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Georgiana Onicescu, ScM

Cancer Prevention and Control Statistics Tutorial

July 9, 2009

paddler cancer survivors

blend of factors that could potentially enhance the quality of the lives of

cancer survivor participants.

Evaluating the efficacy of dragon boating to improve the overall quality of life

among cancer survivors has the potential to advance our understanding of

factors that influence quality-of-life among cancer survivors.

We hypothesize that physical activity conducted within the context of the

social support of a dragon boat team contributes significantly to improved

overall quality of life above and beyond a standard physical activity program

because the collective experience of dragon boating is likely enhanced by

team sport factors such as cohesion, teamwork, and the goal of competition.

Methods: 134 cancer survivors self-selected to an 8-week dragon boat

paddling intervention group or to an organized walking program. Each study

arm was comprised of a series of 3 groups of approximately 20-25

participants, with pre- and post-testing to compare quality of life and

physical performance outcomes between study arms.

We have a concept of what cohesion is, but we

cant measure it directly.

Merriam-Webster:

the act or state of sticking together tightly

the quality or state of being made one

We cannot simply say how cohesive is your

team? or on a scale from 1-10, how do you

rate your team cohesion?

We think it combines several elements of unity

and team spirit and perhaps other factors

Factor Analysis

Data reduction tool

Removes redundancy or duplication from a set of

correlated variables

Represents correlated variables with a smaller set of

derived variables.

Factors are formed that are relatively independent of one

another.

Two types of variables:

latent variables: factors

observed variables

Cohesion Variables:

G1 (I do not enjoy being a part of the social environment of this exercise group)

G2 (I am not going to miss the members of this exercise group when the program

ends)

G3 (I am unhappy with my exercise groups level of desire to exceed)

G4 (This exercise program does not give me enough opportunities to improve my

personal performance)

G5 (For me, this exercise group has become one of the most important social

groups to which I belong)

G6 (Our exercise group is united in trying to reach its goals for performance)

G7 (We all take responsibility for the performance by our exercise group)

G8 (I would like to continue interacting with some of the members of this exercise

group after the program ends)

G9 (If members of our exercise group have problems in practice, everyone wants

to help them)

G10 (Members of our exercise group do not freely discuss each athletes

responsibilities during practice)

G11 (I feel like I work harder during practice than other members of this exercise

group)

Other examples

Diet

Air pollution

Personality

Customer satisfaction

Depression

Quality of Life

1. Identification of Underlying Factors:

clusters variables into homogeneous sets

creates new variables (i.e. factors)

allows us to gain insight to categories

2. Screening of Variables:

identifies groupings to allow us to select one variable to

represent many

useful in regression (recall collinearity)

3. Summary:

Allows us to describe many variables using a few factors

4. Clustering of objects:

Helps us to put objects (people) into categories depending on

their factor scores

[technique] is factor analysis. Few statisticians are neutral about

this technique. Proponents feel that factor analysis is the

greatest invention since the double bed, while its detractors feel

it is a useless procedure that can be used to support nearly any

desired interpretation of the data. The truth, as is usually the case,

lies somewhere in between. Used properly, factor analysis can

yield much useful information; when applied blindly, without

regard for its limitations, it is about as useful and informative as

Tarot cards. In particular, factor analysis can be used to explore

the data for patterns, confirm our hypotheses, or reduce the

Many variables to a more manageable number.

