).

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Appendix B: Designs

D-Optimal algorithm

D-Optimal designs have been criticized for being too dependent on an assumed model.

To reduce the dependence on an assumed model, MODDE has implemented a

Bayesian Modification of the K-Exchange algorithm of Johnson and Nachtsheim

(1983), as described by W. DuMouchel and B. Jones in “A Simple Bayesian

Modification of D-Optimal designs to reduce dependence on an Assumed Model”,

Technometrics (1994).

With this algorithm one can add to the “primary terms” i.e. the terms in the model,

“potential terms”, i.e. additional terms that might be important. The objective is to

select a D-Optimal design, rich enough to guard for potential terms, and enable the

analysis to detect possibly active ones.

In order not to increase the number of runs N, and to avoid a singular estimation, one

assumes that the coefficients of the potential terms are likely to have a mean of 0 and a

finite variance (tau, τ)2.

K-exchange algorithm

The k-exchange algorithm is a compromise between the exchange algorithm of Wynn

(1972) with k=1 and the Federov algorithm with k = N (the selected number of runs).

In MODDE k is set to 3, that is at every iteration of the procedure, the algorithm

considers an exchange between k = 3 points in the design with the smallest prediction

variance and points in the candidate set. If any exchange increases the determinant, the

point(s) (up to 3) are exchanged.

As recommended by W. DuMouchel, tau, τ, is set to 1 in MODDE.

Potential terms

Potential terms are higher order terms not included in the model but taken into account

during the creation of the candidate set. Potential terms are default added but can be

removed by clearing the Use potential terms box.

Depending on the number of factors, the objective and the model, MODDE adds the

following potential terms:

Screening

Factors Model Potential terms

RSM

Factors Model Potential terms

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User Guide to MODDE

Screening

Factors Model Potential terms

RSM

Factors Model Potential terms

7 - 12 Quadratic None

Screening

Factors Model Potential terms

RSM

Factors Model Potential terms

Note: No potential terms are added for investigations with all factors defined

as qualitative.

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Appendix B: Designs

Design evaluation

To evaluate and compare D-Optimal designs, MODDE computes the following

criteria:

LogDetNorm

The log of the determinant of X'X normalized for number of terms in the model p, and

number of runs N.

This is the criterion used, by default, to select the best design. MODDE selects the

design with the largest value (closest to 0) of LogDetNorm.

LogDetNorm = Log10 [ Det(X'X)1/p / N]

The maximum value of LogDetNorm, for an orthogonal design, is 0.

LogDet

The Log of the determinant of the X'X matrix

Condition No

The condition number of the X design matrix coded orthogonal, and extended

according to the model.

G efficiency

G efficiency is a lower bound on D efficiency, which compares the efficiency of a D-

Optimal design to a fractional factorial.

G efficiency is defined as:

Geff = (100*p)/(n*d)

Where

p = number of terms in the model

n = number of runs in the design

d = Maximum relative prediction variance v over the candidate set, where the

prediction variance v = x(X'X)-1x'

MODDE allows you to specify a set of experimental runs as Inclusions specified

under Design | Inclusions. If you enter experiments in Inclusion before creating your

design these runs are default a part of the resulting D-Optimal design.

Inclusions are useful for design augmentation. If you already have performed a few

experiments, and want to add M additional experiments, add the old experiments in

Inclusions, ask for N+M runs and state the desired model. The M runs are selected D-

Optimally from the candidate set with respect to your model.

For more on design augmentation see the Complement design section in the File

chapter.

Note: All of these statistics are computed from the runs selected D-optimally

and do not include the possible center points added to the worksheet.

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User Guide to MODDE

Irregular region

Screening

When the mixture region is an irregular polyhedron, MODDE computes the extreme

vertices (corners) delimiting the region. These extreme vertices constitute the candidate

set and the centers of the high dimensional faces are added to support potential

terms. The design is a D-optimal selection of N (specified by user) runs from the

candidate set.

RSM

MODDE computes the extreme vertices, 1/3, 2/3 centers of edges, centers of faces of

dimension (q-1) and the overall centroid of the experimental region. When there are

too many extreme vertices, only the center of the 25% longest edges is computed.

These experimental points constitute the candidate set.

The design is a D-Optimal selection of N runs (specified by the user) from the

Candidate set.

You can always select to have the mixture factors expressed in pseudo components for

the analysis. MODDE uses the L pseudo component transformation when RL ≤ RU and

the U pseudo component when RU < RL.

Pseudo component transformation is the MODDE default when the method of fit is

MLR as it stretches the experimental region and alleviates the problem of ill

conditioning.

Mixture models

Because of the mixture constraint, (the mixture factors are not independent) the

analysis of mixture data with multiple regression requires a special model form.

The traditional approaches have been:

• Defining the model omitting one mixture factor, hence making the others

independent. This is the Slack Variable approach.

• Omitting some terms from the model, so that the terms remaining in the

model are independent. This is Scheffé model, with the constant term

removed from the linear model and the quadratic terms removed from the

quadratic model.

• Using the complete model including all the mixture terms, but putting

constraints on the coefficients to make them estimable. This is the Cox

reference model, and the constraints on the coefficients are defined with

respect to a standard reference mixture. This standard reference mixture

serves the same function as the centering constant with process variables

models.

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Appendix B: Designs

When you have both process and mixture factors, you can select to treat them as one

model, or to specify separate models for the mixture factors, and the process factors.

With both mixture and process factors, the only model form available is the Cox

reference mixture model.

When the model obeys mixture hierarchy, the PLS coefficients are expressed relative

to a stated standard reference mixture. The following constraints are imposed on the

coefficients:

For linear models

∑bksk = 0

For quadratic models

∑bksk = 0 (1)

∑ckjbkjsk = 0 for k = 1,,,,q (1) and for j = 1,,,,q (2)

Here ckj = 1 when j ≠ k and ckj = 2 when k = j.

and sk are the coordinates of the standard reference mixture.

