** Mx startup successful ** !@human; **MX-PC 1.63h** Job started on 03/05/07 at 09:39:42 ! ESTIMATE GENETIC (QTL) AND ENVIRONMENTAL COMPONENTS - FEQ MODEL - PIHAT APPROACH ! BRISBANE TWIN AND FAMILY STUDY OF COGNITION Note: #loop section begins here #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 ; DEFINITION IBD0M1 IBD1M1 IBD2M1 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M11 IBD1M1 IBD2M1 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M1 IBD1M1 IBD0M1 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2415 0.5058 0.2527 111.9452 111.5210 Variance 0.1157 0.1099 0.0965 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9787 0.9954 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 11 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.3746 3 0.5575 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.7448 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.58 Execution 0: 0: 0: 4.43 TOTAL 0: 0: 0: 5.01 Total number of warnings issued: 0 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M2 IBD1M2 IBD2M2 ; DEFINITION IBD0M2 IBD1M2 IBD2M2 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M12 IBD1M2 IBD2M2 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M2 IBD1M2 IBD0M2 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2256 0.5072 0.2672 111.9452 111.5210 Variance 0.0995 0.0959 0.0980 271.9751 281.1169 Minimum 0.0000 0.0000 0.0001 68.0000 68.0000 Maximum 0.9841 0.9988 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 12 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9280 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7446 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7835 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6277 3 0.2171 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0002 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.5309 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7446 0.0000 183.9280 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6726 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7835 111.7835 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6726 PIQ2 91.7446 275.6726 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 4.13 TOTAL 0: 0: 0: 4.88 Total number of warnings issued: 0 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M3 IBD1M3 IBD2M3 ; DEFINITION IBD0M3 IBD1M3 IBD2M3 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M13 IBD1M3 IBD2M3 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M3 IBD1M3 IBD0M3 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2087 0.5177 0.2736 111.9452 111.5210 Variance 0.1215 0.1382 0.1224 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9987 0.9989 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 13 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7484 3 0.0429 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4171 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 4.41 TOTAL 0: 0: 0: 5.16 Total number of warnings issued: 0 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M4 IBD1M4 IBD2M4 ; DEFINITION IBD0M4 IBD1M4 IBD2M4 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M14 IBD1M4 IBD2M4 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M4 IBD1M4 IBD0M4 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2051 0.5207 0.2742 111.9452 111.5210 Variance 0.1266 0.1508 0.1306 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9992 0.9994 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 14 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 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 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9280 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7446 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7791 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3895 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7446 0.0000 183.9280 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6726 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6726 PIQ2 91.7446 275.6726 Function value of this group: 7203.3503 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 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 4.11 TOTAL 0: 0: 0: 4.84 Total number of warnings issued: 2 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M5 IBD1M5 IBD2M5 ; DEFINITION IBD0M5 IBD1M5 IBD2M5 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M15 IBD1M5 IBD2M5 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M5 IBD1M5 IBD0M5 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2029 0.5236 0.2735 111.9452 111.5210 Variance 0.1216 0.1460 0.1281 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9989 0.9998 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 15 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9279 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7444 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7835 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7363 3 0.0445 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0003 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4127 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7444 0.0000 183.9279 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6724 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7835 111.7835 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6724 PIQ2 91.7444 275.6724 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 4.02 TOTAL 0: 0: 0: 4.77 Total number of warnings issued: 2 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M6 IBD1M6 IBD2M6 ; DEFINITION IBD0M6 IBD1M6 IBD2M6 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M16 IBD1M6 IBD2M6 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M6 IBD1M6 IBD0M6 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2153 0.5154 0.2693 111.9452 111.5210 Variance 0.1258 0.1414 0.1234 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9982 0.9973 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 16 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6177 3 0.1759 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4847 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 4.25 TOTAL 0: 0: 0: 5.00 Total number of warnings issued: 2 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M7 IBD1M7 IBD2M7 ; DEFINITION IBD0M7 IBD1M7 IBD2M7 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M17 IBD1M7 IBD2M7 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M7 IBD1M7 IBD0M7 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2162 0.5152 0.2686 111.9452 111.5210 Variance 0.1257 0.1403 0.1226 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9966 0.9990 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 17 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 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 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9277 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7450 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6111 3 0.1835 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0005 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4890 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7450 0.0000 183.9277 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6727 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5784 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6727 PIQ2 91.7450 275.6727 Function value of this group: 7203.3503 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 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 4.09 TOTAL 0: 0: 0: 4.84 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M8 IBD1M8 IBD2M8 ; DEFINITION IBD0M8 IBD1M8 IBD2M8 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M18 IBD1M8 IBD2M8 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M8 IBD1M8 IBD0M8 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2425 0.5014 0.2561 111.9452 111.5210 Variance 0.1351 0.1431 0.1241 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9955 0.9980 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 18 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 178.2285 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 85.4120 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7861 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6024 3 0.1388 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3.4571 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4400 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 11.9518 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3099 0.0434 0.6467 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 85.4120 11.9518 178.2285 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.5923 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.2419 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.3502 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7861 111.7861 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.5923 PIQ2 90.6709 275.5923 Function value of this group: 7203.2894 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.289 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.289 Bayesian Information Criterion >>>> 916.774 Sample size Adjusted BIC >>>> 2267.492 Deviance Information Criterion >>>> 1698.791 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.061 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.970 Akaike's Information Criterion > -3.939 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.86 TOTAL 0: 0: 0: 4.61 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M9 IBD1M9 IBD2M9 ; DEFINITION IBD0M9 IBD1M9 IBD2M9 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M19 IBD1M9 IBD2M9 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M9 IBD1M9 IBD0M9 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2392 0.5125 0.2483 111.9452 111.5210 Variance 0.1245 0.1275 0.1111 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9974 0.9989 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 19 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 171.3903 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 77.7314 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7940 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6109 3 0.1211 MATRIX L This is a FULL matrix of order 1 by 1 1 1 5.1375 