** Mx startup successful **
**MX-Linux version 1.49**
! The dataset is limited to DZ twin pairs only
!
The following MX script lines were read for group 1
#DEFINE NVAR 1
#DEFINE NVARX2 2
#NGROUPS 1
Note: #NGroup set number of groups to 1
SIMULATED DATA, REAL ALLELE EFFECT
DATA NINPUT=7 ! 7 INPUT VARIABLES
RECTANGULAR FILE=SET1.REC ! READ DATA FROM FILE
NOTE: Rectangular file contained 1000 records with data
LABELS P1 P2 A1S1 A2S1 A1S2 A2S2 TYPE
! aisj is allele i of sibling j
! type is coded: 1: AAAA 2: AAAa 3: AAaa
! 4: AaAA 5: AaAa 6: Aaaa
! 7: aaAA 8: aaAa 9: aaaa
DEFINITION_VARIABLES A1S1 A2S1 A1S2 A2S2 TYPE ;
NOTE: Definition yields 1000 data vectors for analysis
NOTE: Vectors contain a total of 2000 observations
! only p1 and p2 will be analyzed; other variables define the model
BEGIN MATRICES
A LOWER NVARX2 NVARX2 FREE ! ADDITIVE GENETIC INFLUENCES , CHOLESKY
F FULL 2 1 ! A ALLELE COUNT FOR SIB1 (0,1,2)
H FULL 2 1 ! A ALLELE COUNT FOR SIB2
I FULL 1 1 ! TO STORE TYPE
J UNIT 1 1 ! 1.0
K FULL 1 1 ! 2.0
U UNIT 1 2 ! UNIT MATRIX
B FULL 1 1 ! BETA WEIGHT FOR INDIVIDUAL ALLELE COUNT
N FULL 1 1 FREE ! OVERALL MEAN
W FULL 2 1 FREE ! AB AND AW PARAMETERS
V FULL 9 1 !
X FULL 9 1
END MATRICES
MATRIX A 1 0 1
MATRIX I 1
MATRIX K 2
MATRIX V 1 .5 0 .5 0 -.5 0 -.5 -1
MATRIX X 0 .5 1 -.5 0 .5 -1 -.5 0
SPECIFY F A1S1 A2S1
SPECIFY H A1S2 A2S2
SPECIFY I TYPE
BOUND -5 5 B 1 1
BOUND -5 5 N 1 1
BEGIN ALGEBRA;
E = I|J|I|K ; ! TO SELECT ROW OF V|X
Z = \PART((V|X),E)*W | \PART((V|-X),E)*W ; ! SELECTS ROW OF V|X AND V|-X
END ALGEBRA;
MEANS (N + (B@U)*F | N + (B@U)*H) + Z;
COVARIANCE A*A' ;
OPTION ND=4 ! REQUEST 4 DECIMAL PLACES IN OUTPUT
OPTION RS MULTIPLE ! REQUEST RESIDUALS, MULTIPLE FIT
OPTION ISSAT ! THIS IS SATURATED MODEL FOR SUBMODEL COMPARISON
END
Summary of VL file data for group 1
TYPE A2S2 A1S2 A2S1 A1S1 P1 P2
Code -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 1.0000 2.0000
Number 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000
Mean 4.9580 .5030 .4940 .4970 .4900 -.0415 -.1730
Variance 6.6962 .2500 .2500 .2500 .2499 2.7999 2.7401
Minimum 1.0000 .0000 .0000 .0000 .0000 -5.3776 -6.5806
Maximum 9.0000 1.0000 1.0000 1.0000 1.0000 4.8277 5.6065
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
Simulated data, real allele effect
MATRIX A
This is a LOWER TRIANGULAR matrix of order 2 by 2
1 2
1 1
2 2 3
MATRIX B
This is a 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 4
It has no free parameters specified
MATRIX F
This is a FULL matrix of order 2 by 1
1
1 -1
2 -2
MATRIX H
This is a FULL matrix of order 2 by 1
1
1 -3
2 -4
MATRIX I
This is a FULL matrix of order 1 by 1
1
1 -5
MATRIX J
This is a UNIT matrix of order 1 by 1
MATRIX K
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 1
1
1 4
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a FULL matrix of order 9 by 1
It has no free parameters specified
MATRIX W
This is a FULL matrix of order 2 by 1
1
1 5
2 6
MATRIX X
This is a FULL matrix of order 9 by 1
It has no free parameters specified
MATRIX Z
This is a computed FULL matrix of order 1 by 2
It has no free parameters specified
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
Simulated data, real allele effect
MATRIX A
This is a LOWER TRIANGULAR matrix of order 2 by 2
1 2
1 1.6065
2 .5359 1.5306
MATRIX B
This is a FULL matrix of order 1 by 1
1
1 .0000
MATRIX E
This is a computed FULL matrix of order 1 by 4
[=I|J|I|K]
1 2 3 4
1 4.0000 1.0000 4.0000 2.0000
MATRIX F
This is a FULL matrix of order 2 by 1
1
1 .0000
2 1.0000
MATRIX H
This is a FULL matrix of order 2 by 1
1
1 .0000
2 .0000
MATRIX I
This is a FULL matrix of order 1 by 1
1
1 4.0000
MATRIX J
This is a UNIT matrix of order 1 by 1
MATRIX K
This is a FULL matrix of order 1 by 1
1
1 2.0000
MATRIX N
This is a FULL matrix of order 1 by 1
1
1 -.1112
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a FULL matrix of order 9 by 1
1
1 1.0000
2 .5000
3 .0000
4 .5000
5 .0000
6 -.5000
7 .0000
8 -.5000
9 -1.0000
MATRIX W
This is a FULL matrix of order 2 by 1
1
1 .6090
2 .4403
MATRIX X
This is a FULL matrix of order 9 by 1
1
1 .0000
2 .5000
3 1.0000
4 -.5000
5 .0000
6 .5000
7 -1.0000
8 -.5000
9 .0000
MATRIX Z
This is a computed FULL matrix of order 1 by 2
[=\PART((V|X),E)*W|\PART((V|-X),E)*W]
1 2
1 .0843 .5246
