!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 W DIAG NVAR NVAR FREE !DOMINANCE INNOVATIONS Z DIAG NVAR NVAR FREE !SPECIFIC ENVIRONMENTAL INNOVATIONS L DIAG NVAR NVAR FREE !QTL INNOVATIONS N LOWER NVAR NVAR !GENETIC TRANSMISSION PATHS O LOWER NVAR NVAR !DOMINANCE TRANSMISSION PATHS P LOWER NVAR NVAR !SPECIFIC ENVIRONMENTAL TRANSMISSION PATHS F LOWER NVAR NVAR !QTL TRANSMISSION PATHS R DIAG NVAR NVAR !MEASUREMENT ERROR I IDEN NVAR NVAR M FULL NSIB NVAR FREE H FULL 1 1 !.5 B FULL 1 1 !.25 END MATRICES; MATRIX H .5 MATRIX B .25 SPECIFY N 0 13 0 0 14 0 SPECIFY O 0 15 0 0 16 0 SPECIFY P 0 17 0 0 18 0 SPECIFY F 0 19 0 0 20 0 SPECIFY R 21 21 21 !EQUATE MEASUREMENT ERROR VARIANCES FOR IDENTIFICATION SPECIFY M 40 41 42 40 41 42 BEGIN ALGEBRA; A= (I-N)~ & (X*X'); D= (I-O)~ & (W*W'); E= (I-P)~ & (Z*Z') + R*R'; Q= (I-F)~ & (L*L'); V= A+Q+D+E; !TOTAL VARIANCE END ALGEBRA; END The following MX script lines were read for group 2 G2: MONOZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE=MARKER6.DAT NOTE: Rectangular file contained 519 records with data LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT11 PLT12 PLT13 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 PLT11 PLT12 PLT13 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; COVARIANCE A+D+Q+E | A+D+Q _ A+D+Q | A+D+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER6.DAT NOTE: Rectangular file contained 519 records with data LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT11 PLT12 PLT13 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 PIBD0 PIBD1 PIBD2 PLT11 PLT12 PLT13 PLT21 PLT22 PLT23; DEFINITION PIBD0 PIBD1 PIBD2; NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1734 observations BEGIN MATRICES = GROUP 1; NOTE: Definition yields 230 data vectors for analysis NOTE: Vectors contain a total of 1038 observations K FULL 3 1 !IBD PROBABILITIES (FROM GENEHUNTER) I UNIT 3 1 !TO CREATE MEANS FOR ALL MODELS & SIBS *** WARNING! *** Matrix was previously defined for this group. Mx will redefine END MATRICES; SPECIFY K PIBD0 PIBD1 PIBD2 BEGIN ALGEBRA; U= H@A+B@D; !IBD 0 COVARIANCE (=NON-QTL COVARIANCE) S= U+H@Q; !IBD 1 COVARIANCE T= U+Q; !IBD 2 COVARIANCE Y= V|U_ U|V_ !IBD 0 MATRIX V|S_ S|V_ !IBD 1 MATRIX V|T_ T|V; !IBD 2 MATRIX END ALGEBRA; MEANS I@M; COVARIANCE Y; WEIGHTS K; START 0.5 ALL START 2.8 M 1 1 1 M 1 1 2 M 1 1 3 OPTION NDECIMALS=3 OPTION ITERATIONS=10000 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 PLT11 PLT12 PLT13 PLT21 PLT22 PLT23 Code 1.000 2.000 3.000 4.000 5.000 6.000 Number 165.000 145.000 171.000 163.000 140.000 169.000 Mean 2.849 2.696 2.541 2.862 2.711 2.568 Variance 0.293 0.356 0.272 0.302 0.307 0.268 Minimum 1.800 1.150 1.240 1.800 1.220 1.560 Maximum 4.480 4.360 4.050 4.580 4.280 4.070 Summary of VL file data for group 3 PIBD2 PIBD1 PIBD0 PLT11 PLT12 PLT13 PLT21 Code -3.000 -2.000 -1.000 1.000 2.000 3.000 4.000 Number 230.000 230.000 230.000 193.000 205.000 123.000 190.000 Mean 0.241 0.479 0.279 2.866 2.671 2.477 2.796 Variance 0.134 0.138 0.132 0.294 0.297 0.232 0.306 Minimum 0.000 0.000 0.000 1.580 1.310 1.520 1.480 Maximum 1.000 1.000 1.000 4.410 4.350 4.210 4.590 PLT22 PLT23 Code 5.000 6.000 Number 205.000 122.000 Mean 2.634 2.491 Variance 0.357 0.314 Minimum 1.380 1.400 Maximum 4.780 4.110 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 19 0 3 0 20 0 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 L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 10 2 0 11 3 0 0 12 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 19 0 3 0 20 0 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 L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 10 2 0 11 3 0 0 12 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 19 0 3 0 20 0 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 10 2 0 11 3 0 0 12 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX S This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX U This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 computed FULL matrix of order 18 by 6 It has no free parameters specified MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 7 2 0 8 3 0 0 9 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH 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 0.062 0.098 0.049 2 0.098 0.154 0.077 3 0.049 0.077 0.039 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.034 0.005 0.012 2 0.005 0.001 0.002 3 0.012 0.002 0.004 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.003 2 0.011 0.062 