** Mx startup successful **
**MX-OSF version 1.49**
! 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
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
BEGIN ALGEBRA;
A = H@H;
E = W&A;
END ALGEBRA;
MATRIX H .25 .25 .25 .25
BOUND 0 1 H 1 1 TO H 2 2
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
*** WARNING! ***
End of input file but End statement missing!
End statement automatically added...
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 FULL matrix of order 2 by 2
1 2
1 1 2
2 3 4
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 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 FULL matrix of order 2 by 2
1 2
1 1 2
2 3 4
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 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 0.1074 0.0615 0.0615 0.0353
2 0.0501 0.1087 0.0287 0.0623
3 0.0501 0.0287 0.1087 0.0623
4 0.0234 0.0507 0.0507 0.1099
MATRIX E
This is a computed FULL matrix of order 3 by 3
[=W&A]
1 2 3
1 0.1074 0.1231 0.0353
2 0.1002 0.2748 0.1245
3 0.0234 0.1014 0.1099
MATRIX H
This is a FULL matrix of order 2 by 2
1 2
1 0.3277 0.1878
2 0.1529 0.3316
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 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 0.1074 0.0615 0.0615 0.0353
2 0.0501 0.1087 0.0287 0.0623
3 0.0501 0.0287 0.1087 0.0623
4 0.0234 0.0507 0.0507 0.1099
MATRIX E
This is a computed FULL matrix of order 3 by 3
[=W&A]
1 2 3
1 0.1074 0.1231 0.0353
2 0.1002 0.2748 0.1245
3 0.0234 0.1014 0.1099
MATRIX H
This is a FULL matrix of order 2 by 2
1 2
1 0.3277 0.1878
2 0.1529 0.3316
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 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 -3.5226E-06
Your model has 4 estimated parameters and 1 Observed statistics
Observed statistics include 1 constraints.
User defined function value = 496.469
'Degrees of freedom' >>>>>>>>>>>>>>>> -3
This problem used 0.0% 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: 0.03
Total number of warnings issued: 1
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