Vector of OBSERVED means
P1 P2
Mean -.0415 -.1730
Vector of EXPECTED means
P1 P2
Mean -.0269 .4134
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
P1 P2
P1 2.5807
P2 .8609 2.6300
Function value of this group: 7475.1831
Where the fit function is -2 * Log-likelihood of raw data
Your model has 6 estimated parameters and 2000 Observed statistics
-2 times log-likelihood of data >>> 7475.183
Degrees of freedom >>>>>>>>>>>>>>>> 1994
This problem used .9% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.08
Execution 0: 0: 0:22.35
TOTAL 0: 0: 0:24.43
Total number of warnings issued: 0
______________________________________________________________________________
Multiple fit option in effect.
The following MX script lines have been read:
SAVE SET1.MXS
EQUATE W 1 1 1 W 1 2 1
END
Summary of VL file data for group 1
TYPE A2S2 A1S2 A2S1 A1S1 P1 P2
Code -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 1.0000 2.0000
Number 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000
Mean 4.9580 .5030 .4940 .4970 .4900 -.0415 -.1730
Variance 6.6962 .2500 .2500 .2500 .2499 2.7999 2.7401
Minimum 1.0000 .0000 .0000 .0000 .0000 -5.3776 -6.5806
Maximum 9.0000 1.0000 1.0000 1.0000 1.0000 4.8277 5.6065
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
Simulated data, real allele effect
MATRIX A
This is a LOWER TRIANGULAR matrix of order 2 by 2
1 2
1 1
2 2 3
MATRIX B
This is a 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 4
It has no free parameters specified
MATRIX F
This is a FULL matrix of order 2 by 1
1
1 -1
2 -2
MATRIX H
This is a FULL matrix of order 2 by 1
1
1 -3
2 -4
MATRIX I
This is a FULL matrix of order 1 by 1
1
1 -5
MATRIX J
This is a UNIT matrix of order 1 by 1
MATRIX K
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 1
1
1 4
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a FULL matrix of order 9 by 1
It has no free parameters specified
MATRIX W
This is a FULL matrix of order 2 by 1
1
1 5
2 5
MATRIX X
This is a FULL matrix of order 9 by 1
It has no free parameters specified
MATRIX Z
This is a computed FULL matrix of order 1 by 2
It has no free parameters specified
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
Simulated data, real allele effect
MATRIX A
This is a LOWER TRIANGULAR matrix of order 2 by 2
1 2
1 1.6073
2 .5357 1.5317
MATRIX B
This is a FULL matrix of order 1 by 1
1
1 .0000
MATRIX E
This is a computed FULL matrix of order 1 by 4
[=I|J|I|K]
1 2 3 4
1 4.0000 1.0000 4.0000 2.0000
MATRIX F
This is a FULL matrix of order 2 by 1
1
1 .0000
2 1.0000
MATRIX H
This is a FULL matrix of order 2 by 1
1
1 .0000
2 .0000
MATRIX I
This is a FULL matrix of order 1 by 1
1
1 4.0000
MATRIX J
This is a UNIT matrix of order 1 by 1
MATRIX K
This is a FULL matrix of order 1 by 1
1
1 2.0000
MATRIX N
This is a FULL matrix of order 1 by 1
1
1 -.1107
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a FULL matrix of order 9 by 1
1
1 1.0000
2 .5000
3 .0000
4 .5000
5 .0000
6 -.5000
7 .0000
8 -.5000
9 -1.0000
MATRIX W
This is a FULL matrix of order 2 by 1
1
1 .5453
2 .5453
MATRIX X
This is a FULL matrix of order 9 by 1
1
1 .0000
2 .5000
3 1.0000
4 -.5000
5 .0000
6 .5000
7 -1.0000
8 -.5000
9 .0000
MATRIX Z
This is a computed FULL matrix of order 1 by 2
[=\PART((V|X),E)*W|\PART((V|-X),E)*W]
1 2
1 .0000 .5453
Vector of OBSERVED means
P1 P2
Mean -.0415 -.1730
Vector of EXPECTED means
P1 P2
Mean -.1107 .4346
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
P1 P2
P1 2.5835
P2 .8611 2.6330
Function value of this group: 7477.6276
Where the fit function is -2 * Log-likelihood of raw data
Your model has 5 estimated parameters and 2000 Observed statistics
-2 times log-likelihood of data >>> 7477.628
Degrees of freedom >>>>>>>>>>>>>>>> 1995
Saturated model fit* >>>>>>>>>>> 7475.183
Saturated model df* >>>>>>>>>>> 1994
Difference Chi-squared >>>>>>>> 2.445
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> .118
Akaike's Information Criterion > .445
* Saturated model statistic computed earlier in this job
This problem used .9% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: .65
Execution 0: 0: 0:13.58
TOTAL 0: 0: 0:14.23
Total number of warnings issued: 0
______________________________________________________________________________
Multiple fit option in effect.