0.011 3 0.003 0.011 0.057 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.751 0.000 3 0.000 1.081 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.410 2 0.000 -0.112 3 0.000 0.000 0.213 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.880 2.691 2.506 2 2.880 2.691 2.506 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.574 0.000 3 0.000 0.500 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.158 0.000 3 0.000 2.284 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.451 0.000 3 0.000 0.271 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.168 0.126 0.136 2 0.126 0.107 0.116 3 0.136 0.116 0.171 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.141 2 0.000 -0.141 3 0.000 0.000 -0.141 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.308 0.240 0.200 2 0.240 0.325 0.206 3 0.200 0.206 0.271 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.184 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.250 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.155 2 0.000 0.193 3 0.000 0.000 0.185 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 0.062 0.098 0.049 2 0.098 0.154 0.077 3 0.049 0.077 0.039 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.034 0.005 0.012 2 0.005 0.001 0.002 3 0.012 0.002 0.004 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.003 2 0.011 0.062 0.011 3 0.003 0.011 0.057 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.751 0.000 3 0.000 1.081 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.410 2 0.000 -0.112 3 0.000 0.000 0.213 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.880 2.691 2.506 2 2.880 2.691 2.506 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.574 0.000 3 0.000 0.500 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.158 0.000 3 0.000 2.284 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.451 0.000 3 0.000 0.271 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.168 0.126 0.136 2 0.126 0.107 0.116 3 0.136 0.116 0.171 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.141 2 0.000 -0.141 3 0.000 0.000 -0.141 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.308 0.240 0.200 2 0.240 0.325 0.206 3 0.200 0.206 0.271 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.184 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.250 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.155 2 0.000 0.193 3 0.000 0.000 0.185 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 0.062 0.098 0.049 2 0.098 0.154 0.077 3 0.049 0.077 0.039 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.034 0.005 0.012 2 0.005 0.001 0.002 3 0.012 0.002 0.004 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.003 2 0.011 0.062 0.011 3 0.003 0.011 0.057 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.751 0.000 3 0.000 1.081 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.184 3 0.814 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.410 2 0.000 -0.112 3 0.000 0.000 0.213 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.880 2.691 2.506 2 2.880 2.691 2.506 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.574 0.000 3 0.000 0.500 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.158 0.000 3 0.000 2.284 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.451 0.000 3 0.000 0.271 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.168 0.126 0.136 2 0.126 0.107 0.116 3 0.136 0.116 0.171 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.141 2 0.000 -0.141 3 0.000 0.000 -0.141 MATRIX S This is a computed FULL matrix of order 3 by 3 [=U+H@Q] 1 2 3 1 0.124 0.113 0.096 2 0.113 0.131 0.097 3 0.096 0.097 0.106 MATRIX T This is a computed FULL matrix of order 3 by 3 [=U+Q] 1 2 3 1 0.207 0.176 0.164 2 0.176 0.185 0.155 3 0.164 0.155 0.191 MATRIX U This is a computed FULL matrix of order 3 by 3 [=H@A+B@D] 1 2 3 1 0.040 0.050 0.028 2 0.050 0.077 0.039 3 0.028 0.039 0.020 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.308 0.240 0.200 2 0.240 0.325 0.206 3 0.200 0.206 0.271 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.184 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.250 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX Y This is a computed FULL matrix of order 18 by 6 [=V|U_U|V_V|S_S|V_V|T_T|V] 1 2 3 4 5 6 1 0.308 0.240 0.200 0.040 0.050 0.028 2 0.240 0.325 0.206 0.050 0.077 0.039 3 0.200 0.206 0.271 0.028 0.039 0.020 4 0.040 0.050 0.028 0.308 0.240 0.200 5 0.050 0.077 0.039 0.240 0.325 0.206 6 0.028 0.039 0.020 0.200 0.206 0.271 7 0.308 0.240 0.200 