Priors for MCMCglmm with haplodiploid relatedness matrix
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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