! Boulder 2003 ! univariate Mx script for the analysis of one continuous phenotype ! using raw data input file ! MZ en DZ twins ! Evaluated models: ACE, AE, CE, E ! Mx homepage: http://views.vcu.edu/mx 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 TWONVAR 2 ! TWICE NVAR FOR DEFINING THE MEAN G1: CALCULATION GROUP DATA CALC NGROUPS=3 BEGIN MATRICES; X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENT / FACTOR LOADING Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENT / FACTOR LOADING Z LOWER NVAR NVAR FREE ! UNIQUE ENVIRONMENTAL PATH COEFFICIENT / FACTOR LOADING H FULL 1 1 FIX ! .5 FOR DZ COV A END MATRICES; MATRIX H .5 ! 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 V = A%(A+C+E) | C%(A+C+E) | E%(A+C+E) ; !STANDARDIZED VARIANCE COMPONENTS END ALGEBRA; START 1.5 X 1 1 1 ! PROVIDE STARTING VALUES START 1.5 Y 1 1 1 START 1.5 Z 1 1 1 END The following MX script lines were read for group 2 G2: MZ TWINS, DATAGROUP DATA NINPUT_VARS= 14 ! NR OF INPUTVARS PER FAMILY MISSING=-1.00 ! MISSING VALUES = -1.00 NOTE: Missing value *string* set to '-1.00' RECTANGULAR FILE=ALL.DAT ! READ IN RAW DATAFILE, MUST BE IN SAME DIRECTORY Rectangular continuous data read initiated NOTE: Rectangular file contained 2028 records with data that contained a total of 27296 observations LABELS ! TELL MX WHAT IS FOUND IN THE DATAFILE NIH_ID COUNTRY ZYGOT6 REAR AGEA SEXA LDLLNA APOBLNA APOELNA AGEB SEXB LDLLNB APOBLNB APOELNB SELECT IF COUNTRY = 1 ; ! SELECT DUTCH TWINS, YOUNGER SAMPLE (DORRET) NOTE: Select if yields 160 data vectors for analysis NOTE: Vectors contain a total of 2236 observations SELECT IF ZYGOT6 = 3 ; ! SELECT MZM'S NOTE: Select if yields 35 data vectors for analysis NOTE: Vectors contain a total of 490 observations SELECT LDLLNA LDLLNB ; !SELECT ONE PHENOTYPE PER TWIN MEMBER MATRICES = GROUP 1 NOTE: Selection yields 35 data vectors for analysis NOTE: Vectors contain a total of 70 observations M FULL NVAR TWONVAR FREE !MATRIX FOR THE MEANS END MATRICES; MEANS M ; ! MODEL FOR MEANS COVARIANCES ! MODEL FOR MZ VARIANCE/COVARIANCES A+C+E | A+C _ A+C | A+C+E ; ST 15 M 1 1 - M NVAR TWONVAR OPTIONS RSIDUALS END The following MX script lines were read for group 3 G3: DZ TWINS, DATAGROUP DATA NINPUT_VARS= 14 ! NR OF INPUTVARS PER FAMILY MISSING=-1.00 ! MISSING VALUES = -1.00 NOTE: Missing value *string* set to '-1.00' RECTANGULAR FILE=ALL.DAT ! READ IN RAW DATAFILE, MUST BE IN SAME DIRECTORY Rectangular continuous data read initiated NOTE: Rectangular file contained 2028 records with data that contained a total of 27296 observations LABELS ! TELL MX WHAT IS FOUND IN THE DATAFILE NIH_ID COUNTRY ZYGOT6 REAR AGEA SEXA LDLLNA APOBLNA APOELNA AGEB SEXB LDLLNB APOBLNB APOELNB SELECT IF COUNTRY = 1 ; ! SELECT DUTCH TWINS, YOUNGER SAMPLE (DORRET) NOTE: Select if yields 160 data vectors for analysis NOTE: Vectors contain a total of 2236 observations SELECT IF ZYGOT6 = 4; ! SELECT DZM'S NOTE: Select if yields 30 data vectors for analysis NOTE: Vectors contain a total of 420 observations SELECT LDLLNA LDLLNB ; ! SELECT ONE PHENOTYPE PER TWIN MEMBER MATRICES = GROUP 1 NOTE: Selection yields 30 data vectors for analysis NOTE: Vectors contain a total of 60 observations M FULL NVAR TWONVAR FREE !MATRIX FOR THE MEANS END MATRICES; MEANS M; ! MODEL FOR MEANS COVARIANCES ! MODEL FOR DZ VARIANCE/COVARIANCES A+C+E | H@A+C _ H@A+C | A+C+E ; OPTIONS RSIDUALS ! Option Multiple OPTION SAT=600.043, 120 ! -2LL OF SATURATED MODEL, WILL YIELD CHI SQUARE FOR THIS MODEL ! ALLOWS COMPARISON OF SUBMODELS WITH PRESENT MODEL (ACE) ! Interval @95 V 1 1 1 V 1 1 2 V 1 1 3 END Summary of VL file data for group 2 LDLLNA LDLLNB Code 