** 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 ______________________________________________________________________________ ______________________________________________________________________________