If γ (gamma) are the coefficients of the interactions between the process and mixture

factors:

∑γksk = 0

Note: When the model contains terms of order 3, or contains qualitative and

formulation factors, the PLS coefficients are not adjusted relative to a stated

standard mixture.

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User Guide to MODDE

Onion designs can be created for regular process factors, using an imported candidate

set, and using scores from SIMCA-P as design variables. When importing scores, the

scores are automatically loaded from the SIMCA-P usp-file, and the candidate set for

the Onion design is comprised of all objects (rows) in the workset of the SIMCA-P

model selected as the basis of the Onion design.

The design is made in a number of layers (shells), with a separate D-optimal design for

each layer. Typically the number of layers is two or three.

D-Optimal onion designs are similar to space filling designs in that design points are

situated also in the interior of the design space.

D-Optimal onion designs are available in MODDE only when the factors are

quantitative.

Observations in the candidate set are sorted by their distance to the center of the

multivariate space, expressed as percentiles from the center.

The candidate set is then divided into layers, by default three, layer one being the

innermost layer and layer three the outermost layer.

A D-Optimal design is then performed on each layer separately and the final design

and worksheet includes all the runs selected D-Optimally in each layer. This makes the

selected runs fill the multivariate design space.

The model and the number of runs in each layer as well as the percentile of

observations included in each layer can be specified by the user.

The D-Optimal onion design selects runs from each layer separately, ensuring that the

design will have points that fill the space.

When the objective is screening, two D-Optimal Onion design are available. The

recommended design has a full interaction model in the outer layer. The second choice

is with a linear model in the outer layer.

The default number of layers (three when the candidate set allows it) can be changed

from the Layer box. The outer layer is the last layer, and the innermost layer is number

1. The maximum allowed number of layers is default 10. You can change the Max

number of layers in Onion Design in View | General Options, tab General.

For more see the D-Optimal chapter.

When the objective is RSM, the quadratic D-Optimal Onion design is available. The

recommended design has a full quadratic model in the outer layer.

The default number of layers (three when the candidate set allows it) can be changed

from the Layer box. The outer layer is the last layer, and the innermost layer is number

1. The maximum allowed number of layers is default 10. You can change the Max

number of layers in Onion Design in View | General Options, tab General.

For more see the D-Optimal chapter.

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Appendix C: Optimizer

Introduction

The optimizer works according to a given set of specifications. The specification of the

factors and responses are selected according to the desired result. A drawback with this

strategy can be that the best possible solution might not be reached. With unrealistic

response specifications it will be impossible for the optimizer to do a good job. With a

good strategy and by using complementary tools such as contour plots, DPMO

estimates, sweet spot plots and Design Space estimates, a good understanding for the

possibilities can be obtained.

The optimizer is used to find an experimental setpoint that fulfills various criteria. The

optimizer uses a search function to find the best possible solution to an equation

system given a number of operating criteria. The optimizer starts with a number of

criteria set in the optimizer window.

This appendix describes the possibilities and limitations of the optimizer function. The

first part is a description of how the optimizer works and the second part discusses how

different objectives can be reached by selecting different start criteria for the

optimization.

Search function

The optimizer works with a desirability function (f(ds)) that searches for the best

possible combination of factor settings that predicts a result inside the response

specifications and as close as possible to the target(s). When searching for one solution

with many criteria, the result will be a compromise. This compromise is based on a

summary function that is a measure of the distance to target for all results. It is

expressed as f(ds).

How f(ds) works depends on the weight for each response and the limit and target

specifications: the optimizer objective.

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User Guide to MODDE

Optimizer objectives

The optimizer can be set up for different objectives:

1. Limit optimization – where the objective is to reach a solution where all

responses are within the specification limits. This is default in MODDE.

2. Target optimization – where the objective is to reach a solution where all

responses are as close to target as possible. For the target optimization it is

necessary that all responses can be optimized close to or to reach the target.

Otherwise you may end up with an unacceptable solution.

3. Focus optimization – where the objective is to favor one or several responses

over the others using individual weights.

To control the optimization criteria the weight function has a key role, as well as

reasonable limits and targets for the responses. The optimizer works with a desirability

function, f(ds), and will strive to reach the lowest possible value. The shape of the

function is controlled by the weight and the settings of criteria (Min, Target, Max) for

each response. In the following pictures two desirability functions are shown, the first

with weight=1 and the second with weight=0.2.

With the weight 1 the lowest possible f(ds) is -100 and with a weight of 0.2, the lowest

possible f(ds) is -20.

Limit optimization

With weight=1 the desirability function decreases rapidly close to the limit and then

flattens out. As consequence it will be easier to reach a compromise where all

responses are inside the specification limits but maybe not as close to target as

possible.

Weight = 1. The desirability function reached the lowest possible value, -100, just

inside the specification limit. This will work well to find a compromise when many

responses strive to get inside the specification limits. Note that in this plot the 'weight

scaled limit' and the 'limit' are displayed on top of each other.

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Appendix C: Optimizer

Target optimization

If all weights are set to 0.2, the optimizer will search for a target solution for all

responses if that is possible. If that is not possible, the optimizer might find a solution

that will predict some responses very close to target and some outside the specification

limits.

Weight = 0.2. The desirability function will reach the lowest possible value, -20, close

to the target. If the weight is set to 0.2 for all responses it will go for a target solution

due to the slope of the function. This solution might be unacceptable if a common

target solution isn’t present.

Focus optimization

If the weights are set differently for different responses, responses with higher weights

take priority in the search for a solution inside the specifications. The overall

optimization criterion is to reach the lowest sum of f(ds). With the weight 1 the lowest

possible f(ds) is -100 and with a weight of 0.2, the lowest possible f(ds) is -20.

To open the optimizer, click Optimizer on the Prediction menu. MODDE opens a

window with 3 spreadsheets. For detailed information about the optimizer window,

see the Optimizer section in the Prediction chapter.

The start specifications are from the initial factor and response definitions. If no

response specification for Min, Target, and/or Max exists the default criteria is

‘Predict’.

Reaching an optimal result is in many cases an iterative process. If the response

specifications are impossible to reach the criteria will probably have to be reevaluated.

