! Sib pair ACE data The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NVARX2 2 #DEFINE NALLELE 2 #NGROUPS 2 Note: #NGroup set number of groups to 2 ACE DATA DATA NINPUT=13 ! 13 INPUT VARIABLES MISSING=-99.989998 NOTE: Missing value *string* set to '-99.989998' RECTANGULAR FILE=MARKER1.DAT ! READ DATA FROM FILE NOTE: Rectangular file contained 107 records with data LABELS LOCUS PEDNUM ID1 ID2 PIBD0 PIBD1 PIBD2 ACE1 ACE2 A1S1 A2S1 A1S2 A2S2 ! aisj is allele i of sibling j ! select only those sib pairs with no missing marker genotypes SELECT IF A1S1 ^= 0 NOTE: Select if yields 103 data vectors for analysis NOTE: Vectors contain a total of 1331 observations SELECT IF A2S1 ^= 0 NOTE: Select if yields 103 data vectors for analysis NOTE: Vectors contain a total of 1331 observations SELECT IF A1S2 ^= 0 NOTE: Select if yields 102 data vectors for analysis NOTE: Vectors contain a total of 1318 observations SELECT IF A2S2 ^= 0 NOTE: Select if yields 102 data vectors for analysis NOTE: Vectors contain a total of 1318 observations ! Phenotype sib 1, phenotype sib 2, probabilities of sharing 0, 1, and 2 ! alleles ibd, genotype of sib 1, genotype of sib 2 SELECT ACE1 ACE2 PIBD0 PIBD1 PIBD2 A1S1 A2S1 A1S2 A2S2 ; ! use the genotypic information to define the mean and covariance models DEFINITION_VARIABLES PIBD0 PIBD1 PIBD2 A1S1 A2S1 A1S2 A2S2 ; NOTE: Selection yields 102 data vectors for analysis NOTE: Vectors contain a total of 910 observations NOTE: Definition yields 101 data vectors for analysis NOTE: Vectors contain a total of 196 observations BEGIN MATRICES; A LOWER NVAR NVAR FREE ! POLYGENIC COMPONENT Z LOWER NVAR NVAR FREE ! UNIQUE ENVIRONMENTAL COMPONENT Q LOWER NVAR NVAR FREE ! LINKAGE COMPONENT B FULL 3 1 ! IBD PROBABILITIES (FROM GENEHUNTER OR ! Mapmaker/SIBS) D FULL 1 3 ! WILL CONTAIN 0, .5, 1 C FU 1 1 ! CONSTANT TO CONTAIN .5 ! association specification E FULL 1 4 ! FIRST ALLELE OF SIB 1 F FULL 1 4 ! SECOND ALLELE OF SIB 1 G FULL 1 4 ! FIRST ALLELE OF SIB 2 H FULL 1 4 ! SECOND ALLELE OF SIB 2 L FULL 1 4 ! 0 1 0 1 - MATRIX TO OFFSET TO A_W COLUMN M FU 1 1 FREE ! GRAND MEAN U UNIT 4 1 ! UNIT MATRIX W FULL NALLELE 2 FREE ! A_B AND A_W PARAMETERS, ROWS ARE ALLELES, ! a_b is first column, a_w second column END MATRICES; ! fix the constants MATRIX D 0 .5 1 MATRIX C .5 ! starting values for matrices used in linkage component of model MATRIX A .5 MATRIX Z .7 MATRIX Q .1 ! matrices used for association component of model ! which take genotypes in columns 1 and 3, with columns 2 and 4 ! fixed to 1. MATRIX E 1 1 1 1 MATRIX F 1 1 1 1 MATRIX G 1 1 1 1 MATRIX H 1 1 1 1 ! L is a constant MATRIX L 0 1 0 1 MATRIX M 0 ! STARTING VALUE FOR ESTIMATE OF THE OVERALL MEAN ! put ibd probabilities in b SPECIFY B PIBD0 PIBD1 PIBD2 ! put sib genotypes into matrices SPECIFY E A1S1 0 A1S1 0 SPECIFY F A2S1 0 A2S1 0 SPECIFY G A1S2 0 A1S2 0 SPECIFY H A2S2 0 A2S2 0 BEGIN ALGEBRA; ! compute the between effects, which are the sum of all the alleles ! in the sibship, obtained by pulling out the appropriate row of ! the first column of the W matrix, which contains the between ! effects for alleles 1 and 2, and summing those effects I = \PART(W,E) + \PART(W,F) + \PART(W,G) + \PART(W,H) ; ! compute the within effects, which use the second column of the W ! matrix. This is the difference between sib 1 and sib 2's ! genotypic scores. J = \PART(W,(E+L)) + \PART(W,(F+L)) - \PART(W,(G+L)) - \PART(W,(H+L)) ; ! compute pihat from ibd probabilities P = D*B; END ALGEBRA; ! sib 1's mean is composed of the grand mean plus the between effect ! plus the within effect, sib 2's mean is composed of the grand mean, the ! between effect minus the within effect MEANS (M + I + J | M + I - J); ! the expected covariance matrix contains a polygenic component (A), ! a unique environmental component (z) and the QTL component (Q) COVARIANCE A*A' + Z*Z' + Q*Q' | C@A*A' + P@Q*Q' _ C@A*A' + P@Q*Q' | A*A' + Z*Z' + Q*Q' ; OPTION ND=4 ! REQUEST 4 DECIMAL PLACES IN OUTPUT OPTION RS MULTIPLE ! REQUEST RESIDUALS, MULTIPLE FIT OPTION ISSAT ! THIS IS SATURATED MODEL FOR SUBMODEL COMPARISON END The following MX script lines were read for group 2 CONSTRAIN SUM OF WEIGHTS ON DIFFS TO EQUAL 0 ! this is done because a separate parameter was fitted for each ! of the two possible alleles, while it is only possible to estimate ! one parameter less than the number of alleles CONSTRAINT NI=2 BEGIN MATRICES = GROUP 1; O ZERO 1 2 P UNIT 1 NALLELE *** WARNING! *** Matrix was previously defined for this group. Mx will redefine END MATRICES; ! a_b_1 + a_b_2 = 0 ! a_w_1 + a_w_2 = 0 CONSTRAIN P*W = O ; OPTION MULTIPLE OPTION ISSAT ! DEFINE THE FULL MODEL END Summary of VL file data for group 1 A2S2 A1S2 A2S1 A1S1 PIBD2 PIBD1 PIBD0 Code -7.0000 -6.0000 -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 Number 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 Mean 1.5347 1.0693 1.5149 1.0693 0.3437 0.4423 0.2140 Variance 0.2488 0.0645 0.2498 0.0645 0.1649 0.1177 0.0892 Minimum 1.