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4265 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 26.3939 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.2821 0.0958 0.6221 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 77.7314 26.3939 171.3903 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.5156 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 8.8165 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.0916 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7940 111.7940 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.5156 PIQ2 88.9889 275.5156 Function value of this group: 7203.0837 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.084 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.084 Bayesian Information Criterion >>>> 916.672 Sample size Adjusted BIC >>>> 2267.389 Deviance Information Criterion >>>> 1698.688 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.266 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.875 Akaike's Information Criterion > -3.734 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.53 TOTAL 0: 0: 0: 4.28 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M10 IBD1M10 IBD2M10 ; DEFINITION IBD0M10 IBD1M10 IBD2M10 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M110 IBD1M10 IBD2M10 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M10 IBD1M10 IBD0M10 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2353 0.5284 0.2363 111.9452 111.5210 Variance 0.1314 0.1372 0.1084 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9973 0.9993 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 110 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7446 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6986 3 0.0135 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3628 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7446 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6727 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6727 PIQ2 91.7446 275.6727 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 4.07 TOTAL 0: 0: 0: 4.84 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M11 IBD1M11 IBD2M11 ; DEFINITION IBD0M11 IBD1M11 IBD2M11 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M111 IBD1M11 IBD2M11 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M11 IBD1M11 IBD0M11 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2389 0.5260 0.2351 111.9452 111.5210 Variance 0.1325 0.1358 0.1078 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9992 0.9992 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 111 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9282 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7448 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7120 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3560 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7448 0.0000 183.9282 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6729 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6729 PIQ2 91.7448 275.6729 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.88 TOTAL 0: 0: 0: 4.63 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M12 IBD1M12 IBD2M12 ; DEFINITION IBD0M12 IBD1M12 IBD2M12 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M112 IBD1M12 IBD2M12 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M12 IBD1M12 IBD0M12 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2392 0.5248 0.2360 111.9452 111.5210 Variance 0.1435 0.1555 0.1193 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9985 0.9995 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 112 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9280 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7445 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7835 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7567 3 0.0074 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3857 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7445 0.0000 183.9280 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6725 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7835 111.7835 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6725 PIQ2 91.7445 275.6725 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.76 Execution 0: 0: 0: 4.31 TOTAL 0: 0: 0: 5.07 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M13 IBD1M13 IBD2M13 ; DEFINITION IBD0M13 IBD1M13 IBD2M13 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M113 IBD1M13 IBD2M13 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M13 IBD1M13 IBD0M13 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2348 0.5267 0.2386 111.9452 111.5210 Variance 0.1489 0.1677 0.1261 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9991 0.9993 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 113 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7448 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7903 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3951 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7448 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6729 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6729 PIQ2 91.7448 275.6729 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.76 Execution 0: 0: 0: 4.15 TOTAL 0: 0: 0: 4.91 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M14 IBD1M14 IBD2M14 ; DEFINITION IBD0M14 IBD1M14 IBD2M14 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M114 IBD1M14 IBD2M14 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M14 IBD1M14 IBD0M14 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2341 0.5199 0.2460 111.9452 111.5210 Variance 0.1406 0.1426 0.1114 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9997 0.9998 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 114 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7979 3 0.0363 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4353 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.75 TOTAL 0: 0: 0: 4.50 Total number of warnings issued: 4 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M15 IBD1M15 IBD2M15 ; DEFINITION IBD0M15 IBD1M15 IBD2M15 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M115 IBD1M15 IBD2M15 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M15 IBD1M15 IBD0M15 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2340 0.5197 0.2464 111.9452 111.5210 Variance 0.1418 0.1430 0.1109 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9994 0.9979 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 115 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 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 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7450 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8018 3 0.0363 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4372 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7450 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6731 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5784 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6731 PIQ2 91.7450 275.6731 Function value of this group: 7203.3503 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 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.87 TOTAL 0: 0: 0: 4.62 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M16 IBD1M16 IBD2M16 ; DEFINITION IBD0M16 IBD1M16 IBD2M16 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M116 IBD1M16 IBD2M16 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M16 IBD1M16 IBD0M16 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2380 0.5102 0.2518 111.9452 111.5210 Variance 0.1271 0.1214 0.1053 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9982 0.9979 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 116 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8440 3 0.0293 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4513 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.96 TOTAL 0: 0: 0: 4.73 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M17 IBD1M17 IBD2M17 ; DEFINITION IBD0M17 IBD1M17 IBD2M17 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M117 IBD1M17 IBD2M17 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M17 IBD1M17 IBD0M17 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2387 0.5079 0.2534 111.9452 111.5210 Variance 0.1213 0.1110 0.1005 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9958 0.9990 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 117 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.9372 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4686 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.91 TOTAL 0: 0: 0: 4.66 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M18 IBD1M18 IBD2M18 ; DEFINITION IBD0M18 IBD1M18 IBD2M18 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M118 IBD1M18 IBD2M18 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M18 IBD1M18 IBD0M18 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2447 0.5043 0.2510 111.9452 111.5210 Variance 0.1241 0.1226 0.1077 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9970 0.9974 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 118 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7326 3 0.1489 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.5152 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6727 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6727 PIQ2 91.7447 275.6727 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 3.51 TOTAL 0: 0: 0: 4.24 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M19 IBD1M19 IBD2M19 ; DEFINITION IBD0M19 IBD1M19 IBD2M19 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M119 IBD1M19 IBD2M19 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M19 IBD1M19 IBD0M19 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2433 0.5144 0.2423 111.9452 111.5210 Variance 0.1396 0.1374 0.1078 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9998 0.9985 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 119 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6607 3 0.2153 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.5456 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.76 Execution 0: 0: 0: 3.77 TOTAL 0: 0: 0: 4.53 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M20 IBD1M20 