With the help of some raw data analysis and some initial model analysis, you can get a

reasonable understanding of the possibilities.

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User Guide to MODDE

In this example we want to minimize the NOx emission with an upper specification

limit (Max) of 25. Setting the target to 0 might seem logical but it is not possible for

the optimizer function to reach in the experimental region investigated. An inspection

of the raw data, see Replicate Plot below, shows that all NOx data are between 10 and

30. Therefore it should be impossible to get a prediction close to 0 for the current

experimental region. A more reasonable target in this case is NOx=15. The target and

max limit values are supported in the plots that follow.

Replicate Plot: All values for NOx can be found between 10 and 35.

The response Soot is minimized while the response Fuel is set to Target for

illustrational purposes. Generally we also want to minimize the Fuel consumption.

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Appendix C: Optimizer

Optimizer result

The optimizer will search for a solution to the specifications from 8 different starting

points using a Nelder-Mead Simplex algorithm trying to minimize the desirability

value f(ds). The result is expressed as a normalized distance to target Log(D) and

DPMO (Defects Per Million Opportunities outside specifications).

For more information about the calculations, see the Optimizer section in the

Statistical appendix.

After running the optimizer the best proposal (lowest Log(D)) is selected. A Log(D) <

-1 means that all results should be safely within specification limits. The optimal value

of Log(D) is -10; then all response predictions are on target. DPMO gives information

about robustness to small disturbances introduced by the Sensitivity Range specified

for the factors.

In the run list above, row 6 has a DPMO = 0 meaning that with disturbances + 5% on

the factor settings will give a solution inside the specifications. Row 1 has

approximately the same Log(D) but a DPMO = 7000 indicating that a small

disturbance in the factor settings from this point will result in some hits outside the

specifications. Therefore row 6 is preferable.

The result from the optimizer can be evaluated with three main tools:

• Contour Plot Wizard generates a plot around the factor settings of the

selected row, showing the dynamics around the selected point, e.g. if it is a

flat region or very sensitive to small changes. The selected run is displayed

in the plot as lines from the axes with arrows pointing toward the position of

the selected run.

the common region within specifications is shown in green. The selected run

is displayed in the plot as lines from the axes with arrows pointing toward

the position of the selected run.

• Analyze Design Space displays how the factor settings can be varied

around the selected point (optimum) and still fulfill the response criteria. We

can make an estimation of a safe DS region with Monte Carlo simulations on

the factor settings.

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Appendix D: Design Space

Introduction

The calculation of the design space is a search function that expands the possible factor

ranges from a setpoint (optimum) to the largest possible range where all response

predictions are still within the specifications.

Predictions in the design space are done with Monte Carlo simulations. The resulting

distribution of predictions simulates a real situation with a random combination of

factor setting disturbances within a given range.

There are two Design Space features in MODDE:

• Predictive Design Space Estimation for optimization.

• Design Space Validation for robustness testing.

This chapter gives further insight to these features.

The basis for good quality estimates is the use of a proper experimental design. The

Design Space function available by clicking the Analyze Design Space button in the

Optimizer provides:

• A good overview of where the selected point is located in the design region.

• An estimate of the largest possible factor variation that still results in

predictions within specification.

……………………

The “International Conference on Harmonisation (ICH); Draft Guidance: Q8(R1)

Pharmaceutical Development Revision

1” (http://www.fda.gov/cber/ich/ichguid.htm) has outlined quality by design (QbD)

principles for pharmaceutical development which introduced the concept of Design

Space (DS). ICH Q8 defines DS as “the multidimensional combination and interaction

of input variables (e.g. material attributes) that have been demonstrated to provide

assurance of quality”.

……………………

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User Guide to MODDE

The predictive DS estimate shows the factor settings of the selected run in the

optimizer and the accepted variability around these settings that still result in

predictions in the accepted response region.

We can make an estimation of a safe DS region with Monte Carlo simulations on the

factor settings. MODDE will perform a search to identify the largest possible range for

each factor (faded region) that can be used and still meet all response requirements.

The default target is 1000 (0.1%) hits outside the limits (DPMO) for one response. In

this case the limiting response will be Soot, the final predictions will give 0.17% of the

predictions outside the upper limit.

The Monte Carlo simulations are:

• random factor settings according to the selected distribution,

• around their optimum value but within the Low and High limits,

• followed by predictions of the responses. In this case 100 000 predictions are

performed. The distribution as well as the number of simulations and the

range can be changed by the user.

The resulting distributions can be presented as a histogram, one for each response.

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Appendix D: Design Space

If the result in some way is not satisfactory, one option can be to change the starting

point for the DS search (optimum factor setting). Another option is to lock some factor

ranges where setting tighter specifications won’t be a problem. See the Design Space

Validation for robustness testing section later in this chapter.

For alternative start points it can be preferable to step back to the optimizer and select

another start point based on Log(D), DPMO and Sweet Spot evaluation. The modeling

results, e.g. Coefficient Plot, can also be an information source to finding

alternatives. All settings can be changed in the DS estimation table for a user

controlled search in order to find the most appropriate solution.

Previously in this section we showed the results of a DS estimate starting from row 6

in the optimizer. We will now show you how selecting a different starting point can

affect the outcome of the estimation.

An alternative selection of starting point from the optimization can give

approximately the same result but a more extreme factor setting. See the following DS

estimate from the optimizer proposal of row 1. Note that in this design space

estimation we have chosen to not use the model error for a more visual illustration of

the different results. The suggested factor settings are much closer to a limit and likely

represent a less stable point of operations.

These settings give results within specifications but with a combination of factor

settings that is more extreme and close to the experimental limits. Another

consequence is that the accepted region of variability for the proposed factor settings is

narrower than the previous proposal starting from row 6.

1. Develop the best model for each response.

2. Find the optimal settings for the factors that comply with the response

criteria.

3. Check if the proposed optimal factor settings are critical (close to a limit) or

in a safe region.

4. Make an estimation of the safe region with Monte Carlo simulation on the

factor settings.