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Maximum 2.0000 2.0000 2.0000 2.0000 1.0000 1.0000 1.0000 ACE1 ACE2 Code 1.0000 2.0000 Number 95.0000 101.0000 Mean -0.0837 -0.0189 Variance 0.9576 1.0685 Minimum -2.0260 -2.1090 Maximum 2.6860 2.6700 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 6 2 7 8 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 6 2 7 8 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MX PARAMETER ESTIMATES GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3755 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -1.0553 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.2925 MATRIX P This is a computed FULL matrix of order 1 by 1 [=D*B] 1 1 0.0000 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.6321 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2029 -0.2638 2 0.2029 0.2638 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4172 Vector of OBSERVED means ACE1 ACE2 Mean 0.0000 0.0000 Vector of EXPECTED means ACE1 ACE2 Mean -0.7628 1.3478 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 0.7147 ACE2 0.0705 0.7147 Function value of this group: 467.1863 Where the fit function is -2 * Log-likelihood of raw data GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3755 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -1.0553 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.2925 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.6321 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2029 -0.2638 2 0.2029 0.2638 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4172 Your model has 8 estimated parameters and 905 Observed statistics Observed statistics include 2 constraints. -2 times log-likelihood of data >>> 467.186 Degrees of freedom >>>>>>>>>>>>>>>> 897 This problem used 4.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.88 Execution 0: 0: 0:18.29 TOTAL 0: 0: 0:19.17 Total number of warnings issued: 1 ______________________________________________________________________________ ! equate a_b to a_w Multiple fit option in effect. The following MX script lines have been read: SPECIFY 1 W 5 5 6 6 OPTION DF=-1 ! NECESSARY TO GET A SINGLE DF TEST END Summary of VL file data for group 1 A2S2 A1S2 A2S1 A1S1 PIBD2 PIBD1 PIBD0 Code -7.0000 -6.0000 -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 Number 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 Mean 1.5347 1.0693 1.5149 1.0693 0.3437 0.4423 0.2140 Variance 0.2488 0.0645 0.2498 0.0645 0.1649 0.1177 0.0892 Minimum 1.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Maximum 2.0000 2.0000 2.0000 2.0000 1.0000 1.0000 1.0000 ACE1 ACE2 Code 1.0000 2.0000 Number 95.0000 101.0000 Mean -0.0837 -0.0189 Variance 0.9576 1.0685 Minimum -2.0260 -2.1090 Maximum 2.6860 2.6700 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 5 2 6 6 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 5 2 6 6 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MX PARAMETER ESTIMATES GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3593 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -0.9089 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.3311 MATRIX P This is a computed FULL matrix of order 1 by 1 [=D*B] 1 1 0.0000 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.6428 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2272 -0.2272 2 0.2272 0.2272 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4218 Vector of OBSERVED means ACE1 ACE2 Mean 0.0000 0.0000 Vector of EXPECTED means ACE1 ACE2 Mean -0.5778 1.2401 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 0.7203 ACE2 0.0646 0.7203 Function value of this group: 468.5052 Where the fit function is -2 * Log-likelihood of raw data GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3593 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -0.9089 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.3311 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.6428 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2272 -0.2272 2 0.2272 0.2272 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4218 Your model has 6 estimated parameters and 904 Observed statistics Observed statistics include 2 constraints. Note that Observed statistics includes your DF= adjustment of -1 -2 times log-likelihood of data >>> 468.505 Degrees of freedom >>>>>>>>>>>>>>>> 898 Saturated model fit* >>>>>>>>>>> 467.186 Saturated model df* >>>>>>>>>>> 897 Difference Chi-squared >>>>>>>> 1.319 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.251 Akaike's Information Criterion > -0.681 * Saturated model statistic computed earlier in this job This problem used 4.