** Mx startup successful **
**MX-OSF version 1.47c**
! Script to estimate haplotype frequencies
The following MX script lines were read for group 1
#NGROUPS 2
Note: #NGroup set number of groups to 2
TITLE ESTIMATE FREQS
DATA NI=1
BEGIN MATRICES;
I UNIT 1 1
T FULL 1 1
W FULL 3 4
O FULL 3 3 ! OBSERVED GENOTYPE FREQS
P FULL 1 1 FREE ! ALLELE FREQS, LOCUS 1
R FULL 1 1 FREE ! ALLELE FREQS, LOCUS 2
! H full 2 2 free ! haplotype freqs
END MATRICES;
MATRIX O ! OBSERVED FREQS
10 15 5
10 50 13
3 13 10
MATRIX T 2
MATRIX W
1 0 0 0
0 1 1 0
0 0 0 1
MATRIX P .5
MATRIX R .5
BOUND 0 1 P 1 1 R 1 1
BEGIN ALGEBRA;
Q = I-P;
S = I-R;
H = (P_Q)*(R|S);
A = H@H;
E = W&A;
END ALGEBRA;
COMPUTE -T. \SUM(O.\LN(E));
OPTION USER
END GROUP
The following MX script lines were read for group 2
CONSTRAIN HAPLOTYPE FREQS TO SUM TO 1
CONSTRAINT
BEGIN MATRICES = GROUP 1;
END MATRICES;
CONSTRAIN I=\SUM(H);
OPTION RS
END GROUP;
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
Title estimate freqs
MATRIX A
This is a computed FULL matrix of order 4 by 4
It has no free parameters specified
MATRIX E
This is a computed FULL matrix of order 3 by 3
It has no free parameters specified
MATRIX H
This is a computed FULL matrix of order 2 by 2
It has no free parameters specified
MATRIX I
This is a UNIT matrix of order 1 by 1
MATRIX O
This is a FULL matrix of order 3 by 3
It has no free parameters specified
MATRIX P
This is a FULL matrix of order 1 by 1
1
1 1
MATRIX Q
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX R
This is a FULL matrix of order 1 by 1
1
1 2
MATRIX S
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX T
This is a FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX W
This is a FULL matrix of order 3 by 4
It has no free parameters specified
GROUP NUMBER: 2
Constrain haplotype freqs to sum to 1
MATRIX A
This is a computed FULL matrix of order 4 by 4
It has no free parameters specified
MATRIX E
This is a computed FULL matrix of order 3 by 3
It has no free parameters specified
MATRIX H
This is a computed FULL matrix of order 2 by 2
It has no free parameters specified
MATRIX I
This is a UNIT matrix of order 1 by 1
MATRIX O
This is a FULL matrix of order 3 by 3
It has no free parameters specified
MATRIX P
This is a FULL matrix of order 1 by 1
1
1 1
MATRIX Q
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX R
This is a FULL matrix of order 1 by 1
1
1 2
MATRIX S
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX T
This is a FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX W
This is a FULL matrix of order 3 by 4
It has no free parameters specified
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
Title estimate freqs
MATRIX A
This is a computed FULL matrix of order 4 by 4
[=H@H]
1 2 3 4
1 0.0614 0.0663 0.0663 0.0717
2 0.0577 0.0623 0.0623 0.0674
3 0.0577 0.0623 0.0623 0.0674
4 0.0542 0.0586 0.0586 0.0633
MATRIX E
This is a computed FULL matrix of order 3 by 3
[=W&A]
1 2 3
1 0.0614 0.1327 0.0717
2 0.1154 0.2494 0.1347
3 0.0542 0.1172 0.0633
MATRIX H
This is a computed FULL matrix of order 2 by 2
[=(P_Q)*(R|S)]
1 2
1 0.2478 0.2677
2 0.2329 0.2516
MATRIX I
This is a UNIT matrix of order 1 by 1
MATRIX O
This is a FULL matrix of order 3 by 3
1 2 3
1 10.0000 15.0000 5.0000
2 10.0000 50.0000 13.0000
3 3.0000 13.0000 10.0000
MATRIX P
This is a FULL matrix of order 1 by 1
1
1 0.5155
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=I-P]
1
1 0.4845
MATRIX R
This is a FULL matrix of order 1 by 1
1
1 0.4806
MATRIX S
This is a computed FULL matrix of order 1 by 1
[=I-R]
1
1 0.5194
MATRIX T
This is a FULL matrix of order 1 by 1
1
1 2.0000
MATRIX W
This is a FULL matrix of order 3 by 4
1 2 3 4
1 1.0000 0.0000 0.0000 0.0000
2 0.0000 1.0000 1.0000 0.0000
3 0.0000 0.0000 0.0000 1.0000
GROUP NUMBER: 2
Constrain haplotype freqs to sum to 1
MATRIX A
This is a computed FULL matrix of order 4 by 4
[=H@H]
1 2 3 4
1 0.0614 0.0663 0.0663 0.0717
2 0.0577 0.0623 0.0623 0.0674
3 0.0577 0.0623 0.0623 0.0674
4 0.0542 0.0586 0.0586 0.0633
MATRIX E
This is a computed FULL matrix of order 3 by 3
[=W&A]
1 2 3
1 0.0614 0.1327 0.0717
2 0.1154 0.2494 0.1347
3 0.0542 0.1172 0.0633
MATRIX H
This is a computed FULL matrix of order 2 by 2
[=(P_Q)*(R|S)]
1 2
1 0.2478 0.2677
2 0.2329 0.2516
MATRIX I
This is a UNIT matrix of order 1 by 1
MATRIX O
This is a FULL matrix of order 3 by 3
1 2 3
1 10.0000 15.0000 5.0000
2 10.0000 50.0000 13.0000
3 3.0000 13.0000 10.0000
MATRIX P
This is a FULL matrix of order 1 by 1
1
1 0.5155
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=I-P]
1
1 0.4845
MATRIX R
This is a FULL matrix of order 1 by 1
1
1 0.4806
MATRIX S
This is a computed FULL matrix of order 1 by 1
[=I-R]
1
1 0.5194
MATRIX T
This is a FULL matrix of order 1 by 1
1
1 2.0000
MATRIX W
This is a FULL matrix of order 3 by 4
1 2 3 4
1 1.0000 0.0000 0.0000 0.0000
2 0.0000 1.0000 1.0000 0.0000
3 0.0000 0.0000 0.0000 1.0000
CONSTRAINT VALUES (should be near zero)
1
1 0.0000
Your model has 2 estimated parameters and 1 Observed statistics
Observed statistics include 1 constraints.
User defined function value = 505.362
'Degrees of freedom' >>>>>>>>>>>>>>>> -1
This problem used 0.1% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.01
Execution 0: 0: 0: 0.02
TOTAL 0: 0: 0: 0.02
Total number of warnings issued: 0
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