0.124 0.113 0.096 8 0.240 0.325 0.206 0.113 0.131 0.097 9 0.200 0.206 0.271 0.096 0.097 0.106 10 0.124 0.113 0.096 0.308 0.240 0.200 11 0.113 0.131 0.097 0.240 0.325 0.206 12 0.096 0.097 0.106 0.200 0.206 0.271 13 0.308 0.240 0.200 0.207 0.176 0.164 14 0.240 0.325 0.206 0.176 0.185 0.155 15 0.200 0.206 0.271 0.164 0.155 0.191 16 0.207 0.176 0.164 0.308 0.240 0.200 17 0.176 0.185 0.155 0.240 0.325 0.206 18 0.164 0.155 0.191 0.200 0.206 0.271 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.155 2 0.000 0.193 3 0.000 0.000 0.185 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 24 estimated parameters and 1991 Observed statistics -2 times log-likelihood of data >>> 1975.423 Degrees of freedom >>>>>>>>>>>>>>>> 1967 Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 14.8% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.32 Execution 0: 0: 6:21.07 TOTAL 0: 0: 6:22.39 Total number of warnings issued: 3 ______________________________________________________________________________ ! Equate loadings on QTL Multiple fit option in effect. The following MX script lines have been read: DROP @1 F 1 2 1 F 1 3 2 DROP L 1 2 2 L 1 3 3 END Summary of VL file data for group 2 PLT11 PLT12 PLT13 PLT21 PLT22 PLT23 Code 1.000 2.000 3.000 4.000 5.000 6.000 Number 165.000 145.000 171.000 163.000 140.000 169.000 Mean 2.849 2.696 2.541 2.862 2.711 2.568 Variance 0.293 0.356 0.272 0.302 0.307 0.268 Minimum 1.800 1.150 1.240 1.800 1.220 1.560 Maximum 4.480 4.360 4.050 4.580 4.280 4.070 Summary of VL file data for group 3 PIBD2 PIBD1 PIBD0 PLT11 PLT12 PLT13 PLT21 Code -3.000 -2.000 -1.000 1.000 2.000 3.000 4.000 Number 230.000 230.000 230.000 193.000 205.000 123.000 190.000 Mean 0.241 0.479 0.279 2.866 2.671 2.477 2.796 Variance 0.134 0.138 0.132 0.294 0.297 0.232 0.306 Minimum 0.000 0.000 0.000 1.580 1.310 1.520 1.480 Maximum 1.000 1.000 1.000 4.410 4.350 4.210 4.590 PLT22 PLT23 Code 5.000 6.000 Number 205.000 122.000 Mean 2.634 2.491 Variance 0.357 0.314 Minimum 1.380 1.400 Maximum 4.780 4.110 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR 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 L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 10 2 0 0 3 0 0 0 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR 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 L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 10 2 0 0 3 0 0 0 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR 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 a UNIT matrix of order 3 by 1 MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 10 2 0 0 3 0 0 0 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX S This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX U This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 computed FULL matrix of order 18 by 6 It has no free parameters specified MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 7 2 0 8 3 0 0 9 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH 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 0.075 0.085 0.037 2 0.085 0.124 0.053 3 0.037 0.053 0.062 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.048 0.004 0.020 2 0.004 0.000 0.002 3 0.020 0.002 0.008 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.002 2 0.011 0.063 0.011 3 0.002 0.011 0.058 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.000 0.000 3 0.000 1.000 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.375 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.880 2.691 2.508 2 2.880 2.691 2.508 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.135 0.000 3 0.000 0.429 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.094 0.000 3 0.000 4.458 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.351 0.000 3 0.000 0.216 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.140 0.140 0.140 2 0.140 0.140 0.140 3 0.140 0.140 0.140 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.111 2 0.000 -0.111 3 0.000 0.000 -0.111 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.307 0.241 0.199 2 0.241 0.327 0.206 3 0.199 0.206 0.269 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.219 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.274 2 0.000 0.164 3 0.000 0.000 0.199 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.178 2 0.000 0.215 3 0.000 0.000 0.208 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 0.075 0.085 0.037 2 0.085 0.124 0.053 3 0.037 0.053 0.062 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.048 0.004 