-- Norman Streiner, PDQ Statistics

One of the primary goals of factor analysis is

often to identify a measurement model for a

latent variable

This includes

identifying the items to include in the model

identifying how many factors there are in the latent

variable

identifying which items are associated with which

factors

Standard Result

-----------------------------------Variable | Factor1

Factor2 |

-------------+--------------------+

notenjoy | -0.3118

0.5870 |

notmiss | -0.3498

0.6155 |

desireexceed | -0.1919

0.8381 |

personalpe~m | -0.2269

0.7345 |

importants~l |

0.5682

-0.1748 |

groupunited |

0.8184

-0.1212 |

responsibi~y |

0.9233

-0.1968 |

interact |

0.6238

-0.2227 |

problemshelp |

0.8817

-0.2060 |

notdiscuss | -0.0308

0.4165 |

workharder | -0.1872

0.5647 |

-----------------------------------

How to interpret?

between item and factor

High loadings: define a factor

Low loadings: item does not load on

factor

Easy to skim the loadings

This example:

G7, G8 G9

factor 2 is defined by G1, G2,

G3, G4, G10, G11

we need to name factors

important to check their face validity.

These factors can now be calculated

using this model

Each person is assigned a factor score for

each factor

Range between -1 to 1

-----------------------------------Variable | Factor1

Factor2 |

-------------+--------------------+

notenjoy | -0.3118

0.5870 |

notmiss | -0.3498

0.6155 |

desireexceed | -0.1919

0.8381 |

personalpe~m | -0.2269

0.7345 |

importants~l |

0.5682

-0.1748 |

groupunited |

0.8184

-0.1212 |

responsibi~y |

0.9233

-0.1968 |

interact |

0.6238

-0.2227 |

problemshelp |

0.8817

-0.2060 |

notdiscuss | -0.0308

0.4165 |

workharder | -0.1872

0.5647 |

-----------------------------------

in yellow.

How to interpret?

Authors may conclude

something like:

We were able to derive two

factors from the 11 items. The

first factor is defined as

teamwork. The second factor

is defined as personal

competitive nature . These

two factors describe 72% of the

variance among the items.

-----------------------------------Variable | Factor1

Factor2 |

-------------+--------------------+

notenjoy | -0.3118

0.5870 |

notmiss | -0.3498

0.6155 |

desireexceed | -0.1919

0.8381 |

personalpe~m | -0.2269

0.7345 |

importants~l |

0.5682

-0.1748 |

groupunited |

0.8184

-0.1212 |

responsibi~y |

0.9233

-0.1968 |

interact |

0.6238

-0.2227 |

problemshelp |

0.8817

-0.2060 |

notdiscuss | -0.0308

0.4165 |

workharder | -0.1872

0.5647 |

-----------------------------------

in yellow.

Based on the basic Classical Test Theory Idea:

For a case with just one factor:

Ideal:

X1 = F + e1

X2 = F + e2

var(ej) = var(ek) , j k

Xm = F + em

Reality:

X1 = 1F + e1

X2 = 2F + e2

var(ej) var(ek) , j k

Xm = mF + em

(unequal sensitivity to change in factor)

(Related to Item Response Theory (IRT))

Multi-Factor Models

Two factor orthogonal model

ORTHOGONAL = INDEPENDENT

Example: cohesion has two domains

X1 = 11F1 + 12F2 + e1

X2 = 21F1 + 22F2 + e2

.

X1 = 11F1 + 12F2 ++ 1mFm + e1

X2 = 21F1 + 22F2 ++ 2mFm + e2

.

11

21

31

41

51

61

71

81

91

101

111

12 0.31

22 0.35

32 0.19

42 0.23

52 0.57

62 0.82

72 0.92

82 0.62

92 0.88

102 0.03

112 0.19

0.59

0.62

0.84

0.73

0.17

0.12

0.20

0.22

0.21

0.42

0.56

Multiple steps

Stepwise optimal

many choices to be made!

a choice at one step may impact the remaining

decisions

considerable subjectivity

Strong theoretical model is critical

(1) Collect and explore data: choose relevant variables.

(2) Determine the number of factors

(3) Estimate the model using predefined number of factors

(4) Rotate and interpret

(5) (a) Decide if changes need to be made (e.g. drop

item(s), include item(s))

(b) repeat (3)-(4)

(6) Construct scales and use in further analysis

Data Exploration

Histograms

normality

discreteness

outliers

very high or low correlations?

