II. PREPARING THE INPUT FILES 7
II.2. Computation Order: order.dat 7
II.3. Marker/Trait Descriptions: header.dat 8
II.4. Phenotype Data: phen.dat, ascer.dat 8
II.5. Population Information: popln.dat 10
III. USING THE PROGRAMS 11
III.1. Data Preparation Program: preped 12
III.2. Descriptive Statistics Program: descstat 13
III.3. Analysis Preparation Program: prepap 13
III.4. Simulation Program: simul 14
III.5. Analysis Program: papdr 15
III.6. Estimation Program: gpe 16
IV. DEFINING THE MODEL 17
IV.1. Execution Options 17
IV.2. Transmission Parameters 20
IV.3. Recombination Parameters 22
IV.4. Frequency Parameters 22
IV.5. Discrete Trait Parameters 24
IV.6. Quantitative Trait Parameters 27
IV.7. Within-Genotype Parameters 29
IV.8. Multivariate Parameters 30
IV.9. Genotype-Assignment Codes 30
V. PERFORMING THE ANALYSIS 34
V.1. Preparing for the Analysis 34
V.2. Checking for Errors 35
V.3. Maximizing the Likelihoods 36
V.4. Interpreting the Results 37
VI. UNDERSTANDING THE PACKAGE 38
VI.1. Computation Order 38
VI.2. Genotype Order 38
VI.3. Genotype Combining 39
VI.4. Ascertainment Correction 40
VI.5. Use of Logarithms 41
VI.6. Likelihood Calculation 42
VI.7. Genotypic Probabilities 43
VI.8. Penetrance Probabilities 43
VI.9. Genotype Simulation 44
VI.10. Conditioning Process 45
VI.11. Reverse Conditioning 46
VII. WRITING CUSTOM SUBROUTINES 48
VII.1. Frequency: papfq 48
VII.2. Transmission: paptc 48
VII.3. Major Locus Discrete: dmlpr 49
VII.4. Major Locus Quantitative: qmlpr 49
VII.5. Within Genotype: papwg 50
VIII. ACKNOWLEDGMENTS 51
IX. REFERENCES 52
A. FILE LISTS 55
A.1. Command Files 55
A.2. Include Files 55
A.3. Source Files 56
A.4. Input Files 58
A.5. Test Data Files 58
A.6. Parameter Files 59
A.7. Output Files 60
B. FILE FORMATS 61
B.1. Pedigree Structure: trip.dat 61
B.2. Computation Order: order.dat 61
B.3. Trait/Marker Descriptions: header.dat 61
B.4. Phenotype Data: phen.dat and ascer.dat 63
B.5. Population Information: popln.dat 63
B.6. Pedigree and Phenotype Data: papin.dat 64
B.7. Model and Parameter Information: model.dat 65
B.8. Frequency Subroutine List: freq.dat 69
B.9. Transmission Subroutine List: tran.dat 70
B.10. Major Locus Discrete Subroutine List: dmlp.dat 71
B.11. Major Locus Quantitative Subroutine List: qmlp.dat 72
B.12. Within Genotype Subroutine List: wgen.dat 74
C. SUBROUTINE LIBRARIES 76
C.1. Frequency: papfq 76
C.2. Transmission: paptc 77
C.3. Major Locus Discrete: dmlpr 79
C.4. Major Locus Quantitative: qmlpr 80
C.5. Within Genotype: papwg 81
D. TEST EXAMPLES 82
D.1. Execution Options 84
D.2. Transmission Parameters 86
D.3. Recombination Parameters 87
D.4. Frequency Parameters 89
D.5. Discrete Trait Parameters 91
D.6. Quantitative Trait Parameters 93
D.7. Within-Genotype Parameters 94
D.8. Multivariate Parameters 96
D.9. Genotype-Assignment Codes 97
E. ERROR MESSAGES104
E.1. Errors in the Files: filerr104
E.2. Errors in the Data Files: daterr105
E.3. Errors in the Genetic Model: moderr107
E.4. Execution Errors: paperr110
F. CHANGES FROM REVISION 3112
F.1. Files112
F.2. Programs112
F.3. Genetic Models113
F.4. Algorithms113