IBD2M20 ; DEFINITION IBD0M20 IBD1M20 IBD2M20 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M120 IBD1M20 IBD2M20 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M20 IBD1M20 IBD0M20 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2441 0.5137 0.2423 111.9452 111.5210 Variance 0.1414 0.1380 0.1080 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9984 0.9973 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 120 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6496 3 0.2274 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.5522 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.79 TOTAL 0: 0: 0: 4.56 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M21 IBD1M21 IBD2M21 ; DEFINITION IBD0M21 IBD1M21 IBD2M21 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M121 IBD1M21 IBD2M21 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M21 IBD1M21 IBD0M21 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2314 0.5237 0.2449 111.9452 111.5210 Variance 0.1348 0.1342 0.1060 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9981 0.9970 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 121 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7233 3 0.1268 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4884 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.84 TOTAL 0: 0: 0: 4.61 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M22 IBD1M22 IBD2M22 ; DEFINITION IBD0M22 IBD1M22 IBD2M22 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M122 IBD1M22 IBD2M22 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M22 IBD1M22 IBD0M22 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2414 0.5118 0.2468 111.9452 111.5210 Variance 0.1314 0.1266 0.1066 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9990 0.9996 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 122 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7701 3 0.0748 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4599 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.56 TOTAL 0: 0: 0: 4.31 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M23 IBD1M23 IBD2M23 ; DEFINITION IBD0M23 IBD1M23 IBD2M23 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M123 IBD1M23 IBD2M23 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M23 IBD1M23 IBD0M23 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2556 0.4933 0.2511 111.9452 111.5210 Variance 0.1381 0.1265 0.1100 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9978 0.9977 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 123 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8462 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4231 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.90 TOTAL 0: 0: 0: 4.67 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M24 IBD1M24 IBD2M24 ; DEFINITION IBD0M24 IBD1M24 IBD2M24 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M124 IBD1M24 IBD2M24 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M24 IBD1M24 IBD0M24 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2676 0.4744 0.2579 111.9452 111.5210 Variance 0.1597 0.1590 0.1321 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9995 1.0000 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 124 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8968 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4484 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.76 Execution 0: 0: 0: 3.68 TOTAL 0: 0: 0: 4.44 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M25 IBD1M25 IBD2M25 ; DEFINITION IBD0M25 IBD1M25 IBD2M25 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M125 IBD1M25 IBD2M25 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M25 IBD1M25 IBD0M25 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2668 0.4756 0.2576 111.9452 111.5210 Variance 0.1593 0.1584 0.1313 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9996 1.0000 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 125 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8945 3 0.0012 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4484 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.95 TOTAL 0: 0: 0: 4.70 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M26 IBD1M26 IBD2M26 ; DEFINITION IBD0M26 IBD1M26 IBD2M26 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M126 IBD1M26 IBD2M26 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M26 IBD1M26 IBD0M26 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2657 0.4712 0.2630 111.9452 111.5210 Variance 0.1515 0.1481 0.1299 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9993 0.9985 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 126 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8841 3 0.0064 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4485 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.68 TOTAL 0: 0: 0: 4.43 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M27 IBD1M27 IBD2M27 ; DEFINITION IBD0M27 IBD1M27 IBD2M27 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M127 IBD1M27 IBD2M27 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M27 IBD1M27 IBD0M27 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2580 0.4767 0.2653 111.9452 111.5210 Variance 0.1324 0.1226 0.1180 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9925 0.9992 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 127 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7448 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8940 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4470 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7448 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6729 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6729 PIQ2 91.7448 275.6729 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.67 TOTAL 0: 0: 0: 4.42 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M28 IBD1M28 IBD2M28 ; DEFINITION IBD0M28 IBD1M28 IBD2M28 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M128 IBD1M28 IBD2M28 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M28 IBD1M28 IBD0M28 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2288 0.5142 0.2570 111.9452 111.5210 Variance 0.1247 0.1231 0.1064 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9983 0.9992 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 128 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9283 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7445 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.9105 3 0.0136 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4689 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7445 0.0000 183.9283 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7445 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.62 TOTAL 0: 0: 0: 4.37 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M29 IBD1M29 IBD2M29 ; DEFINITION IBD0M29 IBD1M29 IBD2M29 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M129 IBD1M29 IBD2M29 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M29 IBD1M29 IBD0M29 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2280 0.5159 0.2560 111.9452 111.5210 Variance 0.1315 0.1338 0.1110 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9982 0.9998 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 129 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7446 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.9529 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4764 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7446 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6727 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6727 PIQ2 91.7446 275.6727 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.73 TOTAL 0: 0: 0: 4.50 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M30 IBD1M30 IBD2M30 ; DEFINITION IBD0M30 IBD1M30 IBD2M30 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M130 IBD1M30 IBD2M30 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M30 IBD1M30 IBD0M30 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2361 0.5174 0.2465 111.9452 111.5210 Variance 0.1237 0.1151 0.0964 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9988 0.9987 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 130 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5761 3 0.3871 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.6751 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 4.01 TOTAL 0: 0: 0: 4.76 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M31 IBD1M31 IBD2M31 ; DEFINITION IBD0M31 IBD1M31 IBD2M31 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M131 IBD1M31 IBD2M31 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M31 IBD1M31 IBD0M31 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2401 0.5133 0.2466 111.9452 111.5210 Variance 0.1230 0.1134 0.0971 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9976 0.9958 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 131 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9279 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.4772 3 0.4940 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0006 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.7326 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9279 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6726 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6726 PIQ2 91.7447 275.6726 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 4.09 TOTAL 0: 0: 0: 4.86 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M32 IBD1M32 IBD2M32 ; DEFINITION IBD0M32 IBD1M32 IBD2M32 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M132 IBD1M32 IBD2M32 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M32 IBD1M32 IBD0M32 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2346 0.5202 0.2452 111.9452 111.5210 Variance 0.1131 0.0992 0.0863 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9962 0.9987 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 132 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 139.0349 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 42.6969 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7572 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.4918 3 0.4444 MATRIX L This is a FULL matrix of order 1 by 1 