Re: Variogram not plotting and problem with pattern function

Hi Dave,

Thank you for the clarifications!

I tried the asreml version you are currently using and it works fine, I
can generate variograms as before.

Regards,

Fernando

From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On
Behalf Of Butler, David
Sent: Friday, January 22, 2010 12:37 AM
To: ASREML-L_at_DPI.NSW.GOV.AU
Subject: Re: Variogram not plotting and problem with pattern function

Fernando,

The "pattern" argument to coef.asreml() is designed to extract the
coefficients for interaction terms, is those involving ":", such as
"Column_*:Row_*". The "list" argument returns the coefficients in a
named list, so you can get just those coefficients for the "ped" term
via the appropriate list element.

I cannot reproduce the error in plotting the variogram with my test data
set, would you be kind enough to forward me your data file, suitably
disguised if necessary?

Dave.

________________________________

From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On
Behalf Of grignola
Sent: Friday, 22 January 2010 7:06 AM
To: ASREML-L_at_DPI.NSW.GOV.AU
Subject: Variogram not plotting and problem with pattern function

Hello,
A couple of questions.
1. I upgraded to asreml 3.0 and I'm running the model:
met.1.asr <- asreml(yld ~ Site, random =~ diag(Site):geno,
rcov=~at(Site):ar1(Column):ar1(Row), data=mmData). The sample data is
nicely balanced.
1 2 3 4 5 6
SITE1 72 72 72 72 72 72
SITE2 72 72 72 72 72 72
SITE3 72 72 72 72 72 72

However, with this 3.0 version I cannot plot the variogram as I used to
with the previous version. I now get an error:
> plot(variogram(met.1.asr))
Error in `$<-.data.frame`(`*tmp*`, "gamma", value = c(0,
0.415962583409219, :
replacement has 1296 rows, data has 0

2. To extract solutions from a simple genetic model fitting pedigree
as "random =~ ped(Pedigree)".

coef(model1.asr)$random
effect
ped(Pedigree)_GARDEL_URUGUAYO 2.23904

I first tried this code:
coef(model1.asr,pattern='ped(Pedigree)'), but it does not work. It
returns just the name of the effect, but no solutions.
However, I noticed that the following code does work (note that 'ped('
is missing)
coef(model1.asr,pattern='Pedigree)')
Are there any rules that I'm missing when using "pattern"? It looks like
it does not like "("

Thanks for you for your assistance.

Fernando

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Received on Fri Jan 22 2010 - 16:03:42 EST