** Mx startup successful **
  
   **MX-OSF version 1.50c**
 ! 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
 P FULL 3 3 FREE ! EXPECTED PROPORTIONS
 O FULL 3 3 ! OBSERVED GENOTYPE FREQS
 T FULL 1 1
 END MATRICES;
 MATRIX O ! OBSERVED FREQS
 10 15 5
 10 50 13
 3 13 10
 START .111 ALL
 MATRIX T 2
 BEGIN ALGEBRA;
 END ALGEBRA;
 BOUND 0 1 P 1 1 TO P 3 3
 COMPUTE -T. \SUM(O.\LN(P));
 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(P);
 OPTION RS
 END GROUP;
  
  
  PARAMETER SPECIFICATIONS
  
  GROUP NUMBER:           1
  
Title estimate freqs                                                                                                            
  
  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    3 by    3
    1 2 3
 1  1 2 3
 2  4 5 6
 3  7 8 9
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
  It has no free parameters specified
  
  GROUP NUMBER:           2
  
Constrain haplotype freqs to sum to 1                                                                                           
  
  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    3 by    3
    1 2 3
 1  1 2 3
 2  4 5 6
 3  7 8 9
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
  It has no free parameters specified
  
  
  
  
  MX PARAMETER ESTIMATES
  
  GROUP NUMBER:           1
  
Title estimate freqs                                                                                                            
  
  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    3 by    3
          1       2       3
 1   0.0775  0.1163  0.0388
 2   0.0775  0.3876  0.1008
 3   0.0233  0.1008  0.0775
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
             1
 1      2.0000
  
  GROUP NUMBER:           2
  
Constrain haplotype freqs to sum to 1                                                                                           
  
  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    3 by    3
          1       2       3
 1   0.0775  0.1163  0.0388
 2   0.0775  0.3876  0.1008
 3   0.0233  0.1008  0.0775
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
             1
 1      2.0000
  
  CONSTRAINT VALUES (should be near zero)
               1
 1   -1.3136E-07
  
 Your model has    9 estimated parameters and      1 Observed statistics
 Observed statistics include   1 constraints.
  
 User defined function value =   487.169
 'Degrees of freedom' >>>>>>>>>>>>>>>>        -8
  
 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: 0.01
 TOTAL                      0: 0: 0: 0.02
  
 Total number of warnings issued:           0
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