1 1 9.6554 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.6903 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 93.2272 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1553 0.3391 0.5057 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 42.6969 93.2272 139.0349 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.9590 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 6.5343 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.7913 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7572 111.7572 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.9590 PIQ2 107.0530 274.9590 Function value of this group: 7199.5019 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7199.502 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5497.502 Bayesian Information Criterion >>>> 914.881 Sample size Adjusted BIC >>>> 2265.598 Deviance Information Criterion >>>> 1696.897 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 3.848 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.146 Akaike's Information Criterion > -0.152 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.42 TOTAL 0: 0: 0: 4.17 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M33 IBD1M33 IBD2M33 ; DEFINITION IBD0M33 IBD1M33 IBD2M33 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M133 IBD1M33 IBD2M33 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M33 IBD1M33 IBD0M33 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2442 0.5101 0.2456 111.9452 111.5210 Variance 0.1212 0.1034 0.0900 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9948 0.9988 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 133 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 139.7330 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 39.3435 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7604 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5027 3 0.4257 MATRIX L This is a FULL matrix of order 1 by 1 1 1 9.7691 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.6771 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 95.4349 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1433 0.3477 0.5090 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 39.3435 95.4349 139.7330 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.5114 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 6.2724 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.8209 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7604 111.7604 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.5114 PIQ2 103.9582 274.5114 Function value of this group: 7198.9646 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7198.965 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5496.965 Bayesian Information Criterion >>>> 914.612 Sample size Adjusted BIC >>>> 2265.330 Deviance Information Criterion >>>> 1696.629 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 4.385 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.112 Akaike's Information Criterion > 0.385 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.41 TOTAL 0: 0: 0: 4.16 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M34 IBD1M34 IBD2M34 ; DEFINITION IBD0M34 IBD1M34 IBD2M34 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M134 IBD1M34 IBD2M34 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M34 IBD1M34 IBD0M34 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2482 0.4958 0.2561 111.9452 111.5210 Variance 0.1379 0.1273 0.1077 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9975 0.9998 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 134 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 143.9300 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 44.1954 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7595 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7468 3 0.0895 MATRIX L This is a FULL matrix of order 1 by 1 1 1 9.2905 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 86.3132 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1610 0.3145 0.5245 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 44.1954 86.3132 143.9300 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.4386 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 6.6480 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.9971 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7595 111.7595 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.4386 PIQ2 84.1472 274.4386 Function value of this group: 7198.7917 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7198.792 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5496.792 Bayesian Information Criterion >>>> 914.526 Sample size Adjusted BIC >>>> 2265.243 Deviance Information Criterion >>>> 1696.542 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 4.558 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.102 Akaike's Information Criterion > 0.558 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.43 TOTAL 0: 0: 0: 4.18 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M35 IBD1M35 IBD2M35 ; DEFINITION IBD0M35 IBD1M35 IBD2M35 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M135 IBD1M35 IBD2M35 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M35 IBD1M35 IBD0M35 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2512 0.4925 0.2563 111.9452 111.5210 Variance 0.1450 0.1371 0.1137 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9987 0.9971 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 135 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 146.0655 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 45.9485 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7655 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.7966 3 0.0152 MATRIX L This is a FULL matrix of order 1 by 1 1 1 9.0782 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4135 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 82.4139 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1674 0.3003 0.5323 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 45.9485 82.4139 146.0655 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.4279 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 6.7785 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 12.0858 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7655 111.7655 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.4279 PIQ2 80.0303 274.4279 Function value of this group: 7199.0185 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7199.019 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5497.019 Bayesian Information Criterion >>>> 914.639 Sample size Adjusted BIC >>>> 2265.356 Deviance Information Criterion >>>> 1696.656 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 4.331 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.115 Akaike's Information Criterion > 0.331 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.57 TOTAL 0: 0: 0: 4.32 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M36 IBD1M36 IBD2M36 ; DEFINITION IBD0M36 IBD1M36 IBD2M36 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M136 IBD1M36 IBD2M36 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M36 IBD1M36 IBD0M36 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2514 0.4923 0.2563 111.9452 111.5210 Variance 0.1470 0.1403 0.1153 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9994 0.9994 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 136 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 146.4448 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 46.2977 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7667 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.8068 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 9.0380 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4034 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 81.6848 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1687 0.2977 0.5336 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 46.2977 81.6848 146.4448 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.4273 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 6.8042 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 12.1014 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7667 111.7667 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.4273 PIQ2 79.2481 274.4273 Function value of this group: 7199.0634 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7199.063 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5497.063 Bayesian Information Criterion >>>> 914.661 Sample size Adjusted BIC >>>> 2265.379 Deviance Information Criterion >>>> 1696.678 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 4.287 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.117 Akaike's Information Criterion > 0.287 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.76 Execution 0: 0: 0: 3.38 TOTAL 0: 0: 0: 4.14 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M37 IBD1M37 IBD2M37 ; DEFINITION IBD0M37 IBD1M37 IBD2M37 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M137 IBD1M37 IBD2M37 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M37 IBD1M37 IBD0M37 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2557 0.4803 0.2640 111.9452 111.5210 Variance 0.1402 0.1296 0.1165 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9954 0.9980 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 137 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 125.9561 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 29.3357 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7442 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.2430 3 0.0017 MATRIX L This is a FULL matrix of order 1 by 1 1 1 10.9252 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.1232 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 119.3606 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1068 0.4346 0.4586 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 29.3357 119.3606 125.9561 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.6523 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 5.4162 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.2230 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7442 111.7442 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.6523 