5. Evaluate the results and make necessary adjustments.

6. Set your preferred factor specifications.

7. Document the final results.

283

User Guide to MODDE

According to the FDA: “VALIDATION OF ANALYTICAL PROCEDURES:

Definition and terminology. The robustness of an analytical procedure is a measure of

its capacity to remain unaffected by small, but deliberate variations in method

parameters and provides an indication of its reliability during normal usage.”

Design Space validation is a way to test if the system investigated is robust against

disturbances in the investigated region.

The aim of robustness testing is to evaluate if a process, or a system, performs

satisfactory even when some influential factors are allowed to vary. In other words, we

want to investigate the system’s sensitivity (or preferably lack of sensitivity) to

changes in certain critical factors. The advantages of a robust process or system

include simpler process control, a known range of applicability and an ensured quality

of the product or process.

A robustness test is usually carried out before the release of an almost finished product,

or analytical system, as a test to ensure quality. Umetrics recommends the use of DoE

for robustness testing and such a design is usually centered on the factor combination,

which is currently used for running the analytical system, or the process. We call this

the setpoint. The setpoint may have been found through a screening design, an

optimization design, or some other identification principle, such as written quality

documentation. The aim of robustness testing is, therefore, to explore robustness close

to the chosen setpoint.

In Design Space Validation we use Monte Carlo simulations on the regression model

and simulate random disturbances within the investigated range of operation for all

factors. The regression model originates from a low resolution design supporting linear

models since we assume that small disturbances have mainly linear effects. Fractional

factorial resolution III and Placket Burman designs are recommended.

In this example we show that the DoE strategy in combination with Monte Carlo

simulations here gives a proper estimate of the system's robustness.

The investigation chosen to illustrate the Design Space Validation feature originates

from a pharmaceutical company. It represents a typical analytical chemistry problem

within the pharmaceutical industry. In analytical chemistry, the HPLC method is often

mounted for routine analysis of complex mixtures. It is therefore important that such a

system will work reliably for a long time, and be reasonably insensitive to varying

chromatographic conditions. For details about this example, see the tutorial

"Robustness testing".

284

Appendix D: Design Space

Evaluation

The Prediction | Design Space Validation tests the robustness by making a large

number of random disturbances (Monte Carlo Simulation) in the specified region. In

this example the specified region is the Experimental Region. In the DS window

(shown below) the factor part shows the original investigation settings with a specific

selection for the qualitative factor Column. ColA was manually selected as this column

gave the worst results (See Tutorial example for more information about the specific

example). The result is shown as a distribution of random samples including model

prediction errors and it is well within the specification limits for some responses. The

result can be expressed in general statistics as well as capability indexes Cpk or DPMO

= Defects Per Million Opportunities outside specifications.

A description of the details of this window is found in the Design Space window

section in the Design Space chapter.

Factor spreadsheet

All factors are varied within the design limits with Monte Carlo simulations according

to a Normal distribution. These are the default settings.

Response spreadsheet

The result for response k1 is optional; there are no specific demands for this response.

The result for response k2 is partially outside the specification limits.

The result for response Res1 is above the low specification limit.

The result for response PlateN(2) is above the low specification limit

From the above we conclude that this system is robust against disturbances in the

factors for Res1 and PlateN(2). k2 is not robust against disturbances in the factors.

285

User Guide to MODDE

Final adjustments

Design Space can be used to estimate the maximum accepted variability in factors that

still predict all results within the specifications.

The problem in the described example is response k2. The requirement for k2 is that

less than 0.1%, corresponding to DPMO = 1000, of the predictions may be outside the

specification limits.

There are constraints when handling this type of situation;

• Which factors affect the result?

• How can we adjust the factor limits without causing too much problems in

the normal use of the procedure?

First we have to check the model to understand which factors are the most influential.

The model has to be significant for an adjustment in factor ranges to have affect on the

result distribution.

In this example the model for k2 is very significant and the most important factor is

Acetonitrile (ACN).

286

Appendix D: Design Space

Assuming that the factor Temperature is easy to control with a narrower range we start

with this factor by adjusting temperature to +/- 0.5 °C. At the same time we can open

the Role for ACN to 'Free'. This instruction together with the specification limit for k2

(DPMO = 1000) will give an estimate of a range for ACN where we can predict that

the system is robust according to the specifications. The picture below displays the

result of the settings.

The proposed settings for ACN are now 25.51 to 26.49 and the estimated distribution

for k2 is 1410 hits outside the specification limits.

A final step might be to make an adjustment of the factor settings to some practical

new specification within the range for ACN, for instance 25.5 to 26.5. The result

shown below implies that the critical response k2 will have 0.16% of future predictions

outside the specifications.

287

User Guide to MODDE

To open the response histogram, click the Create Histogram button in the Design

Space window.

In the Response box on the Standard toolbar, select which responses to display.

To view statistics, right-click the Design Space window, and then click Design Space

Statistics.

A more detailed description of this example is found in the tutorial named “Robustness

Testing”.

288

References

inference”, A re-issue (J. H. Bennett, Ed.), Oxford University Press, Oxford,

England, (1990).

2. G.E.P.Box, W. G. Hunter, and J. S. Hunter, “Statistics for experimenters”,

Wiley, New York, (1978).

3. G.E.P. Box, The collected works, Vol 1. (G.C. Tiao, Ed.), Wadsworth

Advanced Books and Software, Belmont, CA, 1985.

4. Morgan, Chemometrics: Experimental Design, ACOL, London, and Wiley,

New York, (1991).

5. Wold, “Soft modeling, The basic design and some extensions”, In Vol. II of

K-G. Jöreskog and H. Wold, Ed.s. Systems under indirect observation, Vol.s

I and II, North-Holland, Amsterdam, (1982).

6. Wold, A. Ruhe, H. Wold and W. J. Dunn III, “The Collinearity Problem in

Linear Regression. The Partial Least Squares Approach to Generalized

Inverses”, SIAM J. Sci. Stat. Comput. 5, 735-743, (1984).

