** 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 ______________________________________________________________________________ ______________________________________________________________________________