!David Evans & Nick Martin platelet data ! QTL linkage study of platelet count at age 14, marker 6 !Using MZ and DZ twins #repeat 8 Note: beginning of #Repeat section The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NSIB 2 ! NUMBER OF SIBLINGS G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER1 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER1 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.225 0.518 0.257 2.671 2.634 Variance 0.144 0.168 0.136 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.052 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.047 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.411 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.677 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.169 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.156 0.507 0.142 0.195 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.052 0.169 0.047 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.334 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.228 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.218 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.052 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.047 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 1.000 2 0.000 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.411 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.677 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.000 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.169 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.156 0.507 0.142 0.195 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.052 0.169 0.047 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.334 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.228 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.218 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.677 2.677 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.334 PLT22 0.073 0.334 Function value of this group: 653.072 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1002.193 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 9.928 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.002 Akaike's Information Criterion > 7.928 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 3.81 Execution 0: 0: 0:-0.05 TOTAL 0: 0: 0: 3.76 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER2 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER2 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.239 0.484 0.277 2.671 2.634 Variance 0.137 0.131 0.121 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 0.995 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** 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 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.054 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.048 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.407 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.677 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.165 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.161 0.498 0.144 0.196 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.054 0.165 0.048 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.332 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.232 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.219 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.054 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.048 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.859 2 0.141 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.407 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.677 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.070 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.165 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.161 0.498 0.144 0.196 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.054 0.165 0.048 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.332 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.232 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.219 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.677 2.677 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.332 PLT22 0.086 0.332 Function value of this group: 651.118 Where the fit function is -2 * Log-likelihood of raw data *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1000.260 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 11.861 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 9.861 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.83 Execution 0: 0: 0:-0.01 TOTAL 0: 0: 0: 2.82 Total number of warnings issued: 2 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER3 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER3 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.257 0.456 0.288 2.671 2.634 Variance 0.161 0.168 0.153 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.053 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.043 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.412 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.678 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.170 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.160 0.513 0.131 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.053 0.170 0.043 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.331 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.230 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.208 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.053 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.043 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.901 2 0.099 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.412 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.678 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.049 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.170 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.160 0.513 0.131 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.053 0.170 0.043 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.331 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.230 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.208 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.678 2.678 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.331 PLT22 0.078 0.331 Function value of this group: 648.399 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 997.512 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 14.609 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 12.609 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.86 Execution 0: 0: 0: 0.50 TOTAL 0: 0: 0: 3.36 Total number of warnings issued: 2 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER4 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER4 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.253 0.463 0.284 2.671 2.634 Variance 0.162 0.165 0.145 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.082 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.034 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.386 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.676 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.149 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.249 0.451 0.102 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.082 0.149 0.034 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.287 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.184 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.082 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.034 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 1.000 2 0.000 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.386 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.676 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.000 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.149 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.249 0.451 0.102 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.082 0.149 0.034 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.287 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.184 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.676 2.676 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.330 PLT22 0.075 0.330 Function value of this group: 652.898 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1002.052 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 10.069 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.002 Akaike's Information Criterion > 8.069 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.74 Execution 0: 0: 0: 0.29 TOTAL 0: 0: 0: 3.03 Total number of warnings issued: 2 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER5 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER5 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.252 0.463 0.285 2.671 2.634 Variance 0.152 0.157 0.145 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** 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 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.076 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.034 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.394 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.677 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.155 