Same scale

high = good, low = bad?

NotDiscussPOST

70

WorkHarderPOST

ProblemsHelpPOST

0 30

GroupUnitedPOST

Frequency

Frequency

Frequency

20 40

InteractPOST

30 60

ResponsibilityPOST

DesireExceedPOST

Frequency

Frequency

30 60

ImportantSocialPOST

Frequency

1

PersonalPerformPOST

0 20

Frequency

40 80

NotMissPOST

Frequency

NotEnjoyPOST

0 40

Frequency

1

30

30 60

0 30

Frequency

100

0 40

Frequency

Data exploration

Correlation Matrix

. pwcorr notenjoy-workharder

| notenjoy notmiss desire~d person~m import~l groupu~d respon~y

-------------+--------------------------------------------------------------notenjoy |

1.0000

notmiss |

0.3705

1.0000

desireexceed |

0.2609

0.3987

1.0000

personalpe~m |

0.2552

0.3472

0.5946

1.0000

importants~l | -0.2514 -0.3357 -0.1384 -0.3123

1.0000

groupunited | -0.1732 -0.2460 -0.2384 -0.1359

0.4364

1.0000

responsibi~y | -0.2554 -0.3663 -0.2908 -0.2507

0.4399

0.8016

1.0000

interact | -0.1847 -0.2966 -0.2162 -0.2294

0.4415

0.4251

0.5174

problemshelp | -0.2561 -0.2865 -0.2567 -0.1940

0.4159

0.6498

0.7748

notdiscuss |

0.1610

0.0763

0.2253

0.2193 -0.0242

0.0027 -0.0598

workharder |

0.3482

0.1606

0.3794

0.3848 -0.0010 -0.2765 -0.3083

| interact proble~p notdis~s workha~r

-------------+-----------------------------------interact |

1.0000

problemshelp |

0.5446

1.0000

notdiscuss | -0.0346 -0.0699

1.0000

workharder | -0.1063 -0.2358

0.2660

1.0000

5

3

1

5

3

5

3

1

5

3

1

5

3

1

1

5

3

3

1

5

3

5

5

3

3

1

5

3

1

1

5

3

1

5

3

1

1

5

3

1

Valid correlations?

Data Matrix

Factor analysis is totally dependent on correlations

between variables.

Factor analysis summarizes correlation structure

v1...vk

v1...vk

O1

.

.

.

.

.

.

.

.

On

Data Matrix

F1..Fj

v1

.

.

.

vk

v1

.

.

.

vk

Correlation

Matrix

Factor

Matrix

Important implications

Correlation matrix must be valid measure of

association

Likert scale? i.e. on a scale of 1 to K?

Consider previous set of plots

Is Pearson (linear) correlation a reasonable

measure of association?

Odds ratios? Nope. on the wrong scale.

Need measures on scale of -1 to 1, with zero meaning

no association

Solutions:

tetrachoric correlation: for binary items

polychoric correlation: for ordinal items

-choric corelations

assume that variables are truncated versions of continuous

variables

only appropriate if continuous underlying assumption makes

sense

analysis!

