[R-sig-ME] MCMCglmm error

[Walid Crampton-Mawass]

Thank you Jarrod for your reply!

If I understand correctly then, to stop this error I should just give a
dummy maternal id for the individuals with missing id.

Thank you again for your help

Walid Mawass






On Wed, Mar 20, 2019, 3:34 PM HADFIELD Jarrod <j.hadfield using ed.ac.uk> wrote:

> Hi,
>
> MCMCglmm used to issue a warning if there were NA’s in the random effect
> predictors. However, people seemed to ignore it when it was inappropriate.
> The only case I can think of where it should be ignored is in a multi
> membership model where the number of members varies over observations,
> which is probably a rare type of model. Consequently, I now just stop
> people doing what I *think*they didn’t intend. It may be the case that you
> don’t know who the mother is, but that doesn’t mean they don’t have a
> mother. Fitting a dummy maternal id is the standard solution.
>
> A more informative error message will be in the next release.
>
> Cheers,
>
> Jarrod
>
> > On 20 Mar 2019, at 19:01, Walid Crampton-Mawass <walidmawass10 using gmail.com>
> wrote:
> >
> > Hello everyone,
> >
> > I started getting this error when I run an animal model with a maternal
> > random effect using MCMCglmm. here is my code:
> >
> > *prior1 <- list(R=list(V=1, nu=0.002), G=list(G1=list(V=1,
> > nu=0.002),G2=list(V=1, nu=0.002)))*
> >
> > *model_afr_3_1 <- MCMCglmm(AFR~
> > 1+OffMortality+COEFPAR+I(COEFPAR*COEFPAR)+TWIN+BIRTHYW+mortrate1 ,
> random =
> > ~animal + MOTHERW, rcov = ~units, data = IAC, pedigree = prunedPed,
> family
> > = "gaussian" , nitt = 3500000, burnin = 500000, thin = 3000, prior =
> > prior1, verbose = FALSE, pr=TRUE)*
> > *Error in t(ZZ[[k]]) : invalid object passed to as_cholmod_sparse*
> > *Calls: MCMCglmm -> buildZ -> t -> t*
> >
> > I was able to find out that the variable causing the error is the second
> > random term "MOTHERW" which represents the id of each individual's mother
> > as to model maternal variation. However I started getting this error
> > recently even though it used to work beforehand without any errors. The
> > variable is set as a multi-level factor just as is done to the "animal"
> > variable. But there are a few missing values for some individuals (20 out
> > of 572)
> >
> > *str(dat$MOTHERW)*
> > * Factor w/ 297 levels "100007","100032",..: 114 142 207 12 258 168 261
> 230
> > 179 107 ...*
> >
> > I tried another variable, FATHERW, which is the id of the father of the
> > individual. I get the same error again : *Error in t(ZZ[[k]]) : invalid
> > object passed to as_cholmod_sparse*
> >
> > However, when using another variable in my data as a random variable
> > instead, BIRTHYW (birth year of individual; set as a factor), the model
> > runs without any errors. The only difference is that there are no missing
> > values in this variable compared MOTHERW  and FATHERW.
> >
> > is it probably the case that we can't use a variable with a few missing
> > values as a random variable in MCMCglmm anymore?
> >
> > Thanks for any help!
> > --
> > Walid Mawass
> > Ph.D. candidate in Cellular and Molecular Biology
> > Population Genetics Laboratory
> > University of Québec at Trois-Rivières
> > 3351, boul. des Forges, C.P. 500
> > Trois-Rivières (Québec) G9A 5H7
> > Telephone: 819-376-5011 poste 3384
> >
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> >
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