!Genetic Simplex Model !Analysis of platelet count !Platelet count rescaled by dividing count by 100 to aid optimisation The following MX script lines were read for group 1 #DEFINE NVAR 3 #DEFINE NSIB 2 ! NUMBER OF SIBLINGS #NGROUPS 3 Note: #NGroup set number of groups to 3 TITLE GENETIC STRUCTURE - SIMPLEX CALCULATION BEGIN MATRICES X DIAG NVAR NVAR FREE !GENETIC INNOVATIONS Y DIAG NVAR NVAR FREE !COMMON ENVIRONMENTAL INNOVATIONS Z DIAG NVAR NVAR FREE !SPECIFIC ENVIRONMENTAL INNOVATIONS N LOWER NVAR NVAR FREE !GENETIC TRANSMISSION PATHS O LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL TRANSMISSION PATHS P LOWER NVAR NVAR FREE !SPECIFIC ENVIRONMENTAL PATHS R DIAG NVAR NVAR FREE !MEASUREMENT ERROR I IDEN NVAR NVAR M FULL NSIB NVAR FREE H FULL 1 1 !.5 END MATRICES; MATRIX H .5 SPECIFY N 0 13 0 0 14 0 SPECIFY O 0 17 0 0 18 0 SPECIFY P 0 19 0 0 20 0 SPECIFY M 40 41 42 40 41 42 BEGIN ALGEBRA; A = (I-N)~ & (X*X') ; C = (I-O)~ & (Y*Y') ; E = (I-P)~ & (Z*Z') + R*R' ; END ALGEBRA; EQUATE R 1 1 1 R 1 2 2 R 1 3 3 !EQUATE MEASUREMENT ERROR VARIANCES FOR IDENTIFICATION END GROUP; The following MX script lines were read for group 2 G2: MONOZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE=MARKER1.DAT NOTE: Rectangular file contained 519 records with data LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY <3 ; NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 ; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 277 data vectors for analysis NOTE: Vectors contain a total of 953 observations MEANS M; COVARIANCES A+C+E | A+C_ A+C | A+C+E; END GROUP; The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE=MARKER1.DAT NOTE: Rectangular file contained 519 records with data LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY >2 ; NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 ; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 230 data vectors for analysis NOTE: Vectors contain a total of 1038 observations MEANS M; COVARIANCES A+C+E | H@A+C _ H@A+C | A+C+E; START 0.3 ALL START 2.8 M 2 1 1 M 2 1 2 M 2 1 3 OPTION ITERATIONS=8000 OPTION NDECIMALS=4 END Summary of VL file data for group 2 PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 Code 1.0000 2.0000 3.0000 4.0000 5.0000 6.0000 Number 165.0000 145.0000 171.0000 163.0000 140.0000 169.0000 Mean 2.8489 2.6961 2.5406 2.8618 2.7114 2.5685 Variance 0.2925 0.3559 0.2723 0.3018 0.3070 0.2676 Minimum 1.8000 1.1500 1.2400 1.8000 1.2200 1.5600 Maximum 4.4800 4.3600 4.0500 4.5800 4.2800 4.0700 Summary of VL file data for group 3 PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 Code 1.0000 2.0000 3.0000 4.0000 5.0000 6.0000 Number 193.0000 205.0000 123.0000 190.0000 205.0000 122.0000 Mean 2.8663 2.6707 2.4774 2.7959 2.6339 2.4906 Variance 0.2937 0.2967 0.2315 0.3055 0.3573 0.3141 Minimum 1.5800 1.3100 1.5200 1.4800 1.3800 1.4000 Maximum 4.4100 4.3500 4.2100 4.5900 4.7800 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 Title Genetic structure - Simplex MATRIX A This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 40 41 42 2 40 41 42 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 13 0 3 0 14 0 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 19 0 3 0 20 0 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 28 2 0 28 3 0 0 28 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 1 2 0 2 3 0 0 3 MATRIX Y This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 7 2 0 8 3 0 0 9 GROUP NUMBER: 2 G2: Monozygotic twins MATRIX A This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 40 41 42 2 40 41 42 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 13 0 3 0 14 0 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 19 0 3 0 20 0 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 28 2 0 28 3 0 0 28 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 1 2 0 2 3 0 0 3 MATRIX Y This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 7 2 0 8 3 0 0 9 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 40 41 42 2 40 41 42 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 13 0 3 0 14 0 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 19 0 3 0 20 0 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 28 2 0 28 3 0 0 28 