Re: animal model

Dear Roger,

The job is not set up to process PATH 1, which is the default of no argument is provided on the command line.

Using PATH 1, the job looks like

...
wwt ywt gfw fdm fat ~ Trait Tr.age Tr.brr Tr.sex Tr.age.sex,

!r Tr.tag ,

at(Tr,1).dam, at(Tr,2).dam, -at(Tr,3).dam .003,

at(Tr,1).lit, at(Tr,2).lit, at(Tr,3).lit, at(Tr,4).lit,

at(Trait,1).age.grp .0024,

at(Trait,2).age.grp .0019,

at(Trait,4).age.grp .0020,

at(Trait,5).age.grp .00026,

at(Trait,1).sex.grp .93,

at(Trait,2).sex.grp 16.0,

at(Trait,3).sex.grp .28,

at(Trait,5).sex.grp 1.18,

!f Tr.grp

1 2 3 # One multivariate R structure, 3 G structures

0 0 0 # No structure across lamb records

# First zero lets ASReml count te number of records

Tr 0 US #General structure across traits

7.66

5.33 13

.18 .66 .10

.78 2.1 .27 3.2

.73 2.02 .08 .20 1.44

Tr.tag 2 # Direct animal effects.

tag

at(Tr,1).dam 2 # Maternal effects.

dam

at(Tr,1).lit 2 # Litter effects.

lit

The G structure fails to parse because each of the 3 terms is defined as being a direct product of two terms but only one is supplied.

2)
 PATH 2 ends with 'LogL not converged' although the last 9 LogL values are
LogL=-1425.20. WhY? Well looking at the %change column in
 at(Tr,1).dam CORRelat 2 0.990000 0.990000 0.00 0 F
 at(Tr,1).dam CORRelat 2 1.05652 1.05652 2.80 0 U
 at(Tr,1).dam CORRelat 2 0.407193 0.407193 1.00 2 U
 at(Tr,1).lit FA D(LL'+E)D 1 1 0.636898 0.636898 7.41 -1 P
 at(Tr,1).lit FA D(LL'+E)D 1 2 0.999500 0.999500 0.00 0 B
 at(Tr,1).lit FA D(LL'+E)D 1 3 0.460883 0.460883 2.87 0 P
 at(Tr,1).lit FA D(LL'+E)D 1 4 -0.195717 -0.195717 -0.64 0 P
 shows an issue with the last dam term and the first litter term.

Fnding the convergence sequence in the .res files shows
 Iteration 1 16 17 18 19 20
 LogL -1636.767 -1425.197 -1425.197 -1425.196 -1425.196 -1425.196
 Change % 4 4 4 3 3 2
  66 G 2.540000 0.393028 0.411087 0.395389 0.408824 0.397221 0.407193 2.5
  67 L 0.500000 0.638125 0.636547 0.637927 0.636750 0.637771 0.636898 -0.2

So these two terms are oscillating and slowly converging
ASReml is checking both the change in LogL and the % change in parameters to determine convergence.

For practical purposes, I would say this has converged, and if you wanted a compromise final value, average the final two values, or do something more sophisticated with the last 6 values.

3)
A basic pin file is
# Ignore components 1:8 as adjustemnt factors

# 9:23 is Residual

# 24:38 is Additive

# 39:41 is dam

# 42:51 is litter
F PhenWY 9:11 + 24:26 + 39:41 + 42:44
F PhenWYGD 12:18 + 27:33 + 45:51
F PhenWYGDF 19:23 + 34:38
R Rphen 52:66
R Rgen 24:38
H H2W 24 52
H H2Y 26 54
H H2G 29 57
H H2D 33 61
H H2F 38 66

------------------------
Arthur Gilmour

Retired Principal Research Scientist (Biometrics)

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Received on Sat May 29 2009 - 06:04:22 EST