Polychoric correlation matrix

notenjoy

notmiss

desireexceed

personalperform

importantsocial

groupunited

responsibility

interact

problemshelp

notdiscuss

workharder

notenjoy

1

.64411349

.44814752

.37687346

-.33466689

-.26640575

-.38218019

-.31300025

-.40864072

.28367782

.49864257

notmiss

desireexceed

1

.60971951

.49572253

-.35262233

-.25987331

-.43174724

-.41147172

-.44688816

.2071563

.26866894

1

.74640077

-.18773414

-.32414348

-.34289848

-.28711931

-.34338549

.33714715

.50117974

importantsocial

groupunited

personalperform

importantsocial

groupunited

responsibility

interact

problemshelp

notdiscuss

workharder

personalperform

1

-.42902852

-.22011768

-.32272048

-.37003374

-.31435615

.28191066

.4766736

1

.47698468

.49187407

.51150655

.51458893

-.07289447

.02547056

1

.85603168

.46469124

.75552992

-.0934676

-.35603256

interact

problemshelp

responsibility

interact

problemshelp

notdiscuss

workharder

responsibility

1

.59252523

.84727982

-.11548039

-.37311526

1

.60910395

-.09653691

-.13316066

1

-.11580359

-.30122735

. findit polychoric

. polychoric notenjoy-workharder

. matrix R = r(R)

Intuitively: The number of uncorrelated constructs that

are jointly measured by the Xs.

Only useful if number of factors is less than number of

Xs (recall data reduction).

Use principal components to help decide

type of factor analysis

number of factors is equivalent to number of variables

each factor is a weighted combination of the input variables:

F1 = a11X1 + a12X2 + .

Recall: For a factor analysis, generally,

X1 = a11F1 + a12F2 +...

Eigenvalues

To select how many factors to use, consider

eigenvalues from a principal components analysis

Two interpretations:

eigenvalue equivalent number of variables which the factor

represents

eigenvalue amount of variance in the data described by the

factor.

Rules to go by:

scree plot

% variance explained

comprehensibility

items

Cohesion Example

. factormat R, pcf n(134)

(obs=134)

Factor analysis/correlation

Method: principal-component factors

Rotation: (unrotated)

Number of obs

=

Retained factors =

Number of params =

134

3

30

-------------------------------------------------------------------------Factor |

Eigenvalue

Difference

Proportion

Cumulative

-------------+-----------------------------------------------------------Factor1 |

4.96356

3.14606

0.4512

0.4512

Factor2 |

1.81751

0.76378

0.1652

0.6165

Factor3 |

1.05373

0.27749

0.0958

0.7123

Factor4 |

0.77624

0.02065

0.0706

0.7828

Factor5 |

0.75559

0.22587

0.0687

0.8515

Factor6 |

0.52972

0.05654

0.0482

0.8997

Factor7 |

0.47318

0.24670

0.0430

0.9427

Factor8 |

0.22647

0.02484

0.0206

0.9633

Factor9 |

0.20163

0.07341

0.0183

0.9816

Factor10 |

0.12822

0.05407

0.0117

0.9933

Factor11 |

0.07415

.

0.0067

1.0000

--------------------------------------------------------------------------

5

Eigenvalues

2

3

. screeplot

5

Number

10

. factormat R, n(134) ipf factor(2)

(obs=134)

Factor analysis/correlation

Method: iterated principal factors

Rotation: (unrotated)

Number of obs

=

Retained factors =

Number of params =

.........

Factor loadings (pattern matrix) and unique variances

------------------------------------------------Variable | Factor1

Factor2 |

Uniqueness

-------------+--------------------+-------------notenjoy | -0.6091

0.2661 |

0.5582

notmiss | -0.6566

0.2648 |

0.4988

desireexceed | -0.6712

0.5373 |

0.2608

personalpe~m | -0.6342

0.4344 |

0.4091

importants~l |

0.5538

0.2162 |

0.6466

groupunited |

0.7164

0.4137 |

0.3156

responsibi~y |

0.8456

0.4197 |

0.1088

interact |

0.6271

0.2132 |

0.5613

problemshelp |

0.8187

0.3866 |

0.1802

notdiscuss | -0.2830

0.3072 |

0.8256

workharder | -0.4977

0.3260 |

0.6461

-------------------------------------------------

134

2

21

Interpretability?

Not interpretable at this stage

In an unrotated solution, the first factor describes most of

variability.

Ideally we want to

spread variability more evenly among factors.

make factors interpretable

redefine factors such that loadings on various factors tend to be

very high (-1 or 1) or very low (0)

intuitively, it makes sharper distinctions in the meanings of the

factors

We use factor analysis for rotation NOT principal

components!

