[R-sig-ME] Priors for MCMCglmm with haplodiploid relatedness matrix

[Matthew Wolak]

Hi Mike,

As Jarrod suggests, the singularity could be due to a numerical
dependence among entries in the matrix that could arise either because
of the structure of the pedigree or because of (more or less) rounding
errors. Have you/can you compare your haplo.mat.inverse to what you get
if you run the pedigree through the `makeS()` function in the nadiv
package? Does supplying the makeS inverse matrix allow the model to run?

For example, using the `FG90` example pedigree in nadiv:

nadiv.haplo.mat.inverse <- makeS(FG90, heterogametic = "0", DosageComp =
"ngdc")$Sinv

# Where the `heterogametic` argument gives the code in a 4th column of
the pedigree denoting the haploid sex


Matthew

....................................................
Dr. Matthew E. Wolak
School of Biological Sciences
Zoology Building
University of Aberdeen
Tillydrone Avenue
Aberdeen AB24 2TZ

Zoology room 202
office phone: +44 (0)1224 273255

On 04/10/16 17:00, Michael Sheehan wrote:
> Dear all,
>
>
> I am attempting to examine the heritability of a number of traits in a haplodiplod species using MCMCglmm. This has presented a number of challenges since the standard relatedness matrix calculated from a pedigree as part of the program assumes diploid relatedness, which underestimates relatedness among sisters. I have been able to make a haplodiploid appropriate relatedness matrix but when I run the following:
>
>
> model1=MCglmm(trait~1, random=~animal, ginverse=list(animal=haplo.mat.inverse), data�ta, family="ordinal", prior=prior1, nitt5000, thin0, burninP00, verbose=T)
>
>
> I immediately get the following error:
>
>
> "G-structure 1 is ill-conditioned (possibly because of ginverse): use proper priors if you haven't, or rescale data if you have"
>
>
> If I run the same code with a diploid relatedness matrix (calling it through pedigree or ginverse) the program runs without error. I have tried a wide range of priors and even run without priors and get the same error for the haplodiploid matrix while the diploid matrix runs.
>
>
> I am curious if others have received a similar message and how it was dealt with.
>
>
> Thanks in advance for any help!
>
> Mike Sheehan
>
>
>
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