PIQ2 44.0391 274.6523 Function value of this group: 7193.7599 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7193.760 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5491.760 Bayesian Information Criterion >>>> 912.010 Sample size Adjusted BIC >>>> 2262.727 Deviance Information Criterion >>>> 1694.026 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 9.590 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.008 Akaike's Information Criterion > 5.590 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.44 TOTAL 0: 0: 0: 4.19 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M38 IBD1M38 IBD2M38 ; DEFINITION IBD0M38 IBD1M38 IBD2M38 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M138 IBD1M38 IBD2M38 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M38 IBD1M38 IBD0M38 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2567 0.4811 0.2622 111.9452 111.5210 Variance 0.1493 0.1443 0.1234 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9981 0.9994 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 138 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 123.2851 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 27.8765 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7414 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.0000 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 11.1281 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.0000 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 123.8335 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1014 0.4503 0.4483 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 27.8765 123.8335 123.2851 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 274.9951 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 5.2798 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.1034 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7414 111.7414 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 274.9951 PIQ2 27.8765 274.9951 Function value of this group: 7192.9836 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7192.984 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5490.984 Bayesian Information Criterion >>>> 911.622 Sample size Adjusted BIC >>>> 2262.339 Deviance Information Criterion >>>> 1693.638 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 10.366 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.006 Akaike's Information Criterion > 6.366 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.00 TOTAL 0: 0: 0: 3.75 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M39 IBD1M39 IBD2M39 ; DEFINITION IBD0M39 IBD1M39 IBD2M39 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M139 IBD1M39 IBD2M39 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M39 IBD1M39 IBD0M39 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2485 0.4874 0.2641 111.9452 111.5210 Variance 0.1427 0.1414 0.1226 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9985 0.9996 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 139 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 115.5043 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 24.2472 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7470 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.1521 3 0.0011 MATRIX L This is a FULL matrix of order 1 by 1 1 1 11.6451 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.0771 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 135.6084 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0881 0.4925 0.4195 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 24.2472 135.6084 115.5043 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.3599 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4.9241 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.7473 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7470 111.7470 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.3599 PIQ2 34.7026 275.3599 Function value of this group: 7191.3134 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7191.313 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5489.313 Bayesian Information Criterion >>>> 910.786 Sample size Adjusted BIC >>>> 2261.504 Deviance Information Criterion >>>> 1692.803 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 12.037 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.002 Akaike's Information Criterion > 8.037 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.29 TOTAL 0: 0: 0: 4.06 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M40 IBD1M40 IBD2M40 ; DEFINITION IBD0M40 IBD1M40 IBD2M40 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M140 IBD1M40 IBD2M40 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M40 IBD1M40 IBD0M40 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2463 0.4897 0.2640 111.9452 111.5210 Variance 0.1449 0.1437 0.1228 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9991 0.9962 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 140 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 110.3023 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 21.9747 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7576 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.2062 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 11.9750 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.1031 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 143.4004 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0797 0.5202 0.4001 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 21.9747 143.4004 110.3023 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6775 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4.6877 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.5025 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7576 111.7576 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6775 PIQ2 36.7615 275.6775 Function value of this group: 7189.9854 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7189.985 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5487.985 Bayesian Information Criterion >>>> 910.122 Sample size Adjusted BIC >>>> 2260.840 Deviance Information Criterion >>>> 1692.139 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 13.365 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 9.365 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.33 TOTAL 0: 0: 0: 4.08 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M41 IBD1M41 IBD2M41 ; DEFINITION IBD0M41 IBD1M41 IBD2M41 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M141 IBD1M41 IBD2M41 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M41 IBD1M41 IBD0M41 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2331 0.5006 0.2663 111.9452 111.5210 Variance 0.1302 0.1331 0.1170 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9988 0.9984 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 141 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 101.3190 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 16.6998 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7830 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.2686 3 0.0053 MATRIX L This is a FULL matrix of order 1 by 1 1 1 12.5615 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.1396 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 157.7906 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0605 0.5721 0.3674 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 16.6998 157.7906 101.3190 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.8094 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4.0865 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.0657 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7830 111.7830 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.8094 PIQ2 38.7290 275.8094 Function value of this group: 7188.3866 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7188.387 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5486.387 Bayesian Information Criterion >>>> 909.323 Sample size Adjusted BIC >>>> 2260.040 Deviance Information Criterion >>>> 1691.340 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 14.963 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 10.963 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.50 TOTAL 0: 0: 0: 4.25 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M42 IBD1M42 IBD2M42 ; DEFINITION IBD0M42 IBD1M42 IBD2M42 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M142 IBD1M42 IBD2M42 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M42 IBD1M42 IBD0M42 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2311 0.4918 0.2771 111.9452 111.5210 Variance 0.1295 0.1265 0.1158 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9972 0.9972 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 142 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 109.2216 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 31.4410 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8101 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.4405 3 0.0038 MATRIX L This is a FULL matrix of order 1 by 1 1 1 11.6562 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2241 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 135.8677 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1137 0.4913 0.3950 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 31.4410 135.8677 109.2216 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.5303 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 5.6072 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.4509 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8101 111.8101 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.5303 PIQ2 61.8889 276.5303 Function value of this group: 7193.4965 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7193.497 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5491.497 Bayesian Information Criterion >>>> 911.878 Sample size Adjusted BIC >>>> 2262.595 Deviance Information Criterion >>>> 1693.895 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 9.853 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.007 Akaike's Information Criterion > 5.853 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.48 TOTAL 0: 0: 0: 4.23 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M43 IBD1M43 IBD2M43 ; DEFINITION IBD0M43 IBD1M43 IBD2M43 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M143 IBD1M43 IBD2M43 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M43 IBD1M43 IBD0M43 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2309 0.4923 0.2768 111.9452 111.5210 Variance 0.1333 0.1297 0.1163 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9991 0.9996 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 143 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 108.9966 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 30.8698 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.4639 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 11.6954 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2320 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 136.7823 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1116 0.4944 0.3940 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 30.8698 136.7823 108.9966 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.6487 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 5.5561 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.4401 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8247 111.8247 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.6487 PIQ2 62.5992 276.6487 Function value of this group: 7193.5991 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7193.599 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5491.599 Bayesian Information Criterion >>>> 911.929 Sample size Adjusted BIC >>>> 2262.647 Deviance Information Criterion >>>> 1693.946 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 9.751 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.008 Akaike's Information Criterion > 5.751 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.22 TOTAL 0: 0: 0: 3.97 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M44 IBD1M44 IBD2M44 ; DEFINITION IBD0M44 IBD1M44 IBD2M44 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M144 IBD1M44 IBD2M44 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M44 IBD1M44 IBD0M44 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2333 0.4941 0.2726 111.9452 111.5210 Variance 0.1243 0.1175 0.1081 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9994 0.9989 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 144 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 101.7546 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 19.6404 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8651 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.4835 3 0.0259 MATRIX L This is a FULL matrix of order 1 by 1 1 1 12.4576 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2676 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 155.1906 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0710 0.5611 0.3679 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 19.6404 155.1906 101.7546 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.5856 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4.4317 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.0874 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8651 111.8651 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.5856 PIQ2 61.1740 276.5856 Function value of this group: 7192.3426 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7192.343 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5490.343 Bayesian Information Criterion >>>> 911.301 Sample size Adjusted BIC >>>> 2262.018 Deviance Information Criterion >>>> 1693.318 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 11.007 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.004 Akaike's Information Criterion > 7.007 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.64 TOTAL 0: 0: 0: 4.39 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M45 IBD1M45 IBD2M45 ; DEFINITION IBD0M45 IBD1M45 IBD2M45 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M145 IBD1M45 IBD2M45 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M45 IBD1M45 IBD0M45 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2245 0.5112 0.2643 111.9452 111.5210 Variance 0.1298 0.1323 0.1134 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9979 0.9999 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 145 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 103.5406 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 19.2908 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5184 3 0.0343 MATRIX L This is a FULL matrix of order 1 by 1 1 1 12.4031 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2935 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 153.8357 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0697 0.5560 0.3742 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 19.2908 153.8357 103.5406 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.6670 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4.3921 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.1755 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8834 111.8834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.6670 PIQ2 64.4415 276.6670 Function value of this group: 7194.6059 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7194.606 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5492.606 Bayesian Information Criterion >>>> 912.433 Sample size Adjusted BIC >>>> 2263.150 Deviance Information Criterion >>>> 1694.449 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 8.744 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.013 Akaike's Information Criterion > 4.744 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.74 Execution 0: 0: 0: 3.94 TOTAL 0: 0: 0: 4.68 Total number of warnings issued: 6 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M46 IBD1M46 IBD2M46 ; DEFINITION IBD0M46 IBD1M46 IBD2M46 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M146 IBD1M46 IBD2M46 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M46 IBD1M46 IBD0M46 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2302 0.5077 0.2621 111.9452 111.5210 Variance 0.1312 0.1342 0.1156 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9991 0.9995 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 146 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 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 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 101.6073 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 11.8896 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8764 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5362 3 0.0310 MATRIX L This is a FULL matrix of order 1 by 1 1 1 12.7621 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2991 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 162.8704 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0430 0.5893 0.3677 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 11.8896 162.8704 101.6073 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.3672 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3.4481 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.0800 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8764 111.8764 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.3672 PIQ2 60.6033 276.3672 Function value of this group: 7193.1319 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 856 Observed statistics -2 times log-likelihood of data >>> 7193.132 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5491.132 Bayesian Information Criterion >>>> 911.696 Sample size Adjusted BIC >>>> 2262.413 Deviance Information Criterion >>>> 1693.712 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 10.218 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.006 Akaike's Information Criterion > 6.218 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 3.79 TOTAL 0: 0: 0: 4.56 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M47 IBD1M47 IBD2M47 ; DEFINITION IBD0M47 IBD1M47 IBD2M47 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M147 IBD1M47 IBD2M47 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M47 IBD1M47 IBD0M47 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2199 0.5159 0.2643 111.9452 111.5210 Variance 0.1242 0.1310 0.1146 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9985 0.9951 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 147 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 101.3690 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 9.6567 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8762 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5598 3 0.0230 MATRIX L This is a FULL matrix of order 1 by 1 1 1 12.8571 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3029 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 165.3056 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0349 0.5982 0.3668 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 9.6567 165.3056 101.3690 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.3314 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3.1075 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.0682 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8762 111.8762 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.3314 PIQ2 59.7311 276.3314 Function value of this group: 7194.2299 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7194.230 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5492.230 Bayesian Information Criterion >>>> 912.245 Sample size Adjusted BIC >>>> 2262.962 Deviance Information Criterion >>>> 1694.261 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 9.120 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.010 Akaike's Information Criterion > 5.120 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 4.01 TOTAL 0: 0: 0: 4.78 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M48 IBD1M48 IBD2M48 ; DEFINITION IBD0M48 IBD1M48 IBD2M48 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M148 IBD1M48 IBD2M48 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M48 IBD1M48 IBD0M48 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2209 0.5151 0.2640 111.9452 111.5210 Variance 0.1374 0.1538 0.1275 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9966 0.9984 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 148 