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0:10.65 TOTAL 0: 0: 0:10.65 Total number of warnings issued: 1 ______________________________________________________________________________ Multiple fit option in effect. The following MX script lines have been read: SAVE COMBINED.MXS OPTION ISSAT ! A_B = A_W IS THE NEW BASE MODEL END Summary of VL file data for group 1 A2S2 A1S2 A2S1 A1S1 PIBD2 PIBD1 PIBD0 Code -7.0000 -6.0000 -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 Number 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 Mean 1.5347 1.0693 1.5149 1.0693 0.3437 0.4423 0.2140 Variance 0.2488 0.0645 0.2498 0.0645 0.1649 0.1177 0.0892 Minimum 1.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Maximum 2.0000 2.0000 2.0000 2.0000 1.0000 1.0000 1.0000 ACE1 ACE2 Code 1.0000 2.0000 Number 95.0000 101.0000 Mean -0.0837 -0.0189 Variance 0.9576 1.0685 Minimum -2.0260 -2.1090 Maximum 2.6860 2.6700 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 5 2 6 6 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 5 2 6 6 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MX PARAMETER ESTIMATES GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3593 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -0.9089 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.3311 MATRIX P This is a computed FULL matrix of order 1 by 1 [=D*B] 1 1 0.0000 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.6428 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2272 -0.2272 2 0.2272 0.2272 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4218 Vector of OBSERVED means ACE1 ACE2 Mean 0.0000 0.0000 Vector of EXPECTED means ACE1 ACE2 Mean -0.5778 1.2401 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 0.7203 ACE2 0.0646 0.7203 Function value of this group: 468.5052 Where the fit function is -2 * Log-likelihood of raw data GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3593 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -0.9089 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.3311 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.6428 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2272 -0.2272 2 0.2272 0.2272 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4218 Your model has 6 estimated parameters and 904 Observed statistics Observed statistics include 2 constraints. Note that Observed statistics includes your DF= adjustment of -1 -2 times log-likelihood of data >>> 468.505 Degrees of freedom >>>>>>>>>>>>>>>> 898 This problem used 4.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.33 Execution 0: 0: 0: 2.26 TOTAL 0: 0: 0: 2.59 Total number of warnings issued: 1 ______________________________________________________________________________ ! drop both a_b and a_w against a_b = a_w - overall test of association Multiple fit option in effect. The following MX script lines have been read: DROP W 1 1 1 TO W 2 2 2 OPTION DF=-2 END Summary of VL file data for group 1 A2S2 A1S2 A2S1 A1S1 PIBD2 PIBD1 PIBD0 Code -7.0000 -6.0000 -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 Number 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 Mean 1.5347 1.0693 1.5149 1.0693 0.3437 0.4423 0.2140 Variance 0.2488 0.0645 0.2498 0.0645 0.1649 0.1177 0.0892 Minimum 1.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Maximum 2.0000 2.0000 2.0000 2.0000 1.0000 1.0000 1.0000 ACE1 ACE2 Code 1.0000 2.0000 Number 95.0000 101.0000 Mean -0.0837 -0.0189 Variance 0.9576 1.0685 Minimum -2.0260 -2.1090 Maximum 2.6860 2.6700 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 It has no free parameters specified MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 It has no free parameters specified MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.0000 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 0.0000 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 -0.0312 MATRIX P This is a computed FULL matrix of order 1 by 1 [=D*B] 1 1 0.0000 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.8905 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 0.0000 0.0000 2 0.0000 0.0000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4875 Vector of OBSERVED means ACE1 ACE2 Mean 0.0000 0.0000 Vector of EXPECTED means ACE1 ACE2 Mean -0.0312 -0.0312 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 1.0306 ACE2 0.0000 1.0306 Function value of this group: 530.7570 Where the fit function is -2 * Log-likelihood of raw data GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.0000 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 0.0000 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 -0.0312 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.8905 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 0.0000 0.0000 2 0.0000 0.0000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4875 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 4 estimated parameters and 903 Observed statistics Observed statistics include 2 constraints. Note that Observed statistics includes your DF= adjustment of -2 -2 times log-likelihood of data >>> 530.757 Degrees of freedom >>>>>>>>>>>>>>>> 899 Saturated model fit* >>>>>>>>>>> 468.505 Saturated model df* >>>>>>>>>>> 898 Difference Chi-squared >>>>>>>> 62.252 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 60.252 * Saturated model statistic computed earlier in this job This problem used 4.