** Mx startup successful ** **MX-PC 1.57a** Job started on 03/08/05 at 08:38:51 ! SCRIPT NAME : example_ace.mx (dp) ! GOAL : To calculate variance components ! DATA : continuous ! INPUT : raw data ! UNI/BI/MULTI : uni ! DATA-GROUPS : MZM DZM MZF DZF DOSMF DOSFM ! MEANS MODEL : grand mean, sex effect !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! The following MX script lines were read for group 1 #DEFINE NVAR 1 ! MX READS 1. THIS CORRESPONDS TO ONE PHENOTYPE TO BE ANALYSED #DEFINE NDEF 1 ! NUMBER OF COVARIATES (AGE AND SEX IN THIS SCRIPT) #DEFINE NSIB 2 !TELLS MX THE SIZE OF THE LARGEST SIBSHIP G1: CALCULATION GROUP DATA CALC NGROUPS=3 BEGIN MATRICES; X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENT (STANDARD DEVIATION) Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENT (STANDARD DEVIATION) Z LOWER NVAR NVAR FREE ! UNIQUE ENVIRONMENTAL PATH COEFFICIENT (STANDARD DEVIATION) H FULL 1 1 FIX ! .5 FOR DZ COV A Q FULL 1 1 FIX ! FOR DZ COV IF ESTIMATING C Q=1 IF ESTIMATING D Q=.25 G FULL 1 NSIB FREE ! GRAND MEAN PHENOTYPES P FULL NDEF NVAR FREE ! ESTIMATED EFFECTS OF THE COVARIATES (SEX AGE) END MATRICES; MATRIX H .5 ! MATRIX H IS FIXED AND CONTAINS .5 MATRIX Q 1 ! MATRIX H IS FIXED AND CONTAINS .5 BEGIN ALGEBRA; A= X*X' ; ! ADDITIVE GENETIC VARIANCE C= Y*Y' ; ! COMMON ENVIRONMENTAL VARIANCE E= Z*Z' ; ! UNIQUE ENVIRONMENTAL VARIANCE S = A%(A+C+E) | C%(A+C+E) | E%(A+C+E) ; !STANDARDIZED VARIANCE COMPONENTS END ALGEBRA; ST 6 X 1 1 1 ! PROVIDE STARTING VALUES ST 2 Y 1 1 1 ST 2 Z 1 1 1 ST .2 G 1 1 G 1 2 END The following MX script lines were read for group 2 G2: MZ TWINS, DATAGROUP DATA NINPUT_VARS= 7 MISSING=-9.00 NOTE: Missing value *string* set to '-9.00 ' RECTANGULAR FILE=SIMULATED.DAT Rectangular continuous data read initiated NOTE: Rectangular file contained 250 records with data that contained a total of 1750 observations LABELS ZYG SEX1 SEX2 SEX3 TWIN1 TWIN2 SIB1 SELECT IF ZYG = 1 ; ! SELECT MZ NOTE: Select if yields 100 data vectors for analysis NOTE: Vectors contain a total of 700 observations SELECT SEX1 SEX2 TWIN1 TWIN2 ; DEFINITION SEX1 SEX2 ; NOTE: Selection yields 100 data vectors for analysis NOTE: Vectors contain a total of 400 observations NOTE: Definition yields 100 data vectors for analysis NOTE: Vectors contain a total of 200 observations MATRICES = GROUP 1 Note: definition makes highest ordinal variable category 2 N FULL NDEF NSIB FIX ! OBSERVED COVARIATES END MATRICES; SPECIFY N SEX1 SEX2 MEANS G+(N@P) ; ! MODEL FOR MEANS COVARIANCES ! MODEL FOR MZ VARIANCE/COVARIANCES A+C+E | A+C _ A+C | A+C+E ; OPTIONS RSIDUALS END The following MX script lines were read for group 3 G3: DZ TWINS, DATAGROUP DATA NINPUT_VARS= 7 MISSING=-9.00 NOTE: Missing value *string* set to '-9.00 ' RECTANGULAR FILE=SIMULATED.DAT Rectangular continuous data read initiated NOTE: Rectangular file contained 250 records with data that contained a total of 1750 observations LABELS ZYG SEX1 SEX2 SEX3 TWIN1 TWIN2 SIB1 SELECT IF ZYG = 2 ; ! SELECT MZ NOTE: Select if yields 150 data vectors for analysis NOTE: Vectors contain a total of 1050 observations SELECT SEX1 SEX2 TWIN1 TWIN2 ; DEFINITION SEX1 SEX2 ; NOTE: Selection yields 150 data vectors for analysis NOTE: Vectors contain a total of 600 observations Note: Global variable previously defined. Updating SEX1 Note: Global variable previously defined. Updating SEX2 NOTE: Definition yields 150 data vectors for analysis NOTE: Vectors contain a total of 300 observations MATRICES = GROUP 1 Note: definition makes highest ordinal variable category 2 N FULL NDEF NSIB FIX ! OBSERVED COVARIATES END MATRICES; SPECIFY N SEX1 SEX2 MEANS G+(N@P) ; ! MODEL FOR MEANS COVARIANCES ! MODEL FOR MZ VARIANCE/COVARIANCES A+C+E | H@A+C _ H@A+C | A+C+E ; OPTION MULTI JIGGLE ISSAT ! Interval @95 U 1 1 1 U 1 1 2 U 1 1 3 END Summary of VL file data for group 2 SEX2 SEX1 TWIN1 TWIN2 Code -2.0000 -1.0000 1.0000 2.0000 Number 100.0000 100.0000 100.0000 100.0000 Mean 0.5000 0.5000 0.4696 0.5929 Variance 0.2500 0.2500 10.0539 7.6557 Minimum 0.0000 0.0000 -8.6900 -6.5100 Maximum 1.0000 1.0000 5.9600 7.1800 Summary of VL file data for group 3 SEX2 SEX1 TWIN1 TWIN2 Code -2.0000 -1.0000 1.0000 2.0000 Number 150.0000 150.0000 150.0000 150.0000 Mean 0.5267 0.4933 0.2276 -0.0323 Variance 0.2493 0.2500 9.0769 8.6139 Minimum 0.0000 0.0000 -10.1800 -5.9100 Maximum 1.0000 