Multi-trait - multi-site model
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Multi-trait - multi-site model
I am trying to run a multi-site, multi-trait familymodel. I have what I
think are to equivalent parameterisations, however I come up with slightly
different results.
below is the .AS. file, with the two models, one and two:
Dunnii combined analyses - 2 sites
site 2 REP 6 Block 11 Prov 19 Family 220 Seed TREE DBH98 HT98
DBH981 !=V1 !==1 !*V8 !M 0
DBH982 !=V1 !==2 !*V8 !M 0
HT981 !=V1 !==1 !*V9 !M 0
HT982 !=V1 !==2 !*V9 !M 0
Dun_GE.DAT !skip 1 !MAXIT 30 !DOPART $A
!PART 1
! Between Site Bivariate
DBH98 HT98 ~ Trait Trait.site Trait.site.REP Trait.site.Prov !r
Trait.site.Family !f mv
2 2 1 !step 0.01
5280 0 IDEN !S2==1
Trait 0 US 5.7 3.7 3.6
5280 0 IDEN !S2==1
Trait 0 US 3.3 2.2 1.6
Trait.site.Family 2
Trait.site 0 CORR 0.47 0.88 0.43 0.48 0.97 0.5 0.44 0.41 0.476 0.21
Family 0 IDEN
!PART 2
! between site Bivariate
DBH981 DBH982 HT981 HT982 ~ mu Trait.REP Trait.Prov !r Trait.Family !f mv
1 2 1 !step 0.01
0 0 IDEN
Trait 0 US 5.7 0 3.3 3.7 0 3.6 0 2.2 0 1.6 !GUFUUFUFUFU
Trait.Family 2
Trait 0 CORR 0.4 0.9 0.38 0.48 0.97 0.5 0.44 0.34 0.46 0.22
Family 0 IDEN
the results from model 1 are:
ASREML [ 1 Jul 1999] Dunnii combined analyses - 2 sites
12 Jul 1999 21:49:15.478 64.00 Mbyte DUN
QUALIFIERS: !skip 1 !MAXIT 30 !DOPART 4
Reading Dun_GE.DAT FREE FORMAT skipping 1 lines
! Between Site Bivariate
Bivariate analysis of DBH98 and HT98
Using 10560 records [of 10560 read from 10560 lines of Dun_GE.DAT
]
Model term Size Type COL Minimum Mean Maximum #zero
#miss
1 site 2 Factor 1 1 1.5000 2 0
0
2 REP 6 Factor 2 1 3.5000 6 0
0
3 Block 11 Factor 3 1 6.0000 11 0
0
4 Prov 19 Factor 4 1 9.3182 19 0
0
5 Family 220 Factor 5 1 110.5000 220 0
0
6 Seed 1 Covariat 6 1.000 110.5 220.0 0
0
7 TREE 1 Covariat 7 1.000 2.500 4.000 0
0
8 DBH98 1 Variate 8 1.000 7.112 17.40 0
1616
9 HT98 1 Variate 9 1.500 7.706 18.60 0
1396
10 DBH981 1 Covariat 10 2.500 9.958 17.40 0
6210
11 DBH982 1 Covariat 11 1.000 4.417 11.40 0
5966
12 HT981 1 Covariat 12 3.900 11.39 18.60 0
6220
13 HT982 1 Covariat 13 1.500 4.389 9.700 0
5736
14 Trait 2 Traits/Variat
15 Trait.site 4 Interaction 14 Trait : 2 1 site :
2
16 site.REP 12 Interaction 1 site : 2 2 REP :
6
17 Trait.site.R 24 Interaction 14 Trait : 2 16 site.REP :
12
18 site.Prov 38 Interaction 1 site : 2 4 Prov :
19
19 Trait.site.P 76 Interaction 14 Trait : 2 18 site.Prov :
38
20 site.Family 440 Interaction 1 site : 2 5 Family :
220
21 Trait.site.F 880 Interaction 14 Trait : 2 20 site.Family :
440
22 mv_estimates 3012 Missing value
5280 identity
2 US=UnStr 5.70 3.70 3.60
10560 records assumed sorted 2 within 5280
10560 units in section 1; initial variance 1.0000
5280 identity
2 US=UnStr 3.30 2.20 1.60
10560 records assumed sorted 2 within 5280
10560 units in section 2; initial variance 1.0000
4 CORRelat 0.47 0.88 0.43 0.48 0.97 0.50 0.44
0.41
0.48 0.21
220 identity
Structure of Trait.site.F has 880 levels defined
Forming 3999 equations: 107 dense
Initial updates will be shrunk by factor 0.010
NOTICE: 3038 (more) singularities,
LogL=-13956.4 S2= 1.0000 21040 df 1.000 5.700 3.700
3.600 1.000 3.300 2.200 1.600 0.4700 0.8800
0.4300 0.4800 0.9700 0.5000 0.4400 0.4100 0.4760
0.2100
...