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.230 0.470 0.102 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.076 0.155 0.034 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.276 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.184 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.076 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.034 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.234 2 0.766 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.394 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.677 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.383 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.155 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.230 0.470 0.102 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.076 0.155 0.034 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.276 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.184 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.677 2.677 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.330 PLT22 0.131 0.330 Function value of this group: 652.644 Where the fit function is -2 * Log-likelihood of raw data *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1001.784 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 10.337 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 8.337 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.76 Execution 0: 0: 0: 0.12 TOTAL 0: 0: 0: 2.88 Total number of warnings issued: 4 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER6 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER6 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.256 0.475 0.269 2.671 2.634 Variance 0.138 0.136 0.129 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.097 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.032 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.368 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.676 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.135 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.294 0.411 0.097 0.198 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.097 0.135 0.032 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.311 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.179 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.097 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.032 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 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 FULL matrix of order 1 by 1 1 1 0.368 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.676 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.906 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.135 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.294 0.411 0.097 0.198 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.097 0.135 0.032 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.311 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.179 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.676 2.676 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.330 PLT22 0.203 0.330 Function value of this group: 654.683 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1003.858 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 8.263 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.004 Akaike's Information Criterion > 6.263 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.74 Execution 0: 0: 0: 0.67 TOTAL 0: 0: 0: 3.41 Total number of warnings issued: 4 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER7 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER7 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.284 0.476 0.239 2.671 2.634 Variance 0.141 0.118 0.102 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** 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 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.179 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.025 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.247 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.674 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.061 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.542 0.186 0.075 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.179 0.061 0.025 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.423 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.157 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.179 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.025 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.051 3 0.949 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.247 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.674 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.974 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.061 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.542 0.186 0.075 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.179 0.061 0.025 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.423 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.157 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.674 2.674 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.330 PLT22 0.174 0.330 Function value of this group: 661.509 Where the fit function is -2 * Log-likelihood of raw data *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1010.732 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 1.389 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.239 Akaike's Information Criterion > -0.611 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 3.64 Execution 0: 0: 0:-1.20 TOTAL 0: 0: 0: 2.44 Total number of warnings issued: 6 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 ! NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE = MARKER8 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E; END; The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS DATA NINPUT=13 RECTANGULAR FILE = MARKER8 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations 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 PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1106 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 206 data vectors for analysis NOTE: Vectors contain a total of 410 observations BEGIN MATRICES = GROUP 1 K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI HAT END ALGEBRA; MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT OPTION SUB 1012.121, 691 EXIT Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 2.696 2.711 Variance 0.000 0.000 0.000 0.356 0.307 Minimum 1.000 0.000 0.000 1.150 1.220 Maximum 1.000 0.000 0.000 4.360 4.280 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 206.000 206.000 206.000 205.000 205.000 Mean 0.279 0.492 0.229 2.671 2.634 Variance 0.134 0.108 0.085 0.297 0.357 Minimum 0.000 0.000 0.000 1.310 1.380 Maximum 1.000 1.000 1.000 4.350 4.780 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a FULL matrix of order 1 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 K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.179 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.026 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.245 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.675 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.060 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.543 0.182 0.079 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.179 0.060 0.026 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.423 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.161 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.179 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.026 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.065 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.003 2 0.096 3 0.902 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.245 MATRIX M This is a FULL matrix of order 1 by 1 1 1 2.675 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.950 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.060 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.543 0.182 0.079 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 0.179 0.060 0.026 0.065 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.330 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.423 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.161 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.255 Vector of OBSERVED means PLT2 PLT22 Mean 2.671 2.634 Vector of EXPECTED means PLT2 PLT22 Mean 2.675 2.675 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 0.330 PLT22 0.172 0.330 Function value of this group: 661.830 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 695 Observed statistics -2 times log-likelihood of data >>> 1011.031 Degrees of freedom >>>>>>>>>>>>>>>> 690 Submodel fit* >>>>>>>>>>> 1012.121 Submodel df* >>>>>>>>>>> 691 Difference Chi-squared >>>>>>>> 1.090 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.296 Akaike's Information Criterion > -0.910 * Submodel statistic supplied by user This problem used 1.3% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 3.03 Execution 0: 0: 0: 0.34 TOTAL 0: 0: 0: 3.37 Total number of warnings issued: 6 ______________________________________________________________________________ Note: repeat section completed