1.0000 7.4500 7.6300 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: calculation group MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 2 1 2 1 4 5 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX P This is a FULL matrix of order 1 by 1 1 1 6 MATRIX Q This is a 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 X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins, datagroup MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 2 1 2 1 4 5 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX N This is a FULL matrix of order 1 by 2 1 2 1 -1 -2 MATRIX P This is a FULL matrix of order 1 by 1 1 1 6 MATRIX Q This is a 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 X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: DZ twins, datagroup MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 2 1 2 1 4 5 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX N This is a FULL matrix of order 1 by 2 1 2 1 -1 -2 MATRIX P This is a FULL matrix of order 1 by 1 1 1 6 MATRIX Q This is a 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 X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Jiggling parameter estimates... Mx starting optimization; number of parameters = 6 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: calculation group MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 4.9765 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 2.2310 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 1.6885 MATRIX G This is a FULL matrix of order 1 by 2 1 2 1 0.2115 0.1888 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX P This is a FULL matrix of order 1 by 1 1 1 0.1063 MATRIX Q This is a FULL matrix of order 1 by 1 1 1 1.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=A%(A+C+E)|C%(A+C+E)|E%(A+C+E)] 1 2 3 1 0.5594 0.2508 0.1898 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2.2308 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.4937 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -1.2994 GROUP NUMBER: 2 G2: MZ twins, datagroup MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 4.9765 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 2.2310 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 1.6885 MATRIX G This is a FULL matrix of order 1 by 2 1 2 1 0.2115 0.1888 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX N This is a FULL matrix of order 1 by 2 1 2 1 1.0000 1.0000 MATRIX P This is a FULL matrix of order 1 by 1 1 1 0.1063 MATRIX Q This is a FULL matrix of order 1 by 1 1 1 1.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=A%(A+C+E)|C%(A+C+E)|E%(A+C+E)] 1 2 3 1 0.5594 0.2508 0.1898 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2.2308 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.4937 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -1.2994 Vector of OBSERVED means TWIN1 TWIN2 Mean 0.4696 0.5929 Vector of EXPECTED means TWIN1 TWIN2 Mean 0.3178 0.2951 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX TWIN1 TWIN2 TWIN1 8.8960 TWIN2 7.2075 8.8960 Function value of this group: 899.0534 Where the fit function is -2 * Log-likelihood of raw data GROUP NUMBER: 3 G3: DZ twins, datagroup MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 4.9765 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 2.2310 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 1.6885 MATRIX G This is a FULL matrix of order 1 by 2 1 2 1 0.2115 0.1888 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX N This is a FULL matrix of order 1 by 2 1 2 1 1.0000 1.0000 MATRIX P This is a FULL matrix of order 1 by 1 1 1 0.1063 MATRIX Q This is a FULL matrix of order 1 by 1 1 1 1.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=A%(A+C+E)|C%(A+C+E)|E%(A+C+E)] 1 2 3 1 0.5594 0.2508 0.1898 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2.2308 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.4937 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -1.2994 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 6 estimated parameters and 500 Observed statistics -2 times log-likelihood of data >>> 2355.338 Degrees of freedom >>>>>>>>>>>>>>>> 494 This problem used 4.9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0:16.64 Execution 0: 0: 0:***** TOTAL 0: 0: 0: 3.73 Total number of warnings issued: 2 ______________________________________________________________________________