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 107.3281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 16.3998 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8358 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6086 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 12.3559 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3043 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 152.6686 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0593 0.5524 0.3883 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 16.3998 152.6686 107.3281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 276.3966 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4.0497 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 10.3599 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8358 111.8358 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 276.3966 PIQ2 62.8546 276.3966 Function value of this group: 7195.1902 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7195.190 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5493.190 Bayesian Information Criterion >>>> 912.725 Sample size Adjusted BIC >>>> 2263.442 Deviance Information Criterion >>>> 1694.742 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 8.160 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.017 Akaike's Information Criterion > 4.160 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.95 TOTAL 0: 0: 0: 4.70 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M49 IBD1M49 IBD2M49 ; DEFINITION IBD0M49 IBD1M49 IBD2M49 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M149 IBD1M49 IBD2M49 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M49 IBD1M49 IBD0M49 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2315 0.5141 0.2544 111.9452 111.5210 Variance 0.1355 0.1439 0.1201 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9994 0.9991 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 149 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 124.1476 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 26.3413 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8080 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6255 3 0.0046 MATRIX L This is a FULL matrix of order 1 by 1 1 1 11.1833 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3174 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 125.0654 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.0956 0.4539 0.4505 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 26.3413 125.0654 124.1476 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.5543 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 5.1324 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.1422 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8080 111.8080 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.5543 PIQ2 66.0314 275.5543 Function value of this group: 7197.7506 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7197.751 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5495.751 Bayesian Information Criterion >>>> 914.005 Sample size Adjusted BIC >>>> 2264.722 Deviance Information Criterion >>>> 1696.022 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 5.599 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.061 Akaike's Information Criterion > 1.599 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.94 TOTAL 0: 0: 0: 4.69 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M50 IBD1M50 IBD2M50 ; DEFINITION IBD0M50 IBD1M50 IBD2M50 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M150 IBD1M50 IBD2M50 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M50 IBD1M50 IBD0M50 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2335 0.5151 0.2514 111.9452 111.5210 Variance 0.1372 0.1408 0.1149 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9975 0.9992 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 150 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 139.1274 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 41.7822 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7915 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6470 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 9.7180 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3235 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 94.4387 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.1517 0.3430 0.5053 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 41.7822 94.4387 139.1274 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.3483 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 6.4639 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 11.7952 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7915 111.7915 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.3483 PIQ2 72.3317 275.3483 Function value of this group: 7199.9016 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7199.902 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5497.902 Bayesian Information Criterion >>>> 915.081 Sample size Adjusted BIC >>>> 2265.798 Deviance Information Criterion >>>> 1697.097 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 3.448 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.178 Akaike's Information Criterion > -0.552 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.40 TOTAL 0: 0: 0: 4.15 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M51 IBD1M51 IBD2M51 ; DEFINITION IBD0M51 IBD1M51 IBD2M51 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M151 IBD1M51 IBD2M51 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M51 IBD1M51 IBD0M51 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2299 0.5163 0.2538 111.9452 111.5210 Variance 0.1230 0.1238 0.1066 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9989 0.9976 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 151 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 160.4575 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 67.7143 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7839 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.6126 3 0.0854 MATRIX L This is a FULL matrix of order 1 by 1 1 1 6.8827 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.3916 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 47.3718 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.2457 0.1719 0.5823 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 67.7143 47.3718 160.4575 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.5436 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 8.2289 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 12.6672 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7839 111.7839 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.5436 PIQ2 86.2672 275.5436 Function value of this group: 7202.4331 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7202.433 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5500.433 Bayesian Information Criterion >>>> 916.346 Sample size Adjusted BIC >>>> 2267.064 Deviance Information Criterion >>>> 1698.363 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.917 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.632 Akaike's Information Criterion > -3.083 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.75 Execution 0: 0: 0: 3.35 TOTAL 0: 0: 0: 4.10 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M52 IBD1M52 IBD2M52 ; DEFINITION IBD0M52 IBD1M52 IBD2M52 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M152 IBD1M52 IBD2M52 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M52 IBD1M52 IBD0M52 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2439 0.5195 0.2366 111.9452 111.5210 Variance 0.1295 0.1199 0.0954 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9972 0.9913 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 152 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 179.5106 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 86.7921 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7874 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5811 3 0.1812 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3.0531 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4717 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 9.3215 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3149 0.0338 0.6513 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 86.7921 9.3215 179.5106 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6242 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.3162 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.3982 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7874 111.7874 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6242 PIQ2 91.1894 275.6242 Function value of this group: 7203.3152 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.315 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.315 Bayesian Information Criterion >>>> 916.787 Sample size Adjusted BIC >>>> 2267.505 Deviance Information Criterion >>>> 1698.804 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.035 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.983 Akaike's Information Criterion > -3.965 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 3.98 TOTAL 0: 0: 0: 4.71 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M53 IBD1M53 IBD2M53 ; DEFINITION IBD0M53 IBD1M53 IBD2M53 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M153 IBD1M53 IBD2M53 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M53 IBD1M53 IBD0M53 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2464 0.5160 0.2377 111.9452 111.5210 Variance 0.1332 0.1255 0.1002 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9980 0.9998 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 153 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 158.3317 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 62.3561 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5608 3 0.2510 MATRIX L This is a FULL matrix of order 1 by 1 1 1 7.3887 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.5315 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 54.5936 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.2265 0.1983 0.5752 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 62.3561 54.5936 158.3317 