F2

F2

2

2

1

F1

4

F1

x1

x2

x3

x4

Factor 1

Factor 2

0.5

0.8

-0.7

-0.5

0.5

0.8

0.7

-0.5

x1

x2

x3

x4

Factor 1

Factor 2

0

0

-0.9

0

0.6

0.9

0

-0.9

. rotate

Factor analysis/correlation

Method: iterated principal factors

Rotation: orthogonal varimax (Kaiser off)

Rotated Solution

Number of obs

=

Retained factors =

Number of params =

134

2

21

-------------------------------------------------------------------------Factor |

Variance

Difference

Proportion

Cumulative

-------------+-----------------------------------------------------------Factor1 |

3.35544

0.72180

0.5603

0.5603

Factor2 |

2.63364

.

0.4397

1.0000

-------------------------------------------------------------------------LR test: independent vs. saturated: chi2(55) = 959.26 Prob>chi2 = 0.0000

Rotated factor loadings (pattern matrix) and unique variances

------------------------------------------------Variable | Factor1

Factor2 |

Uniqueness

-------------+--------------------+-------------notenjoy | -0.3118

0.5870 |

0.5582

notmiss | -0.3498

0.6155 |

0.4988

desireexceed | -0.1919

0.8381 |

0.2608

personalpe~m | -0.2269

0.7345 |

0.4091

importants~l |

0.5682

-0.1748 |

0.6466

groupunited |

0.8184

-0.1212 |

0.3156

responsibi~y |

0.9233

-0.1968 |

0.1088

interact |

0.6238

-0.2227 |

0.5613

problemshelp |

0.8817

-0.2060 |

0.1802

notdiscuss | -0.0308

0.4165 |

0.8256

workharder | -0.1872

0.5647 |

0.6461

-------------------------------------------------

Rotation options

Orthogonal

more commonly seen

usually at least one option

Stata: varimax, quartimax, equamax, parsimax, etc.

Oblique

allows dependence of factors

make distinctions sharper (loadings closer to 0s and

1s

can be harder to interpret once you lose

independence of factors

Uniqueness

Should all items be retained?

Uniquess for each item describes the proportion of the

item described by the factor model

Recall an R-squared:

proportion of variance in Y explained by X

1-Uniqueness:

proportion of the variance in Xk explained by F1, F2, etc.

Uniqueness:

represents what is left over that is not explained by factors

error that remainese

Rotated factor loadings (pattern matrix) and unique variances

------------------------------------------------Variable | Factor1

Factor2 |

Uniqueness

-------------+--------------------+-------------notenjoy | -0.3118

0.5870 |

0.5582

notmiss | -0.3498

0.6155 |

0.4988

desireexceed | -0.1919

0.8381 |

0.2608

personalpe~m | -0.2269

0.7345 |

0.4091

importants~l |

0.5682

-0.1748 |

0.6466

groupunited |

0.8184

-0.1212 |

0.3156

responsibi~y |

0.9233

-0.1968 |

0.1088

interact |

0.6238

-0.2227 |

0.5613

problemshelp |

0.8817

-0.2060 |

0.1802

notdiscuss | -0.0308

0.4165 |

0.8256

workharder | -0.1872

0.5647 |

0.6461

-------------------------------------------------

Rotated factor loadings (pattern matrix) and unique variances

------------------------------------------------Variable | Factor1

Factor2 |

Uniqueness

-------------+--------------------+-------------notenjoy | -0.3093

0.5811 |

0.5667

notmiss | -0.3345

0.6455 |

0.4715

desireexceed | -0.1783

0.8483 |

0.2486

personalpe~m | -0.2119

0.7551 |

0.3849

importants~l |

0.5618

-0.2057 |

0.6420

groupunited |

0.8265

-0.1271 |

0.3008

responsibi~y |

0.9247

-0.2089 |

0.1012

interact |

0.6160

-0.2469 |

0.5596

problemshelp |

0.8784

-0.2224 |

0.1789

workharder | -0.2023

0.5271 |

0.6813

-------------------------------------------------

Principal Factor Method

Iterated Principal Factor / Least Squares

Maximum Likelihood (ML)

Unfortunately, default is often not the best approach!