0.020 2 0.004 0.000 0.002 3 0.020 0.002 0.008 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.002 2 0.011 0.063 0.011 3 0.002 0.011 0.058 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.000 0.000 3 0.000 1.000 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.375 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.880 2.691 2.508 2 2.880 2.691 2.508 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.135 0.000 3 0.000 0.429 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.094 0.000 3 0.000 4.458 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.351 0.000 3 0.000 0.216 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.140 0.140 0.140 2 0.140 0.140 0.140 3 0.140 0.140 0.140 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.111 2 0.000 -0.111 3 0.000 0.000 -0.111 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.307 0.241 0.199 2 0.241 0.327 0.206 3 0.199 0.206 0.269 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.219 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.274 2 0.000 0.164 3 0.000 0.000 0.199 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.178 2 0.000 0.215 3 0.000 0.000 0.208 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 0.075 0.085 0.037 2 0.085 0.124 0.053 3 0.037 0.053 0.062 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.048 0.004 0.020 2 0.004 0.000 0.002 3 0.020 0.002 0.008 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.002 2 0.011 0.063 0.011 3 0.002 0.011 0.058 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.000 0.000 3 0.000 1.000 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.184 3 0.814 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.375 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.880 2.691 2.508 2 2.880 2.691 2.508 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.135 0.000 3 0.000 0.429 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.094 0.000 3 0.000 4.458 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.351 0.000 3 0.000 0.216 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.140 0.140 0.140 2 0.140 0.140 0.140 3 0.140 0.140 0.140 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.111 2 0.000 -0.111 3 0.000 0.000 -0.111 MATRIX S This is a computed FULL matrix of order 3 by 3 [=U+H@Q] 1 2 3 1 0.120 0.114 0.094 2 0.114 0.132 0.097 3 0.094 0.097 0.103 MATRIX T This is a computed FULL matrix of order 3 by 3 [=U+Q] 1 2 3 1 0.190 0.184 0.164 2 0.184 0.202 0.167 3 0.164 0.167 0.174 MATRIX U This is a computed FULL matrix of order 3 by 3 [=H@A+B@D] 1 2 3 1 0.050 0.044 0.023 2 0.044 0.062 0.027 3 0.023 0.027 0.033 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.307 0.241 0.199 2 0.241 0.327 0.206 3 0.199 0.206 0.269 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.219 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.274 2 0.000 0.164 3 0.000 0.000 0.199 MATRIX Y This is a computed FULL matrix of order 18 by 6 [=V|U_U|V_V|S_S|V_V|T_T|V] 1 2 3 4 5 6 1 0.307 0.241 0.199 0.050 0.044 0.023 2 0.241 0.327 0.206 0.044 0.062 0.027 3 0.199 0.206 0.269 0.023 0.027 0.033 4 0.050 0.044 0.023 0.307 0.241 0.199 5 0.044 0.062 0.027 0.241 0.327 0.206 6 0.023 0.027 0.033 0.199 0.206 0.269 7 0.307 0.241 0.199 0.120 0.114 0.094 8 0.241 0.327 0.206 0.114 0.132 0.097 9 0.199 0.206 0.269 0.094 0.097 0.103 10 0.120 0.114 0.094 0.307 0.241 0.199 11 0.114 0.132 0.097 0.241 0.327 0.206 12 0.094 0.097 0.103 0.199 0.206 0.269 13 0.307 0.241 0.199 0.190 0.184 0.164 14 0.241 0.327 0.206 0.184 0.202 0.167 15 0.199 0.206 0.269 0.164 0.167 0.174 16 0.190 0.184 0.164 0.307 0.241 0.199 17 0.184 0.202 0.167 0.241 0.327 0.206 18 0.164 0.167 0.174 0.199 0.206 0.269 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.178 2 0.000 0.215 3 0.000 0.000 0.208 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 20 estimated parameters and 1991 Observed statistics -2 times log-likelihood of data >>> 1982.328 Degrees of freedom >>>>>>>>>>>>>>>> 1971 Saturated model fit* >>>>>>>>>>> 1975.423 Saturated model df* >>>>>>>>>>> 1967 Difference Chi-squared >>>>>>>> 6.905 Difference d.f. >>>>>>>>>>>>>>> 4 Probability >>>>>>>>>>>>>>>>>>>> 0.141 Akaike's Information Criterion > -1.095 * Saturated model statistic computed earlier in this job Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 14.8% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 4:51.05 TOTAL 0: 0: 4:51.05 Total number of warnings issued: 5 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: START 0.5 ALL START 