Re: animal model

Dear Roger,
Thanks for your copies of coop.fmt and mt.as

The first issue is that your version of coop.fmt had different coding of 'dam'
to mine. Originally the data was analysed under a sire and dam model with sire coded 1:92 and dam coded 1:3591 as in the file you have. However,
obviously sire 1 is not the same animal as dam 1.
My version of the file had 10000 added to the 'dam' number to create a
dam id. This is the file 'pcoop.fmt' used in the published job.

i.e.
==> coop.fmt <== My version
500001 1 10001 18 2 2 2737 31. 37.0 48.0 3.2 0.0 0.0
500002 1 10002 18 2 3 2738 40. 28.5 42.5 2.7 0.0 0.0
500003 1 10002 18 1 3 2738 40. 30.0 49.0 2.5 0.0 0.0
500004 1 10003 18 1 2 2739 46. 44.0 53.5 3.0 0.0 0.0
500005 1 10004 18 1 1 2740 54. 43.0 59.5 2.5 0.0 0.0

==> coop.FMT <== Your version
  500001 1 1 18 2 2 2737 31. 37.0 48.0 3.2 0.0 0.0

  500002 1 2 18 2 3 2738 40. 28.5 42.5 2.7 0.0 0.0

  500003 1 2 18 1 3 2738 40. 30.0 49.0 2.5 0.0 0.0

  500004 1 3 18 1 2 2739 46. 44.0 53.5 3.0 0.0 0.0

  500005 1 4 18 1 1 2740 54. 43.0 59.5 2.5 0.0 0.0

========================

2) There is an inconsequential error in thhe code as reported in the User Guide in that

4 0 FA1 !GP # Factor Analytic

.5 .5 .01 .1 .01

4.95 4.63 0.037 0.941 0.102

has 10 rather than 8 initial values.
At some stage, I recoded the job to drop the litter variance component for the fifth trait 'fat' by replacing Tr.lit by at(Tr,1).lit, at(Tr,2).lit, at(Tr,3).lit, at(Tr,4).lit,

in the model. However, I neglected to remove the corresponding staring value for the FA1 model.

Now the G header line is
at(Tr,1).lit 2

but the G structure is for a term representing 4 sets of 'litter'.
I.e. The variance structure actually applies to all four terms in
at(Tr,1).lit at(Tr,2).lit at(Tr,3).lit at(Tr,4).lit

Your version of the code had 'Tr 0 FA1 !GP'
which is wrong because Trait has 5 levels but only 4 are present.

3) In your coding, there were 2 lines with the comment

        # changed 2 into Tr
This change is wrong because we are just defining the structure for two traits
at(Tr,1).dam, at(Tr,2).dam,

4) So,
after using the data file with dam recoded, and changing
Tr to 2 in the dam structure definitions
Tr to 4 in the litter structure definitions,

the job runs.

I attach the revised data and job and outputs.

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

Retired Principal Research Scientist (Biometrics)

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Received on Fri May 28 2009 - 12:23:47 EST