Caution! ipf and ml may not converge to the right

answer! Look for uniqueness of 0 or 1. Problem of

identifiability or getting stuck.

Interpretation

Naming of Factors

Wrong Interpretation: Factors represent separate

groups of people.

Right Interpretation: Each factor represents a continuum

along which people vary (and dimensions are orthogonal

if orthogonal)

Each object (e.g. each cancer survivor) gets a factor score for

each factor.

Old data vs. New data

The factors themselves are variables

An individuals score is weighted combination of scores on input

variables

These weights are NOT the factor loadings!

Loadings and weights determined simultaneously so that there is

no correlation between resulting factors.

Factor Scoring

. predict f1 f2

(regression scoring assumed)

Scoring coefficients

(method = regression; based on varimax rotated factors)

---------------------------------Variable | Factor1

Factor2

-------------+-------------------notenjoy | -0.03322

0.19223

notmiss | 0.04725

0.13279

desireexceed | 0.15817

0.54996

personalpe~m | -0.04037

0.21452

importants~l | 0.02971 -0.02168

groupunited | 0.12273

0.12938

responsibi~y | 0.60379

0.07719

interact | 0.04594 -0.00870

problemshelp | 0.31516

0.06376

workharder | 0.11750

0.10810

----------------------------------

Factors are generally

scaled to have

variance 1.

Mean is arbitrary.

* If based on Pearson correlation

mean will be zero.

3

4

5

3

4

Scores for factor 2

2

5

4

3

2

Graphs by progrm

Dragon Boat

Walking

2

Dragon Boat

Walking

4

3

2

1

Graphs by progrm

Labels of factors can be arbitrary or lack scientific basis

Derived factors often very obvious

defense: but we get a quantification

Garbage in, garbage out

really a criticism of input variables

factor analysis reorganizes input matrix

Too many steps that could affect results

Too complicated

Correlation matrix is often poor measure of association of input

variables.

Our example?

Preliminary analysis of pilot data!

Concern: negative items hang together, positive items

hang together:

Is separation into two factors:

based on two different factors (teamwork, pers. comp. nature)

based on negative versus positive items?

Validity?

boxplots of factor 1 suggest something

additional reliability and validity needs to be considered

Stata Code

pwcorr notenjoy-workharder

polychoric notenjoy-workharder

matrix R = r(R)

factormat R, pcf n(134)

screeplot

factormat R, n(134) ipf factor(2)

rotate

matrix R = r(R)

factormat R, n(134) ipf factor(2)

rotate

predict f1 f2

scatter f1 f2

graph box f1, by(progrm)

graph box f2, by(progrm)

factor notenjoy-workharder, pcf

screeplot

factor notenjoy-workharder, ipf factor(2)

rotate

factor notenjoy notmiss desire personal

important group respon interact problem

workharder, ipf factor(2)

rotate

predict f1 f2

scatter f1 f2

graph box f1, by(progrm)

graph box f2, by(progrm)

Stata Options

Pearson correlation

Use factor for principal components and factor analysis

choose estimation approach: ipf, pcf, ml, pf

choose to retain n factors: factor(n)

Polychoric correlation

Use factormat for principal components and factor analysis

choose estimation approach: ipf, pcf, ml, pf

choose to retain n factors: factor(n)

include n(xxx) to describe the sample size

Rotate: choose rotation type: varimax (default), promax, etc.

Create factor variables

predict: list as many new variable names as there are retained

factors.

Example: for 3 retained factors,

factor teamwork competition hardworks

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