7. Höskuldsson, “PLS Regression Methods”, J.Chemometrics, 2, 211-228,

(1988).

8. Wold. “Cross validatory estimation of the number of components in factor

and principal components models”, Technometrics 20, 397, (1978).

9. Draper and Smith, “Applied Regression Analysis”, Second Edition, Wiley,

New York.

10. Cornell, “Experiments with Mixtures”, New York: Wiley, (1990).

11. Cox, “A Note on Polynomial Response Functions for Mixtures”, Biometrica,

58, 155-159, (1971).

12. Crosier, “Mixture Experiments: geometry and Pseudo components”,

Technometrics, 26, 209-216, (1984).

13. Kettaneh-Wold, “Analysis of mixture data with partial least squares”,

Chemometrics and Intelligent laboratory Systems, 14, 57-69, (1992).

14. Rechtschaffner R.L., Saturated fractions of 2n and 3n factorial designs,

Technometrics, 1967, Vol.9, N°4, 569-575.

15. Ing-Marie Olsson, Erik Johansson, Martin Berntsson, Lennart Eriksson,

Johan Gottfries, and Svante Wold, “Rational DOE-protocols for 96 well

plates”, Chemometrics and Intelligent Laboratory Systems, 2006.

16. Doehlert, D.H., “Uniform shell designs”, Journal of the Royal Statistical

Society, 1970, Serie C, N°19, 231-239.

17. Snee, “Test Statistics for Mixture Models”, Technometrics, Nov. 1974.

289

User Guide to MODDE

Type III Secretion, Infection and Immunity, 73, 3104-3114.

19. Design space; ICH Q8(R1) Pharmaceutical Development Revision 1,

http://www.ich.org/cache/compo/276-254-1.html.

20. Quality by Design; http://en.wikipedia.org/wiki/Quality_by_Design

290

Analysis

Index Fit............................................ 136, 137

Menu ......................................... 15, 133

Of variance ............................. 150, 238

Phase ............................................... 2, 9

Wizard ............................................ 135

Analysis Advisor ................................... 45

Analysis menu

2 Organization ................................... 133

Select Fit Method ............................ 136

2D contour ................................... 167, 187

Analysis of Variance ................... 150, 238

3 Analysis phase ......................................... 2

3D Analysis Wizard .................................. 135

Labels..............................................216

Onion plots......................................115 Arrow .................................................... 41

Rotation response surface .................41 Audit trail .............................................. 53

Scatter ............................. 115, 126, 176

Augmenting designs .............................. 23

Surface ............................................172

Zoom and rotate ................ 41, 214, 220 Auto update predictions....................... 176

Auto, MLR, PLS, Scheffé ................... 137

4

Automatic fit ......................................... 59

4D

Contour ...........................................169 Automatic update .......................... 59, 205

Sweet spot .......................................177 Autoscale modifier ................................ 77

Accelerators ......... 30, 31, 45, 64, 221, 224 AXR .................................................... 265

Activation ............................................229 B

Add Balanced ...................................... 106, 257

Command to Favorites ......................46

Block

Experiments ....................................131

Blocking............................................ 56

Factor .......................................... 27, 65

Blocks ....................................... 95, 102

Inclusions ..........................................90

BlockV ............................................ 131

Response ..................................... 32, 75

D-Optimal designs .......................... 252

Row ...................................................32

Interactions ............................. 102, 250

Squares and interactions.............. 34, 38

Mark ................................................. 41

Terms ................................................34

Orthogonal ...................................... 250

To Favorites ......................................51

Random..................................... 56, 253

To Report .................................. 51, 228

RSM designs ................................... 252

Add to Favorites ....................................51 Screening designs ........................... 251

Add to Report ........................................51 Box Behnken designs .......................... 260

Adjust according reference .......... 174, 243 Box Whisker........................................ 128

Alpha level ............................................54 Box-Cox plot ............................... 147, 243

291

User Guide to MODDE

Command menu bar ........................222 Screening to RSM Rechtschaffner .... 28

Format bar .......................................226 Condition Number ............................... 236

Generate report bar .........................226

Optimizer buttons............................185 Confidence interval for predictions ..... 242

Plot bar ..............................................41 Confidence level

Spreadsheet bar .................................41 Changing ........................................... 56

Standard bar ......................................39 Used in .... 145, 149, 150, 173, 175, 176

Status bar ..........................................44

Confoundings .............................. 152, 202

Window bar.......................................44

Constraint

C Candidate set..................................... 89

Candidate runs .....................................112 Constraints supported ....................... 86

Defining ................................ 85, 86, 87

Candidate set Mixture ........................................... 264

Constraints in qualitative and Modifying graphically ...................... 88

multilevel ..........................................89 Qualitative or multilevel ................... 89

Created by MODDE .......................268 Why .................................................. 85

Imported ..........................................111

Max size ............................................59 Continue Edit Report With .......... 222, 226

Customize ............................... 213, 214

Case sensitivity ......................................10 From Optimizer .............................. 187

CCC Insert text .......................................... 41

Design .............................................260 Labels ............................................. 214

Settings .............................................99 Levels ............................................. 214

Options............................................ 214

CCF .....................................................260

Plot .................................. 167, 169, 187

Central Composite design Wizard .................................... 166, 187

Circumscribed

Contour levels ..................................... 214

Design .............................................260

Settings .............................................99 Controlled.............................................. 68

Centroid ................................. 34, 265, 272 Convention ............................................ 10

Classical mixture designs ....................265 Coordinate Reader ................................. 41

Coding qualitative factors....................241 Copy .................................................... 188

Coefficients ................... 55, 152, 240, 241 Correlation................... 129, 162, 163, 232

Collinearity ..........................................264 Correlation matrix ......................... 60, 129

Color Correlation plot ................................... 129

Scatter plot ......................................176 Cross-validation rules .......................... 234

Sweet spot plot ................................177

Worksheet .......................................131 Cubic centroid ................................. 6, 265

Doehlert ............................................27 Contour plot ............................ 213, 214

D-Optimal .........................................25 Header and footer............................ 209

Estimate square term .........................24 Properties of the axes ...................... 207