Final parameter values 1.0000 5.6725 3.6825
3.5977 1.0000 2.9963 1.8869 1.4147 0.45086 0.87853
0.41097 0.47504 0.97053 0.49009 0.44346 0.43495 0.46642
0.21331
Source Model terms Gamma Component Comp/SE %
C
Residual 21120 21040
Residual US=UnStr 1 5.67255 5.67255 45.42 0
U
Residual US=UnStr 1 3.68246 3.68246 40.57 0
U
Residual US=UnStr 2 3.59767 3.59767 45.39 0
U
Residual US=UnStr 1 2.99635 2.99635 47.36 0
U
Residual US=UnStr 1 1.88694 1.88694 44.79 0
U
Residual US=UnStr 2 1.41467 1.41467 47.71 0
U
Trait.site.Family CORRelat 4 0.450861 0.450861 4.99 0
U
Trait.site.Family CORRelat 4 0.878530 0.878530 32.40 0
U
Trait.site.Family CORRelat 4 0.410971 0.410971 4.91 0
U
Trait.site.Family CORRelat 4 0.475040 0.475040 5.37 0
U
Trait.site.Family CORRelat 4 0.970529 0.970529 145.12 0
U
Trait.site.Family CORRelat 4 0.490085 0.490085 6.25 0
U
Trait.site.Family CORRelat 4 0.443462 0.443462 6.08 0
U
Trait.site.Family CORRelat 4 0.434953 0.434953 7.65 0
U
Trait.site.Family CORRelat 4 0.466420 0.466420 7.22 0
U
Trait.site.Family CORRelat 4 0.213314 0.213314 7.74 0
U
Covariance/Variance/Correlation Matrix US=UnStructu
5.673 0.8152
3.682 3.598
Covariance/Variance/Correlation Matrix US=UnStructu
2.996 0.9165
1.887 1.415
Covariance/Variance/Correlation Matrix CORRelation
0.4435 0.4509 0.8785 0.4750
0.1980 0.4350 0.4110 0.9705
0.3996 0.1851 0.4664 0.4901
0.1461 0.2956 0.1546 0.2133
Analysis of Variance DF F-incr F-adj StndErrDiff
14 Trait 2 17829.63 2581.90
15 Trait.site 2 9598.88 1149.92
17 Trait.site.REP 20 126.74 126.65
19 Trait.site.Prov 56 1.97 1.97
the results from model two are:
ASREML [ 1 Jul 1999] Dunnii combined analyses - 2 sites
12 Jul 1999 21:38:44.010 64.00 Mbyte DUN
QUALIFIERS: !skip 1 !MAXIT 30 !DOPART 7
Reading Dun_GE.DAT FREE FORMAT skipping 1 lines
! between site Bivariate
Multivariate analysis of DBH981 DBH982 HT981 HT982
t.Family mv
Using 10560 records [of 10560 read from 10560 lines of Dun_GE.DAT
]
Model term Size Type COL Minimum Mean Maximum #zero
#miss
1 site 2 Factor 1 1 1.5000 2 0
0
2 REP 6 Factor 2 1 3.5000 6 0
0
3 Block 11 Factor 3 1 6.0000 11 0
0
4 Prov 19 Factor 4 1 9.3182 19 0
0
5 Family 220 Factor 5 1 110.5000 220 0
0
6 Seed 1 Covariat 6 1.000 110.5 220.0 0
0
7 TREE 1 Covariat 7 1.000 2.500 4.000 0
0
8 DBH98 1 Covariat 8 1.000 7.112 17.40 0
1616
9 HT98 1 Covariat 9 1.500 7.706 18.60 0
1396
10 DBH981 1 Variate 10 2.500 9.958 17.40 0
6210
11 DBH982 1 Variate 11 1.000 4.417 11.40 0
5966
12 HT981 1 Variate 12 3.900 11.39 18.60 0
6220