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.2814 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 7.8966 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 12.5830 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8237 111.8237 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.2814 PIQ2 91.3709 275.2814 Function value of this group: 7201.8129 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7201.813 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5499.813 Bayesian Information Criterion >>>> 916.036 Sample size Adjusted BIC >>>> 2266.754 Deviance Information Criterion >>>> 1698.053 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 1.537 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.464 Akaike's Information Criterion > -2.463 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 3.50 TOTAL 0: 0: 0: 4.23 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M54 IBD1M54 IBD2M54 ; DEFINITION IBD0M54 IBD1M54 IBD2M54 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M154 IBD1M54 IBD2M54 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M54 IBD1M54 IBD0M54 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2435 0.5183 0.2382 111.9452 111.5210 Variance 0.1375 0.1312 0.1014 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9985 0.9991 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 154 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 169.3974 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 74.5755 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.8029 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5512 3 0.2842 MATRIX L This is a FULL matrix of order 1 by 1 1 1 5.6026 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.5598 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 31.3895 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.2708 0.1140 0.6152 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 74.5755 31.3895 169.3974 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.3624 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 8.6357 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.0153 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.8029 111.8029 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.3624 PIQ2 92.1484 275.3624 Function value of this group: 7202.8842 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7202.884 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5500.884 Bayesian Information Criterion >>>> 916.572 Sample size Adjusted BIC >>>> 2267.289 Deviance Information Criterion >>>> 1698.589 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.466 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.792 Akaike's Information Criterion > -3.534 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.74 Execution 0: 0: 0: 3.46 TOTAL 0: 0: 0: 4.20 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M55 IBD1M55 IBD2M55 ; DEFINITION IBD0M55 IBD1M55 IBD2M55 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M155 IBD1M55 IBD2M55 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M55 IBD1M55 IBD0M55 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2486 0.5121 0.2393 111.9452 111.5210 Variance 0.1295 0.1175 0.0950 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9980 0.9980 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 155 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 171.7176 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 76.7429 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7964 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5617 3 0.2107 MATRIX L This is a FULL matrix of order 1 by 1 1 1 5.1848 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.4916 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 26.8824 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.2787 0.0976 0.6236 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 76.7429 26.8824 171.7176 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.3430 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 8.7603 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.1041 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7964 111.7964 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.3430 PIQ2 89.9581 275.3430 Function value of this group: 7203.0217 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.022 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.022 Bayesian Information Criterion >>>> 916.641 Sample size Adjusted BIC >>>> 2267.358 Deviance Information Criterion >>>> 1698.657 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.328 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> 0.849 Akaike's Information Criterion > -3.672 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.74 Execution 0: 0: 0: 3.52 TOTAL 0: 0: 0: 4.26 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M56 IBD1M56 IBD2M56 ; DEFINITION IBD0M56 IBD1M56 IBD2M56 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M156 IBD1M56 IBD2M56 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M56 IBD1M56 IBD0M56 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2664 0.4830 0.2506 111.9452 111.5210 Variance 0.1385 0.1260 0.1077 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9983 0.9978 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 156 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.5170 3 0.0376 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2961 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.74 Execution 0: 0: 0: 4.62 TOTAL 0: 0: 0: 5.36 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M57 IBD1M57 IBD2M57 ; DEFINITION IBD0M57 IBD1M57 IBD2M57 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M157 IBD1M57 IBD2M57 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M57 IBD1M57 IBD0M57 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2753 0.4767 0.2480 111.9452 111.5210 Variance 0.1406 0.1196 0.1033 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9995 0.9991 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 157 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9280 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7446 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.4861 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.2431 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7446 0.0000 183.9280 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6726 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6726 PIQ2 91.7446 275.6726 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 4.54 TOTAL 0: 0: 0: 5.27 Total number of warnings issued: 8 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M58 IBD1M58 IBD2M58 ; DEFINITION IBD0M58 IBD1M58 IBD2M58 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M158 IBD1M58 IBD2M58 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M58 IBD1M58 IBD0M58 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2975 0.4600 0.2426 111.9452 111.5210 Variance 0.1646 0.1435 0.1125 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9997 0.9973 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 158 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 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 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9283 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7449 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.0000 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0004 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.0000 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7449 0.0000 183.9283 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6732 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5784 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6732 PIQ2 91.7449 275.6732 Function value of this group: 7203.3503 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 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 4.52 TOTAL 0: 0: 0: 5.25 Total number of warnings issued: 10 ______________________________________________________________________________ #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M59 IBD1M59 IBD2M59 ; DEFINITION IBD0M59 IBD1M59 IBD2M59 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M159 IBD1M59 IBD2M59 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION NDECIMALS=4 OPTION RSIDUALS OPTION SUB=7203.35,853 ! LIKELIHOOD, DF FROM FE MODEL EXIT Summary of VL file data for group 1 IBD2M59 IBD1M59 IBD0M59 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2975 0.4600 0.2426 111.9452 111.5210 Variance 0.1646 0.1435 0.1125 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9997 0.9973 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 159 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 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 Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS GENOTYPED MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9282 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7450 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0100 2 0.0000 3 0.0000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0003 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.0000 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7450 0.0000 183.9282 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6732 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5784 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6732 PIQ2 91.7450 275.6732 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 851 Akaike's Information Criterion >>>> 5501.350 Bayesian Information Criterion >>>> 916.805 Sample size Adjusted BIC >>>> 2267.522 Deviance Information Criterion >>>> 1698.822 Submodel fit* >>>>>>>>>>> 7203.350 Submodel df* >>>>>>>>>>> 853 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 2 Probability incalculable Akaike's Information Criterion > -4.000 * Submodel statistic supplied by user This problem used 0.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.73 Execution 0: 0: 0: 4.23 TOTAL 0: 0: 0: 4.96 Total number of warnings issued: 10 ______________________________________________________________________________ Note: #Loop section ends here ! TEST SIGNIFICANCE OF QTL EFFECT ! DROP L 1 1 1 !EXIT ______________________________________________________________________________