Hi,
I am working with the fitting a Poisson repeatability model to ovulation
rate records. The model is
or !POI !LOG ~ mu breed year age !r animal perm
With Asreml, this eventually sends both animal and perm variance
components to zero (tornd.asr).
Source Model terms Gamma Component Comp/SE
% C
animal 854 854 0.258454E-02 0.258454E-02 0.16
-28 P
perm 358 358 0.888961E-07 0.888961E-07 0.00
-99 P
Variance 937 921 1.00000 1.00000 0.00
0 F
However, if I include the dispersion option (!DISP) I get reasonable
values (torn2.asr):
Source Model terms Gamma Component Comp/SE
% C
animal 854 854 0.421773E-01 0.702392E-02 1.38
0 P
perm 358 358 0.921755E-01 0.153503E-01 2.98
0 P
Variance 937 921 1.00000 0.166533 17.95
0 U
I am hoping that would be able to explain this to me, especially the
intrepretation of the dispersion parameter in this context and providing
estimates of heritability and repeatability.
Thanks in advance,
Bruce
ASREML [21 Mar 2000] Generalized mixed models
Wed Apr 12 17:34:25 2000 8.00 Mbyte Unix torn2
*****************************************************
* ASREML 2000 Residuals now written to .yht file, *
* convergence monitoring of parameters to .res file *
*********************************************** ARG *
A-inverse retrieved from ainverse.bin
PEDIGREE [ped.coded ] has 854 identities, 2823 Non zero elements
QUALIFIERS: !NODISPLAY
Reading asreml.data FREE FORMAT skipping 0 lines
Univariate analysis of or
Using 937 records [of 948 read from 948 lines of asreml.data ]
Model term Size Type COL Minimum Mean Maximum #zero #miss
1 animal 854 Direct 1 215.0 581.8 837.0 0 0
2 perm 358 Factor 2 1 161.9733 358 0 0
3 breed 6 Factor 3 1 2.3927 6 0 0
4 year 8 Factor 4 1 4.4440 8 0 0
5 age 4 Factor 5 1 2.5955 4 0 0
6 or 1 Variate 6 0.5000 2.572 9.000 0 0
7 nlb 1 Covariat 7 1.000 2.017 5.000 0 159
8 mu 1 Constant Term
Forming 1231 equations: 19 dense
Initial updates will be shrunk by factor 0.010
Distribution and link: Poisson; Log Mu=exp(XB) V=Mu
NOTICE: 3 (more) singularities,
LogL= 640.120 S2= 1.0000 921 df 0.1000 0.1000 1.000
LogL= 627.491 S2= 1.0000 921 df 0.8906E-01 0.8890E-01 1.000
LogL= 708.005 S2= 1.0000 921 df 0.8906E-02 0.8890E-02 1.000
LogL= 714.419 S2= 1.0000 921 df 0.2936E-02 0.8890E-03 1.000
LogL= 714.424 S2= 1.0000 921 df 0.3638E-02 0.8890E-05 1.000
Final parameter values 0.25845E-020.88896E-07 1.0000
Deviance from GLM fit -204.01
Variance heterogenity factor [Deviance/DF] 0.22
Source Model terms Gamma Component Comp/SE % C
animal 854 854 0.258454E-02 0.258454E-02 0.16 -28 P
perm 358 358 0.888961E-07 0.888961E-07 0.00 -99 P
Variance 937 921 1.00000 1.00000 0.00 0 F
Analysis of Variance DF F-incr F-adj StndErrDiff
8 mu 1 1717.95 99.84
3 breed 5 34.97 31.71 0.1037
4 year 7 1.27 1.11 0.8591E-01
5 age 3 3.69 3.69 0.6120E-01
Solution Standard Error T-value T-prev
5 age
4 -0.378294E-01 0.614788E-01 -0.62
3 -0.828053E-01 0.594600E-01 -1.39 -0.71
2 -0.192746 0.604171E-01 -3.19 -1.88
4 year
1993 0.489248E-02 0.883469E-01 0.06
1994 -0.451166E-01 0.856120E-01 -0.53 -0.59
1995 -0.419165E-01 0.848745E-01 -0.49 0.04
1996 0.800418E-01 0.902823E-01 0.89 1.55
1997 0.680066E-01 0.891103E-01 0.76 -0.15
1998 -0.691629E-01 0.939238E-01 -0.74 -1.73
1999 0.925343E-01 0.985045E-01 0.94 1.83