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 1 2 0 2 3 0 0 3 MATRIX Y This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 7 2 0 8 3 0 0 9 MX PARAMETER ESTIMATES GROUP NUMBER: 1 Title Genetic structure - Simplex MATRIX A This is a computed FULL matrix of order 3 by 3 [=(I-N)~&(X*X')] 1 2 3 1 0.2646 0.2322 0.1977 2 0.2322 0.2418 0.2058 3 0.1977 0.2058 0.2114 MATRIX C This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(Y*Y')] 1 2 3 1 0.0000 0.0000 0.0000 2 0.0000 0.0174 -0.0061 3 0.0000 -0.0061 0.0021 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.0450 0.0092 0.0028 2 0.0092 0.0662 0.0076 3 0.0028 0.0076 0.0584 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.8792 2.6895 2.5073 2 2.8792 2.6895 2.5073 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 0.8776 0.0000 3 0.0000 0.8513 0.0000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 0.7301 0.0000 3 0.0000 -0.3511 0.0000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 2.6779 0.0000 3 0.0000 0.3071 0.0000 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.2038 2 0.0000 -0.2038 3 0.0000 0.0000 -0.2038 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.5144 2 0.0000 0.1950 3 0.0000 0.0000 0.1901 MATRIX Y This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.0000 2 0.0000 0.1319 3 0.0000 0.0000 0.0000 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.0586 2 0.0000 0.0000 3 0.0000 0.0000 0.1204 GROUP NUMBER: 2 G2: Monozygotic twins MATRIX A This is a computed FULL matrix of order 3 by 3 [=(I-N)~&(X*X')] 1 2 3 1 0.2646 0.2322 0.1977 2 0.2322 0.2418 0.2058 3 0.1977 0.2058 0.2114 MATRIX C This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(Y*Y')] 1 2 3 1 0.0000 0.0000 0.0000 2 0.0000 0.0174 -0.0061 3 0.0000 -0.0061 0.0021 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.0450 0.0092 0.0028 2 0.0092 0.0662 0.0076 3 0.0028 0.0076 0.0584 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.8792 2.6895 2.5073 2 2.8792 2.6895 2.5073 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 0.8776 0.0000 3 0.0000 0.8513 0.0000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 0.7301 0.0000 3 0.0000 -0.3511 0.0000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 2.6779 0.0000 3 0.0000 0.3071 0.0000 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.2038 2 0.0000 -0.2038 3 0.0000 0.0000 -0.2038 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.5144 2 0.0000 0.1950 3 0.0000 0.0000 0.1901 MATRIX Y This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.0000 2 0.0000 0.1319 3 0.0000 0.0000 0.0000 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.0586 2 0.0000 0.0000 3 0.0000 0.0000 0.1204 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 3 by 3 [=(I-N)~&(X*X')] 1 2 3 1 0.2646 0.2322 0.1977 2 0.2322 0.2418 0.2058 3 0.1977 0.2058 0.2114 MATRIX C This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(Y*Y')] 1 2 3 1 0.0000 0.0000 0.0000 2 0.0000 0.0174 -0.0061 3 0.0000 -0.0061 0.0021 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.0450 0.0092 0.0028 2 0.0092 0.0662 0.0076 3 0.0028 0.0076 0.0584 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.8792 2.6895 2.5073 2 2.8792 2.6895 2.5073 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 0.8776 0.0000 3 0.0000 0.8513 0.0000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 0.7301 0.0000 3 0.0000 -0.3511 0.0000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.0000 2 2.6779 0.0000 3 0.0000 0.3071 0.0000 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.2038 2 0.0000 -0.2038 3 0.0000 0.0000 -0.2038 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.5144 2 0.0000 0.1950 3 0.0000 0.0000 0.1901 MATRIX Y This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.0000 2 0.0000 0.1319 3 0.0000 0.0000 0.0000 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.0586 2 0.0000 0.0000 3 0.0000 0.0000 0.1204 Your model has 19 estimated parameters and 1991 Observed statistics -2 times log-likelihood of data >>> 1997.139 Degrees of freedom >>>>>>>>>>>>>>>> 1972 This problem used 13.9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.32 Execution 0: 0: 0:44.71 TOTAL 0: 0: 0:46.03 Total number of warnings issued: 0 ______________________________________________________________________________