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United States

Department of

Agriculture

Agricultural

Research

Service

August 1993 Rev: April 1995

A Manual for Use of MTDFREML

A Set of Programs to Obtain Estimates of Variances and Covariances

Draft

Boldman, K. G., L. A. Kriese, L. D. Van Vleck, C. P. Van Tassell and S. D. Kachman. 1995. A Manual for Use of MTDFREML. A Set of Programs To Obtain Estimates of Variances and Covariances [DRAFT]. U.S. Department of Agriculture, Agricultural Research Service.

The manual in eight chapters describes how to compile and run the FORTRAN programs for multiple-trait-restricted-maximum-likelihood estimation of genetic variances and covariances for animal models. Chapters also describe various models that can be analyzed, suggestions for computing strategies, the theory behind the method, the algorithms used so that modifications can be made, and technical descriptions of the search algorithm and its properties. The purpose is to provide not only step-by-step instructions but also background for successful use of the programs.

Note: This manual is a draft version of the technical documentation that will accompany the MTDFREML. It is being released with the software on an interim basis until the official documentation has been prepared as a publication of the U.S. Department of Agriculture's Agricultural Research Service.

Boldman, Kriese, Van Vleck, and Van Tassell are with the Roman L. Hruska U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture (A218 Animal Sciences, University of Nebraska, Lincoln, NE 68583-0908). Kachman is with the Institute of Agriculture and Natural Resources, University of Nebraska, Lincoln, (Department of Biometry, University of Nebraska, Lincoln, NE 68583-0712).

Microsoft and Microsoft FORTRAN are registered trademarks and Windows is a trademark of Microsoft Corporation. Microway is a registered trademark and NDP FORTRAN is a trademark of Microway, Inc. SPARSPAK is copyrighted 1984, University of Waterloo, Waterloo, Ontario, Canada. CMS and MVS/TSO are trademarks of International Business Machines Corporation.

Mention of trade names or commercial products in this report is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

Revised April 1995

All programs and services of the U.S. Department of Agriculture are offered on a nondiscriminatory basis without regard to race, color, national origin, religion, sex, age, marital status, or handicap.

Introduction

Contents

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. Program Installation

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iv

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Introduction and Flow Charts

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v

Compile Summary

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vii

CHAPTER ONE: User Notes for MTDFREML

. Computing Considerations

Introduction

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1

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. Using an INCLUDE statement

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Microsoft FORTRAN 5.1

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3

MTDFREML Programs

. MTDFNRM: Set Up A -1 MTDFPREP: Set Up MME

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MTDFRUN: Solve MME for (Co)Variance Components and Solutions

 

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MTDFNRM: Computing Inverse of Numerator Relationship Matrix

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Running MTDFNRM

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MTDFPREP: Preparation for forming mixed model equations

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Running MTDFPREP

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MTDFRUN: Estimating Variance Components and Solving MME

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Initial run or cold start of MTDFRUN

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Running MTDFRUN

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15

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. Continuation of previous run

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20

. Starting or Restarting MTDFRUN

Convergence???

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CHAPTER TWO: Illustrations for MTDFREML

MTDFNRM

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23

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. Variance Component Estimation

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25

Single Trait Model

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25

MTDFPREP

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MTDFRUN

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28

Multiple Trait Model

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MTDFPREP

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32

MTDFRUN

Contrasts, Sampling Variances and Expectations of Solutions

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MTDFRUN

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i

CHAPTER THREE: Alternative Models and Shared Experiences with MTDFREML

45

Sex-Limited Traits and Genetic-Environmental Interactions

Sire Models

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45

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Sire model

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46

Sire and maternal grandsire model

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Sire and dam model

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Local vs Global Maximization

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49

Standardization of Data

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50

Sparseness

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. Number of Traits

Contrasts

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Insufficient

Memory

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52

CHAPTER FOUR: Theoretical Considerations for MTDFREML

Mixed Models

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53

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. Henderson's Mixed Model Equations

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MME for Variance Component Estimation

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Derivative-Free REML

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