2.8 M 1 1 1 M 1 1 2 M 1 1 3 DROP L 1 1 1 END Summary of VL file data for group 2 PLT11 PLT12 PLT13 PLT21 PLT22 PLT23 Code 1.000 2.000 3.000 4.000 5.000 6.000 Number 165.000 145.000 171.000 163.000 140.000 169.000 Mean 2.849 2.696 2.541 2.862 2.711 2.568 Variance 0.293 0.356 0.272 0.302 0.307 0.268 Minimum 1.800 1.150 1.240 1.800 1.220 1.560 Maximum 4.480 4.360 4.050 4.580 4.280 4.070 Summary of VL file data for group 3 PIBD2 PIBD1 PIBD0 PLT11 PLT12 PLT13 PLT21 Code -3.000 -2.000 -1.000 1.000 2.000 3.000 4.000 Number 230.000 230.000 230.000 193.000 205.000 123.000 190.000 Mean 0.241 0.479 0.279 2.866 2.671 2.477 2.796 Variance 0.134 0.138 0.132 0.294 0.297 0.232 0.306 Minimum 0.000 0.000 0.000 1.580 1.310 1.520 1.480 Maximum 1.000 1.000 1.000 4.410 4.350 4.210 4.590 PLT22 PLT23 Code 5.000 6.000 Number 205.000 122.000 Mean 2.634 2.491 Variance 0.357 0.314 Minimum 1.380 1.400 Maximum 4.780 4.110 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR 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 L This is a DIAGONAL matrix of order 3 by 3 It has no free parameters specified 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR 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 L This is a DIAGONAL matrix of order 3 by 3 It has no free parameters specified 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 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 B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D 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 F This is a LOWER TRIANGULAR 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 a UNIT matrix of order 3 by 1 MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 It has no free parameters specified 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 15 0 3 0 16 0 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0 2 17 0 3 0 18 0 MATRIX Q This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 21 2 0 21 3 0 0 21 MATRIX S This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX U This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 3 by 3 It has no free parameters specified MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 4 2 0 5 3 0 0 6 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 computed FULL matrix of order 18 by 6 It has no free parameters specified MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 7 2 0 8 3 0 0 9 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH 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 0.220 0.232 0.174 2 0.232 0.262 0.197 3 0.174 0.197 0.200 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.044 -0.003 0.024 2 -0.003 0.000 -0.002 3 0.024 -0.002 0.013 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.002 2 0.011 0.062 0.011 3 0.002 0.011 0.058 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.000 0.000 3 0.000 1.000 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.000 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.879 2.689 2.507 2 2.879 2.689 2.507 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.055 0.000 3 0.000 0.752 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 -0.063 0.000 3 0.000 -8.603 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.331 0.000 3 0.000 0.205 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.000 0.000 0.000 2 0.000 0.000 0.000 3 0.000 0.000 0.000 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.101 2 0.000 -0.101 3 0.000 0.000 -0.101 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.307 0.240 0.200 2 0.240 0.324 0.206 3 0.200 0.206 0.271 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.210 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.469 2 0.000 0.132 3 0.000 0.000 0.228 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.184 2 0.000 0.220 3 0.000 0.000 0.213 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 0.220 0.232 0.174 2 0.232 0.262 0.197 3 0.174 0.197 0.200 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.044 -0.003 0.024 2 -0.003 0.000 -0.002 3 0.024 -0.002 0.013 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.002 2 0.011 0.062 0.011 3 0.002 0.011 0.058 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.000 0.000 3 0.000 1.000 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is an IDENTITY matrix of order 3 by 3 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.000 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.879 2.689 2.507 2 2.879 2.689 2.507 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.055 