The following MX script lines have been read:
DROP W 1 1 1
END
Summary of VL file data for group 1
TYPE A2S2 A1S2 A2S1 A1S1 P1 P2
Code -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 1.0000 2.0000
Number 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000
Mean 4.9580 .5030 .4940 .4970 .4900 -.0415 -.1730
Variance 6.6962 .2500 .2500 .2500 .2499 2.7999 2.7401
Minimum 1.0000 .0000 .0000 .0000 .0000 -5.3776 -6.5806
Maximum 9.0000 1.0000 1.0000 1.0000 1.0000 4.8277 5.6065
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
Simulated data, real allele effect
MATRIX A
This is a LOWER TRIANGULAR matrix of order 2 by 2
1 2
1 1
2 2 3
MATRIX B
This is a 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 4
It has no free parameters specified
MATRIX F
This is a FULL matrix of order 2 by 1
1
1 -1
2 -2
MATRIX H
This is a FULL matrix of order 2 by 1
1
1 -3
2 -4
MATRIX I
This is a FULL matrix of order 1 by 1
1
1 -5
MATRIX J
This is a UNIT matrix of order 1 by 1
MATRIX K
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 1
1
1 4
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a FULL matrix of order 9 by 1
It has no free parameters specified
MATRIX W
This is a FULL matrix of order 2 by 1
It has no free parameters specified
MATRIX X
This is a FULL matrix of order 9 by 1
It has no free parameters specified
MATRIX Z
This is a computed FULL matrix of order 1 by 2
It has no free parameters specified
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
Simulated data, real allele effect
MATRIX A
This is a LOWER TRIANGULAR matrix of order 2 by 2
1 2
1 1.6746
2 .5872 1.5490
MATRIX B
This is a FULL matrix of order 1 by 1
1
1 .0000
MATRIX E
This is a computed FULL matrix of order 1 by 4
[=I|J|I|K]
1 2 3 4
1 4.0000 1.0000 4.0000 2.0000
MATRIX F
This is a FULL matrix of order 2 by 1
1
1 .0000
2 1.0000
MATRIX H
This is a FULL matrix of order 2 by 1
1
1 .0000
2 .0000
MATRIX I
This is a FULL matrix of order 1 by 1
1
1 4.0000
MATRIX J
This is a UNIT matrix of order 1 by 1
MATRIX K
This is a FULL matrix of order 1 by 1
1
1 2.0000
MATRIX N
This is a FULL matrix of order 1 by 1
1
1 -.1084
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a FULL matrix of order 9 by 1
1
1 1.0000
2 .5000
3 .0000
4 .5000
5 .0000
6 -.5000
7 .0000
8 -.5000
9 -1.0000
MATRIX W
This is a FULL matrix of order 2 by 1
1
1 .0000
2 .0000
MATRIX X
This is a FULL matrix of order 9 by 1
1
1 .0000
2 .5000
3 1.0000
4 -.5000
5 .0000
6 .5000
7 -1.0000
8 -.5000
9 .0000
MATRIX Z
This is a computed FULL matrix of order 1 by 2
[=\PART((V|X),E)*W|\PART((V|-X),E)*W]
1 2
1 .0000 .0000
Vector of OBSERVED means
P1 P2
Mean -.0415 -.1730
Vector of EXPECTED means
P1 P2
Mean -.1084 -.1084
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
P1 P2
P1 2.8044
P2 .9834 2.7442
Function value of this group: 7582.1661
Where the fit function is -2 * Log-likelihood of raw data
Your model has 4 estimated parameters and 2000 Observed statistics
-2 times log-likelihood of data >>> 7582.166
Degrees of freedom >>>>>>>>>>>>>>>> 1996
Saturated model fit* >>>>>>>>>>> 7475.183
Saturated model df* >>>>>>>>>>> 1994
Difference Chi-squared >>>>>>>> 106.983
Difference d.f. >>>>>>>>>>>>>>> 2
Probability >>>>>>>>>>>>>>>>>>>> .000
Akaike's Information Criterion > 102.983
* Saturated model statistic computed earlier in this job
This problem used .9% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: .00
Execution 0: 0: 0: 8.48
TOTAL 0: 0: 0: 8.48
Total number of warnings issued: 0
______________________________________________________________________________
______________________________________________________________________________