[R-sig-ME] Specifying starting point for MCMCglmm()

[sree datta]

Hi Emily

What are the specifications of your data you are using in the model that it
is taking so long (14 days)? How many variables and records are you using?
Have you attempted to run the model with a smaller subset of the data? If
yes, what were the results?

Sree


On Thu, Jun 4, 2020 at 4:10 PM Ruhs, Emily <ecruhs using usf.edu> wrote:

> Hi everyone~
>
> I am running a series of large models in R using MCMCglmm. After running
> the models for 14 days (complicated, multivariate models), I found that the
> models have not converged yet and I need to run more iterations. I know you
> can use the start= to specify a starting function, but I’m having
> difficulties getting the model to run.
>
> model_EC <- parLapply(cl=cl,listEC, function(i) {
>   MCMCglmm(i[[1]],
>            random = ~us(trait):phylo, family=rep("gaussian", 6),
> rcov=~us(trait):units,
>
>  ginverse=list(phylo=inv.phyloEC$Ainv),prior=prior.1,data=i[[2]],
> start=1820000,
>            nitt=2600000,thin=1400,burnin=0)})
>
> As the code is written, I have the start=1820000, which is where the last
> iteration left off. Can anyone explain what I’m doing wrong in specifying
> the start function?
>
> Any help or suggestions would be greatly appreciated!
>
> Best,
> Emily Cornelius Ruhs
> Postdoctoral Scholar
> University of South Florida
>
>
>
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