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0:10.60 TOTAL 0: 0: 0:10.60 Total number of warnings issued: 3 ______________________________________________________________________________ ! get the a_b = a_w result ! and then drop the linkage parameter Multiple fit option in effect. The following MX script lines have been read: GET COMBINED.MXS Note: 4415 binary records read DROP Q 1 1 1 ! TEST FOR LINKAGE IN THE PRESENCE OF ASSOCIATION OPTION DF=-1 END Summary of VL file data for group 1 A2S2 A1S2 A2S1 A1S1 PIBD2 PIBD1 PIBD0 Code -7.0000 -6.0000 -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 Number 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 101.0000 Mean 1.5347 1.0693 1.5149 1.0693 0.3437 0.4423 0.2140 Variance 0.2488 0.0645 0.2498 0.0645 0.1649 0.1177 0.0892 Minimum 1.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Maximum 2.0000 2.0000 2.0000 2.0000 1.0000 1.0000 1.0000 ACE1 ACE2 Code 1.0000 2.0000 Number 95.0000 101.0000 Mean -0.0837 -0.0189 Variance 0.9576 1.0685 Minimum -2.0260 -2.1090 Maximum 2.6860 2.6700 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 It has no free parameters specified MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 5 2 6 6 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX B This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX C This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX D This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 -4 0 -4 0 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 -5 0 -5 0 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 -6 0 -6 0 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 -7 0 -7 0 MATRIX I This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 4 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 It has no free parameters specified MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 5 5 2 6 6 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 ACE data MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.7709 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -0.9310 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.3297 MATRIX P This is a computed FULL matrix of order 1 by 1 [=D*B] 1 1 0.0000 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.0000 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2328 -0.2328 2 0.2328 0.2328 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3564 Vector of OBSERVED means ACE1 ACE2 Mean 0.0000 0.0000 Vector of EXPECTED means ACE1 ACE2 Mean -0.6013 1.2607 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 0.7213 ACE2 0.2971 0.7213 Function value of this group: 474.5157 Where the fit function is -2 * Log-likelihood of raw data GROUP NUMBER: 2 Constrain sum of weights on diffs to equal 0 MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.7709 MATRIX B This is a FULL matrix of order 3 by 1 1 1 1.0000 2 0.0000 3 0.0000 MATRIX C This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX D This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX E This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX F This is a FULL matrix of order 1 by 4 1 2 3 4 1 1.0000 1.0000 1.0000 1.0000 MATRIX G This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX H This is a FULL matrix of order 1 by 4 1 2 3 4 1 2.0000 1.0000 2.0000 1.0000 MATRIX I This is a computed FULL matrix of order 1 by 1 [=\PART(W,E)+\PART(W,F)+\PART(W,G)+\PART(W,H)] 1 1 0.0000 MATRIX J This is a computed FULL matrix of order 1 by 1 [=\PART(W,(E+L))+\PART(W,(F+L))-\PART(W,(G+L))-\PART(W,(H+L))] 1 1 -0.9310 MATRIX L This is a FULL matrix of order 1 by 4 1 2 3 4 1 0.0000 1.0000 0.0000 1.0000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 0.3297 MATRIX O This is a NULL matrix of order 1 by 2 MATRIX P This is a UNIT matrix of order 1 by 2 MATRIX Q This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.0000 MATRIX U This is a UNIT matrix of order 4 by 1 MATRIX W This is a FULL matrix of order 2 by 2 1 2 1 -0.2328 -0.2328 2 0.2328 0.2328 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3564 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 904 Observed statistics Observed statistics include 2 constraints. Note that Observed statistics includes your DF= adjustment of -1 -2 times log-likelihood of data >>> 474.516 Degrees of freedom >>>>>>>>>>>>>>>> 899 Saturated model fit* >>>>>>>>>>> 468.505 Saturated model df* >>>>>>>>>>> 898 Difference Chi-squared >>>>>>>> 6.011 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.014 Akaike's Information Criterion > 4.011 * Saturated model statistic computed earlier in this job This problem used 4.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.11 Execution 0: 0: 0:14.28 TOTAL 0: 0: 0:14.39 Total number of warnings issued: 5 ______________________________________________________________________________