1.0000 2.0000 Number 35.0000 35.0000 Mean 20.5186 20.2783 Variance 6.6600 7.4321 Minimum 16.1000 12.4700 Maximum 25.3000 24.9500 Summary of VL file data for group 3 LDLLNA LDLLNB Code 1.0000 2.0000 Number 30.0000 30.0000 Mean 19.8897 18.9287 Variance 8.5730 10.8826 Minimum 12.9300 9.9000 Maximum 24.9300 23.8900 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 H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX V 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 H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 4 5 MATRIX V 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 H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 6 7 MATRIX V 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 Mx starting optimization; number of parameters = 7 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 5.3328 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 1.4834 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 1.6578 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX V 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 0.6293 0.1751 0.1956 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -2.3093 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.2179 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.2875 GROUP NUMBER: 2 G2: MZ twins, datagroup MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 5.3328 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 1.4834 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 1.6578 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 20.5186 20.2783 MATRIX V 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 0.6293 0.1751 0.1956 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -2.3093 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.2179 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.2875 Vector of OBSERVED means LDLLNA LDLLNB Mean 20.5186 20.2783 Vector of EXPECTED means LDLLNA LDLLNB Mean 20.5186 20.2783 EXPECTED COVARIANCE MATRIX LDLLNA LDLLNB LDLLNA 8.4739 LDLLNB 6.8162 8.4739 Function value of this group: 304.6332 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 5.3328 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 1.4834 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 1.6578 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 19.8897 18.9287 MATRIX V 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 0.6293 0.1751 0.1956 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -2.3093 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.2179 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1.2875 Vector of OBSERVED means LDLLNA LDLLNB Mean 19.8897 18.9287 Vector of EXPECTED means LDLLNA LDLLNB Mean 19.8897 18.9287 EXPECTED COVARIANCE MATRIX LDLLNA LDLLNB LDLLNA 8.4739 LDLLNB 4.1498 8.4739 Function value of this group: 297.4272 Where the fit function is -2 * Log-likelihood of raw data Your model has 7 estimated parameters and 130 Observed statistics -2 times log-likelihood of data >>> 602.060 Degrees of freedom >>>>>>>>>>>>>>>> 123 Saturated model fit* >>>>>>>>>>> 600.043 Saturated model df* >>>>>>>>>>> 120 Difference Chi-squared >>>>>>>> 2.017 Difference d.f. >>>>>>>>>>>>>>> 3 Probability >>>>>>>>>>>>>>>>>>>> 0.569 Akaike's Information Criterion > -3.983 * Saturated model statistic supplied by user This problem used 1.5% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0:19.77 Execution 0: 0: 0:***** TOTAL 0: 0: 0: 0.41 Total number of warnings issued: 0 ______________________________________________________________________________ !Save ACE.mxs ! AE model !Drop Y 1 1 1 !end !get ace.mxs !CE model !Drop X 1 1 1 !end ! E model !Drop X 1 1 1 !Drop Y 1 1 1 !end