General..............................................23 Properties of the plot area ............... 210

Inclusions .................................. 90, 271 Scatter plot ...................................... 216

292

Index

to model .......................................... 146

D to target ........................................... 186

Decimal ......................................... 71, 207 DModY ............................................... 146

Default options ......................................52 Dockable Windows ............................... 44

Default plot settings.............................206 Doehlert ......................................... 27, 262

Default template .......................... 222, 226 D-Optimal

Degrees of freedom .............................239 Algorithm........................................ 269

Complement...................................... 25

Delete investigation ...............................21 Onion design ........................... 113, 274

Deleted Studentized Residuals .... 146, 241 Pages ....................................... 108, 122

Results ............................................ 108

Derived responses

Summary ......................................... 203

Defining ............................................78

What ....................................... 103, 268

Operators...........................................81

When....................................... 103, 272

Qualitative factors .............................82

Sets of variables ................................80 E

Syntax ...............................................81

Edge ............................................ 203, 265

Description button ...............................101

Edit menu .............................................. 31

Descriptive Statistics ...........................128

Edit model ............................... 34, 99, 104

Design

Advanced designs .............................18 Effects ................................................. 155

Import design from file .....................21 E-format ................................................ 52

Traditional designs ............................18

Eigenvalues ................................. 134, 236

Design augmentation ...........................271

Email ..................................................... 22

Design Region ............................. 201, 202

Encrypt .................................................. 29

Design Runs .......................... 97, 104, 112

Estimate squares .................................... 23

Design Runs Span ...............................106

Evaluate ............................... 109, 134, 271

Design Space

Buttons ............................................194 Evaluation plot .................................... 184

Estimation ............................... 190, 191 Exclude button ...................................... 41

Statistics .................................. 197, 254 Exclude tool .......................................... 41

Validation .......................................284

Window...........................................192 Execute folder ....................................... 46

Design Wizard ............................... 64, 117 Exit ........................................................ 30

Desirability ..........................................248 Experiment Name .......................... 52, 131

Detect curvature .......................... 124, 125 Experiment Number ...................... 52, 131

Determinant Experimental cycle .................................. 1

Criteria .................................... 106, 271 Experimental design .......................... 5, 10

D-Optimal design maximizes ..........268

Exporting Favorites configuration ......... 50

Log .......................................... 109, 271

Normalized Log ..............................109 Extended................................ 57, 200, 204

DF residuals.........................................134 Extended Axial .................................... 265

DFresid ................................................239 External variability ...................... 124, 250

Diagnostic part ....................................152 Extreme Vertices ................................. 203

Diagnostics .................................. 125, 143

293

User Guide to MODDE

Factor Full Factorial Mixed ............................ 257

Add ...................................................32 Full Screen ...................................... 44, 51

Advanced page ..................................69

Definition ..........................................65 G

Max number ......................................67 G-efficiency......................... 108, 112, 203

Mixture and process ........................ 263

Modifying .........................................73 General Options

Name .................................................10 General page ..................................... 59

Qualitative................................. 82, 241 List presentation................................ 57

Scaling ...................................... 70, 235 Restore .............................................. 61

Setting ...............................................67 General page.................................... 59, 66

Spreadsheet .......................................72

Generate D-Optimal button ................. 107

Transformation..................................70

Types ................................................67 Generate new ............................... 107, 186

Use ....................................................68 Generate Report bar ............................ 226

Factorial designs .......................... 257, 260 Generate Report window ..................... 222

Favorites Generators ................................. 37, 38, 99

Add command ...................................46

Add to Favorites................................51 Grab Plot ..................................... 224, 226

Button ...............................................39 Graeco-Latin square ............................ 258

Create a new folder ...........................46

Gridlines ...................................... 207, 212

Restore ..............................................61

Window....................................... 45, 46 H

F-distribution ............................... 149, 150 Hat matrix ........................... 239, 241, 242

Filler ................................................ 67, 68 Header ......................................... 209, 214

Fit Help ............................................. 226, 229

Goodness of ....................................239

Lack of ............................ 140, 149, 150 Help menu ........................................... 229

Model ...................................... 136, 137 Help-button ......................................... 229

Multiple Linear Regression (MLR).231

Hierarchy ............................................. 234

Partial Least Squares (PLS) ............232

Summary .........................................139 High Limit ........................................... 181

Fit methods .............................. 7, 231, 232 Histogram ............................................ 127

Fold over ......................................... 23, 24 Hypercube ........................................... 260

Folder .............................................. 45, 46 Hyperlink ............................................ 224

Footer .......................................... 209, 214 Hyper-triangles .................................... 262

Format I

Axes ................................................207

Bar in report ....................................226 Image................................................... 224

Header/Footer .................................209 Import

Menu in report ................................225 Candidate set............................. 18, 111

Plot area ..........................................210 Design from file ................................ 21

Formulation ............................. 67, 68, 263 Favorites configuration ..................... 50

Scores ....................................... 18, 111

Fractional factorial Worksheet to inclusions .................... 92

Complement ......................................23

Design .............................................257

Free Mark ..............................................41

294

Index

Inclusions M

Added to the worksheet.....................90

Design augmentation ......................271 Main Effect.................................... 58, 157

Editing inclusions..............................92 Manage licenses .................................. 229

Generating.........................................92

Maximum runs .................................... 199

Part of the design ..............................91

vs. complement design ......................90 Menu item ............................................. 10

Increment.............................................207 Mid-range ...................... 70, 235, 236, 240

Insert Image .........................................226 Minimum ..................................... 207, 248

Insert Rows.............................. 32, 92, 176 Mip-file ................................................. 11

Installation ...............................................1 Missing ................................................ 237

Interactions .............................. 34, 99, 158 Mixture

and process factors .................. 247, 263

Interior points ......................................265

Constraint........................................ 264

Interpreting the model .........................152 Contour plot wizard ........................ 166

Investigation Options.............................52 Data................................................. 243

Designs ........................................... 263

Irregular region ....................................272 Experimental region ........................ 264