3 breed
6 0.507577 0.651190E-01 7.79
3 -0.850997E-01 0.106344 -0.80 -5.36
4 0.580041 0.851034E-01 6.82 4.93
5 0.499146 0.561617E-01 8.89 -0.89
2 -0.109632 0.101933 -1.08 -5.76
8 mu
19 0.825678 0.826323E-01 9.99
1 animal 854 effects fitted
2 perm 358 effects fitted
5 possible outliers: see .res file
Finished: Wed Apr 12 17:34:30 2000 WARNING: LogL Converged; Parameters Not Converged
ASREML [21 Mar 2000] Generalized mixed models
Wed Apr 12 17:30:55 2000 8.00 Mbyte Unix torn2
*****************************************************
* ASREML 2000 Residuals now written to .yht file, *
* convergence monitoring of parameters to .res file *
*********************************************** ARG *
A-inverse retrieved from ainverse.bin
PEDIGREE [ped.coded ] has 854 identities, 2823 Non zero elements
QUALIFIERS: !NODISPLAY
Reading asreml.data FREE FORMAT skipping 0 lines
Univariate analysis of or
Using 937 records [of 948 read from 948 lines of asreml.data ]
Model term Size Type COL Minimum Mean Maximum #zero #miss
1 animal 854 Direct 1 215.0 581.8 837.0 0 0
2 perm 358 Factor 2 1 161.9733 358 0 0
3 breed 6 Factor 3 1 2.3927 6 0 0
4 year 8 Factor 4 1 4.4440 8 0 0
5 age 4 Factor 5 1 2.5955 4 0 0
6 or 1 Variate 6 0.5000 2.572 9.000 0 0
7 nlb 1 Covariat 7 1.000 2.017 5.000 0 159
8 mu 1 Constant Term
Forming 1231 equations: 19 dense
Initial updates will be shrunk by factor 0.010
Distribution and link: Poisson; Log Mu=exp(XB) V=Mu
NOTICE: 3 (more) singularities,
LogL= 1118.23 S2= 0.15158 921 df 0.1000 0.1000 1.000
LogL= 1081.26 S2= 0.15803 921 df 0.9933E-01 0.1000 1.000
LogL= 1081.86 S2= 0.15893 921 df 0.9175E-01 0.9909E-01 1.000
LogL= 1083.29 S2= 0.16162 921 df 0.7175E-01 0.9633E-01 1.000
LogL= 1084.29 S2= 0.16476 921 df 0.5291E-01 0.9277E-01 1.000
LogL= 1084.58 S2= 0.16672 921 df 0.4236E-01 0.9107E-01 1.000
LogL= 1084.55 S2= 0.16651 921 df 0.4218E-01 0.9228E-01 1.000
LogL= 1084.55 S2= 0.16653 921 df 0.4218E-01 0.9216E-01 1.000
Final parameter values 0.42177E-010.92176E-01 1.0000
Deviance from GLM fit -133.67
Variance heterogenity factor [Deviance/DF] 0.15
Source Model terms Gamma Component Comp/SE % C
animal 854 854 0.421773E-01 0.702392E-02 1.38 0 P
perm 358 358 0.921755E-01 0.153503E-01 2.98 0 P
Variance 937 921 1.00000 0.166533 17.95 0 U
Analysis of Variance DF F-incr F-adj StndErrDiff
8 mu 1 2318.23 360.66
3 breed 5 90.78 79.34 0.5700E-01
4 year 7 8.66 6.69 0.3951E-01
5 age 3 16.70 16.70 0.2773E-01
Solution Standard Error T-value T-prev
5 age
4 -0.423435E-01 0.271356E-01 -1.56
3 -0.870193E-01 0.281661E-01 -3.09 -1.65
2 -0.202955 0.305604E-01 -6.64 -4.66
4 year
1993 0.292374E-02 0.373854E-01 0.08
1994 -0.581240E-01 0.373076E-01 -1.56 -1.74
1995 -0.710062E-01 0.383299E-01 -1.85 -0.40
1996 0.461848E-01 0.421068E-01 1.10 3.50
1997 0.507821E-01 0.438866E-01 1.16 0.14
1998 -0.102984 0.474361E-01 -2.17 -4.55
1999 0.733845E-01 0.512010E-01 1.43 4.70
3 breed
6 0.494528 0.400377E-01 12.35
3 -0.487666E-01 0.530696E-01 -0.92 -9.88
4 0.564815 0.568147E-01 9.94 8.17
5 0.504536 0.374205E-01 13.48 -1.04
2 -0.101050 0.517223E-01 -1.95 -11.13
8 mu
19 0.832114 0.438158E-01 18.99
1 animal 854 effects fitted
2 perm 358 effects fitted
4 possible outliers: see .res file
Finished: Wed Apr 12 17:31:02 2000 LogL Converged