13 HT982 1 Variate 13 1.500 4.389 9.700 0
5736
14 mu 4 Traits/Variat
15 Trait 4 Traits/Variat
16 Trait.REP 24 Interaction 15 Trait : 4 2 REP :
6
17 Trait.Prov 76 Interaction 15 Trait : 4 4 Prov :
19
18 Trait.Family 880 Interaction 15 Trait : 4 5 Family :
220
19 mv_estimat 24132 Missing value
10560 identity
4 US=UnStr 5.70 0.00 3.30 3.70 0.00 3.60 0.00
2.20
0.00 1.60
42240 records assumed sorted 4 within10560
4 CORRelat 0.40 0.90 0.38 0.48 0.97 0.50 0.44
0.34
0.46 0.22
220 identity
Structure of Trait.Family has 880 levels defined
Forming 25117 equations: 105 dense
Initial updates will be shrunk by factor 0.010
NOTICE: 24156 (more) singularities,
LogL=-13981.7 S2= 1.0000 42160 df 1.000 5.700 0.000
3.300 3.700 0.000 3.600 0.000 2.200 0.000
1.600 0.4000 0.9000 0.3800 0.4800 0.9700 0.5000
0.4400 0.3400 0.4600 0.2200
.....
Final parameter values 1.0000 5.6726 0.0000
3.7022 3.6825 0.0000 3.5977 0.0000 2.2249 0.0000
1.5551 0.46927 0.87855 0.42817 0.48155 0.97079 0.49728
0.44342 0.40871 0.46639 0.20660
Source Model terms Gamma Component Comp/SE %
C
Residual US=UnStr 1 5.67256 5.67256 45.42 0
U
Residual US=UnStr 1 0.00000 0.00000 0.00 0
F
Residual US=UnStr 2 3.70223 3.70223 47.30 0
U
Residual US=UnStr 1 3.68246 3.68246 40.57 0
U
Residual US=UnStr 2 0.00000 0.00000 0.00 0
F
Residual US=UnStr 3 3.59768 3.59768 45.39 0
U
Residual US=UnStr 1 0.00000 0.00000 0.00 0
F
Residual US=UnStr 2 2.22486 2.22486 45.95 0
U
Residual US=UnStr 3 0.00000 0.00000 0.00 0
F
Residual US=UnStr 4 1.55505 1.55505 47.99 0
U
Trait.Family CORRelat 4 0.469273 0.469273 5.03 0
U
Trait.Family CORRelat 4 0.878553 0.878553 32.40 0
U
Trait.Family CORRelat 4 0.428171 0.428171 4.96 0
U
Trait.Family CORRelat 4 0.481549 0.481549 5.37 0
U
Trait.Family CORRelat 4 0.970790 0.970790 138.38 0
U
Trait.Family CORRelat 4 0.497284 0.497284 6.25 0
U
Trait.Family CORRelat 4 0.443421 0.443421 6.08 0
U
Trait.Family CORRelat 4 0.408711 0.408711 7.11 0
U
Trait.Family CORRelat 4 0.466387 0.466387 7.22 0
U
Trait.Family CORRelat 4 0.206596 0.206596 7.50 0
U
Covariance/Variance/Correlation Matrix US=UnStructu
5.673 0.000 0.8152 0.000
0.000 3.702 0.000 0.9273
3.682 0.000 3.598 0.000
0.000 2.225 0.000 1.555
Covariance/Variance/Correlation Matrix CORRelation
0.4434 0.4693 0.8786 0.4815
0.1998 0.4087 0.4282 0.9708
0.3995 0.1869 0.4664 0.4973
0.1458 0.2821 0.1544 0.2066
Analysis of Variance DF F-incr F-adj StndErrDiff
14 mu 4 13906.61 1601.05
16 Trait.REP 20 123.51 123.42
17 Trait.Prov 56 1.97 1.97
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