Factor definition.............................. 263

L Hierarchy ........................................ 243

Labels ..................................................176 Irregular region ............................... 272

Lack of Fit Models ............................................ 243

Alpha level ........................................54 Prediction plot wizard ..................... 173

ANOVA ..........................................238 MLR scaling .................... 70, 77, 235, 236

DF ...................................................134 MLR solution from PLS ...................... 234

Model validity .................................140

Plot ..................................................149 MODDE .................................... 1, 11, 230

Latent structures ..................................232 Model

Distance .......................................... 146

Layers .................... 59, 112, 258, 261, 274 Fit............................................ 136, 137

Layers overlap .....................................112 Hierarchy ........................................ 234

L-designs ................................... 5, 18, 258 Individual ........................................ 134

Interpret .......................................... 152

Legend ......................................... 210, 214 List .................................................. 204

Line style .............................................210 Saturated ......................................... 142

Select .......................................... 38, 95

Linked responses ...................................82

What is ................................................ 5

List presentation ....................................57

Model bar .............................................. 44

Loading plot ................................ 162, 163

Model predictive power....................... 233

Lock

Model validity ..................................... 140

Contour levels .................................213

Investigation......................................29 Multilevel factor .................................... 67

Log Multiple Linear Regression ............. 7, 231

Determinant ............................ 109, 271 Multiplots ...................................... 39, 206

In audit trail.......................................53

Multivariate ................................... 18, 232

LogDet.................................................271

LogdetNorm ................................ 109, 271 N

Low Limit............................................181 Network installation ............................ 229

New ......................................... 11, 17, 226

295

User Guide to MODDE

New worksheet from file .......................21 Customize ......................................... 61

Default .............................................. 52

Next Component General.............................................. 58

Analysis menu......................... 137, 138 List .................................................... 60

Extract .............................................138 Scaling .............................................. 70

MLR solution from PLS .................234

Options button ..................................... 169

No Mark ................................................41

Organization .................................. 12, 133

Non-English ........................................214

Orthogonal

Normal probability ...................... 143, 156 Blocking.................................. 102, 250

Normalized coefficients................. 55, 152 Correlation ...................................... 129

Scaling .............................. 70, 235, 236

Normalized Log Determinant ..............109

Scaling by MODDE ................ 111, 264

Number format ................................ 52, 60 Settings ........................................... 200

Number of decimals ...................... 71, 207 Outliers ........................ 143, 146, 162, 232

N-value ................................................237 Output.............................................. 50, 59

Overlay prediction ....................... 173, 174

Objective ................................... 5, 94, 199

Observed vs Predicted ................... 41, 148 P

Office 2003.............................. 59, 61, 224 Partial Least Squares ....................... 7, 232

Older MODDE versions ........................11 Password protect ................................... 29

Onion Paste Design .......................................... 94

Candidate set ...................................111

Paste unformatted ................................ 224

Design ............................. 258, 261, 274

Generate .................................... 18, 113 PBSS ................................................... 258

Layers max........................................59 Percent......................................... 113, 177

Plots ................................................115

Placeholders ........................ 224, 226, 227

Onion D-Optimal ......................... 112, 113

Plackett Burman .................................. 258

Open All Items ......................................46

Plackett Burman Super-Saturated........ 258

Open investigation .................................21

Plate-Size ...................................... 18, 259

Operators ...............................................81

Plot area....................................... 210, 214

Optimization criteria............................181

Plot bar .................................................. 41

Optimizer

Copy to prediction list .....................188 Plot Labels............................................. 52

Definition ........................................248 Plot Loadings .............................. 163, 242

Generate new ..................................186 Plot options.................................. 166, 213

Generating the start runs .................185

Lists ........................................ 181, 183 Plot Settings

Log ..................................................183 3D scatter ........................................ 216

Play button ......................................186 Axis................................................. 207

Running the Optimizer ....................186 Header and footer............................ 209

Plot area .......................................... 210

Optimizer buttons ................................185

Plots....................................... 16, 205, 228

Optimizer runs .....................................186

PLS plots ............................. 162, 163, 242

PLS Scaling ............................. 71, 77, 235

296

Index

PLS Summary plots ..................... 139, 141 Contour level range ......................... 214

Curvature ................................ 124, 125

Potential terms ............................. 203, 269 Factor ........................................ 67, 181

Prediction Recalculate Scale button ..................... 207

Copy from optimizer .......................188

Derived responses .............................78 Rechtschaffner design ................. 259, 261

Formula ...........................................242 Recommended designs .................. 95, 274

Linked responses ...............................82 RED-MUP ....................... 18, 59, 259, 261

Plot wizard ......................................173

Response prediction plot .................175 Reduced Axial ..................................... 265

Scatter plot ......................................176 Reduced CCC ...................................... 260

Sweet spot plot ................................177

Reduced CFF ....................................... 260

Prediction List .....................................176

Reference mixture ......................... 34, 204

Prediction plot wizard..........................173

Regions................................................ 214

Predictivity ..............................................4

Register ............................................... 229

PRESS/SSY .............................................7

Regression ........................................... 231

Print .......................................................30

Regular presentation ...................... 57, 200

Print format dialog.................................30

Regular responses .................................. 77

Print preview ................................... 30, 39

Remove

Print setup..............................................30 All Placeholders .............................. 225

Print-button............................................30 Button ................................. 32, 34, 214

Encryption ........................................ 29

Process and mixture factors .................263 or add header/footer ........................ 209

Product ID ...........................................229 Placeholder ............................. 225, 226

Program limits ............................... 59, 107 Terms ................................................ 34

Pseudo components ..................... 137, 200 Replicate tolerance ................ 59, 130, 201

Pure error ..................................... 134, 150 Report Generator ........................... 22, 221

Report Generator FAQ window .......... 226

Q Report/template ................................... 226

Q2 ................................................ 140, 239

Reproducibility ............................ 140, 141

Qualitative factors ................... 67, 82, 241

Reset button........................................... 34

Quantitative ............................. 67, 69, 263

Residual Standard Deviation ............... 237

Quantitative multilevel .............. 67, 68, 69

Residual types ..................................... 146

R Residuals ....................... 58, 144, 145, 241

R2 .................................. 57, 139, 142, 239 Residuals plots .................................... 144