0.000 3 0.000 0.752 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 -0.063 0.000 3 0.000 -8.603 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.331 0.000 3 0.000 0.205 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.000 0.000 0.000 2 0.000 0.000 0.000 3 0.000 0.000 0.000 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.101 2 0.000 -0.101 3 0.000 0.000 -0.101 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.307 0.240 0.200 2 0.240 0.324 0.206 3 0.200 0.206 0.271 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.210 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.469 2 0.000 0.132 3 0.000 0.000 0.228 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.184 2 0.000 0.220 3 0.000 0.000 0.213 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 0.220 0.232 0.174 2 0.232 0.262 0.197 3 0.174 0.197 0.200 MATRIX B This is a FULL matrix of order 1 by 1 1 1 0.250 MATRIX D This is a computed FULL matrix of order 3 by 3 [=(I-O)~&(W*W')] 1 2 3 1 0.044 -0.003 0.024 2 -0.003 0.000 -0.002 3 0.024 -0.002 0.013 MATRIX E This is a computed FULL matrix of order 3 by 3 [=(I-P)~&(Z*Z')+R*R'] 1 2 3 1 0.044 0.011 0.002 2 0.011 0.062 0.011 3 0.002 0.011 0.058 MATRIX F This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.000 0.000 3 0.000 1.000 0.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.184 3 0.814 MATRIX L This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.000 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX M This is a FULL matrix of order 2 by 3 1 2 3 1 2.879 2.689 2.507 2 2.879 2.689 2.507 MATRIX N This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 1.055 0.000 3 0.000 0.752 0.000 MATRIX O This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 -0.063 0.000 3 0.000 -8.603 0.000 MATRIX P This is a LOWER TRIANGULAR matrix of order 3 by 3 1 2 3 1 0.000 2 0.331 0.000 3 0.000 0.205 0.000 MATRIX Q This is a computed FULL matrix of order 3 by 3 [=(I-F)~&(L*L')] 1 2 3 1 0.000 0.000 0.000 2 0.000 0.000 0.000 3 0.000 0.000 0.000 MATRIX R This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 -0.101 2 0.000 -0.101 3 0.000 0.000 -0.101 MATRIX S This is a computed FULL matrix of order 3 by 3 [=U+H@Q] 1 2 3 1 0.121 0.115 0.093 2 0.115 0.131 0.098 3 0.093 0.098 0.103 MATRIX T This is a computed FULL matrix of order 3 by 3 [=U+Q] 1 2 3 1 0.121 0.115 0.093 2 0.115 0.131 0.098 3 0.093 0.098 0.103 MATRIX U This is a computed FULL matrix of order 3 by 3 [=H@A+B@D] 1 2 3 1 0.121 0.115 0.093 2 0.115 0.131 0.098 3 0.093 0.098 0.103 MATRIX V This is a computed FULL matrix of order 3 by 3 [=A+Q+D+E] 1 2 3 1 0.307 0.240 0.200 2 0.240 0.324 0.206 3 0.200 0.206 0.271 MATRIX W This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.210 2 0.000 0.000 3 0.000 0.000 0.000 MATRIX X This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.469 2 0.000 0.132 3 0.000 0.000 0.228 MATRIX Y This is a computed FULL matrix of order 18 by 6 [=V|U_U|V_V|S_S|V_V|T_T|V] 1 2 3 4 5 6 1 0.307 0.240 0.200 0.121 0.115 0.093 2 0.240 0.324 0.206 0.115 0.131 0.098 3 0.200 0.206 0.271 0.093 0.098 0.103 4 0.121 0.115 0.093 0.307 0.240 0.200 5 0.115 0.131 0.098 0.240 0.324 0.206 6 0.093 0.098 0.103 0.200 0.206 0.271 7 0.307 0.240 0.200 0.121 0.115 0.093 8 0.240 0.324 0.206 0.115 0.131 0.098 9 0.200 0.206 0.271 0.093 0.098 0.103 10 0.121 0.115 0.093 0.307 0.240 0.200 11 0.115 0.131 0.098 0.240 0.324 0.206 12 0.093 0.098 0.103 0.200 0.206 0.271 13 0.307 0.240 0.200 0.121 0.115 0.093 14 0.240 0.324 0.206 0.115 0.131 0.098 15 0.200 0.206 0.271 0.093 0.098 0.103 16 0.121 0.115 0.093 0.307 0.240 0.200 17 0.115 0.131 0.098 0.240 0.324 0.206 18 0.093 0.098 0.103 0.200 0.206 0.271 MATRIX Z This is a DIAGONAL matrix of order 3 by 3 1 2 3 1 0.184 2 0.000 0.220 3 0.000 0.000 0.213 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 19 estimated parameters and 1991 Observed statistics -2 times log-likelihood of data >>> 1994.513 Degrees of freedom >>>>>>>>>>>>>>>> 1972 Saturated model fit* >>>>>>>>>>> 1975.423 Saturated model df* >>>>>>>>>>> 1967 Difference Chi-squared >>>>>>>> 19.090 Difference d.f. >>>>>>>>>>>>>>> 5 Probability >>>>>>>>>>>>>>>>>>>> 0.002 Akaike's Information Criterion > 9.090 * Saturated model statistic computed earlier in this job Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 14.8% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 7:25.34 TOTAL 0: 0: 7:25.34 Total number of warnings issued: 7 ______________________________________________________________________________