Random ................................... 56, 61, 253 Resolution III ................................ 23, 257

Resolution IV designs ......................... 257

297

User Guide to MODDE

Add ........................................... 32, 119 Scale

Box............................................ 39, 206 Contour plot ............................ 213, 214

Definition .................................... 75, 83 Options.............................................. 70

Exclude using modifier .....................77

Manipulations ...................................84 Scale XY ............................................... 41

Name .................................................10 Scaled coefficients............................... 240

Regular..............................................77

Scatter plot

Spreadsheet .......................................83

3D or 2D ......................... 115, 126, 176

Sweet spot .......................................177

Loading ................................... 162, 163

Response box................................. 39, 206 Onion .............................................. 115

Response Surface Modeling ...... 6, 94, 260 Plot settings..................................... 216

Score ............................................... 162

Response value label .............................41

Scheffé ........................................ 137, 236

Restore...................................................61

Scientific ....................................... 52, 207

Revert ....................................................22

Score ............................. 18, 111, 162, 274

Rich Text Format...................................50

Score column plot................................ 162

Robustness ................................... 192, 284

Score vectors ....................................... 162

Role .....................................................181

Screening ....................................... 94, 257

Rotate ............................................ 41, 220

Screening complemented ...................... 23

Rotation ................................. 41, 207, 220

ScreenTips ............................................. 61

RSD ............................................. 237, 239

SD ............................................... 149, 150

RSD*sqrt .............................................150

SD Regression ..................................... 150

RSM Objective ................................ 94, 95

SD-LoF................................................ 149

Run list ................................................183

SD-pe .................................................. 149

Run Optimizer ............................. 185, 186

SD-pe*sqrt........................................... 149

Run order ....................... 52, 124, 131, 144

SDY..................................................... 141

Runs....................................... 97, 186, 268

Select all ................................................ 31

S Select fit method.................................. 137

Safe Region ................................. 190, 191 Send by e-mail....................................... 22

Saturated Models .................................142 Set Run Order ................................ 15, 124

Save Settings

Audit trail ..........................................53 Button ............................................... 38

Button ....................................... 39, 226 Copy factor settings ........................ 188

Inclusions ..........................................90 D-Optimal ....................................... 122

Investigation......................................21 Factor ................................................ 67

Plot or list .................................. 21, 205 Investigation ..................................... 59

Plot settings ............................. 206, 212 Plot .................. 206, 207, 209, 210, 214

Save As.......................................... 21, 205 Restore .............................................. 61

Saving ..................................... 206, 212

Save Format dialog ................................21

Show ............................................... 200

Save List As .................................. 21, 205

Shaded ................................................. 214

Save Plot As .................................. 21, 205

Shortcut menu ..................................... 205

Save Settings ............................... 206, 212

298

Index

All Placeholders ..............................225 Text file ................... 21, 92, 107, 111, 224

Details button ....................................58

Menu .................................................16 Theme.................................................... 59

Placeholder...................... 225, 226, 227 Tile Windows ........................................ 44

ScreenTips on toolbars ......................61

Time .................................................... 207

SimC ....................................................265

Time stamp .......................................... 209

SIMCA-P............................... 18, 111, 274

Title ............................................. 207, 209

SimF ....................................................265

Toolbars

SimM ...................................................265 Command menu in report ............... 222

Simplex ...............................................264 Customize ......................................... 61

Format bar in report ........................ 226

SimSC .................................................265 Generate report bar in report ........... 226

Slack variable ......................................272 Model ................................................ 44

Slide.......................................................61 Plot .................................................... 41

Reset ................................................. 61

Sort ................................................ 32, 155 Spreadsheet ....................................... 41

Special Cubic Model ...........................265 Standard ............................................ 39

Status ................................................ 44

Split objective .................................. 94, 99

Window ............................................ 44

Spreadsheet................................ 41, 72, 83

Tools menu .......................................... 225

Square terms ..........................................95

Traditional designs ................................ 18

SS ........................................ 139, 140, 238

Transformations .............. 70, 77, 147, 264

SS explained ........................................232

Treat folder as item ............................... 46

Standard bar...........................................39

Txt ........................... 21, 92, 107, 111, 224

Standardized residuals ................. 146, 241

Star Distance .........................................99

U

Start runs .............................................185 Uncentered .......................................... 236

Summary plot .............................. 139, 141 Unit Variance .......................... 70, 71, 235

Sweet Spot Plot ........................... 177, 189 Unit variance scaling ..................... 70, 235

Constraint-button .............................. 88

System default .......................................61 Placeholder button .......................... 227

Placeholders .................... 225, 226, 227

T Predictions ...................................... 176

Tagushi ....................................................5 Report ....................................... 22, 225

Target in Optimizer ..................... 181, 248 URL..................................................... 224

T-button ................................. 41, 167, 169 Use True Type ..................................... 214

299

User Guide to MODDE

Add experiment ................................ 32

V Copy ................................................. 31

Variable importance ............................161 Description...................................... 131

Design matrix.................................. 200

View menu .................................... 14, 224 Menu ............................................... 123

View/Hide Toolbars ..............................14 Missing data .................................... 237

Open ................................... 39, 41, 123

W Sort ................................................... 32

WC plots...................................... 163, 242

X

Weight ......................................... 163, 181

X Mark .................................................. 41

Window

X'X

Bar ....................................................44

Condition number ........................... 236

Dockable ...........................................44

Eigenvalues ............................. 134, 236

Menu .................................................16

Matrix ..................... 258, 260, 268, 271

Toolbar..............................................44

Wizard Y

Analysis Wizard ..............................135

Y Mark .................................................. 41

Contour plot wizard ........................166

Design wizard ...................................64 Y-miss ................................................. 237

Prediction plot wizard .....................173

Z

Workset ....................................... 111, 274

Zoom ............................................. 41, 220

300

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