[R-sig-ME] HPDinterval MCMCglmm and using transformed variables in MCMCglmm
j.hadfield at ed.ac.uk
Mon Jul 12 12:30:33 CEST 2010
You probably need to load MCMCglmm (library(MCMCglmm)) or at least
load coda. At the moment the response needs to be logged externally:
but the next version will "fix" this.
On 12 Jul 2010, at 10:31, Rebecca Ross wrote:
> Dear ME users,
> Apologies if this is a naive question, I am new to using MCMC glmm.
> I have been working through the tutorial, using some of my own data,
> and I thought I had followed the steps correctly. The model I have
> been fitting is:
> Briefly, I want to see how the Distance variable (continuous)
> affects stem weight, which I have log transformed as the raw data is
> heteroscedastic. Block is field block, and I am fitting the animal
> random effect to take into account different relatedness between
> individuals (I'm not at the moment trying to estimate Va).
> When I tried this model last night, I could get the 95% CIs using
> this function
> When I tried this morning, I get the following error message
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "HPDinterval", for
> signature "mcmc"
> Can anyone explain what has gone wrong? I've tried changing the
> terms in the model, but that doesn't help, so I think I must have
> changed something in R elsewhere? Or else missing something
> completely obvious.
> Question 2: I dont think MCMCglmm is actually logging my stem
> variable because the fixed effect parameter estimate from the model
> above (AMstem3) are about a factor of 10 out from the fixed effect
> estimate from
> a similar model, fit in lme4, without the animal effect and very
> similar to the same model using the raw stem weight (see below). Do
> I need to specify the log transform differently?
> AMstem3c Dist_fr_A posterior mode: -0.004236659
> Fixed effect Estimate: Dist_fr_A -0.0004442 (SE=0.00006136)
> Fixed effect Estimate: Dist_fr_A -0.004342 (SE=0.0006714)
> Thank you very much for your help,
> Rebecca Ross
> DPhil Candidate,
> University of Oxford.
> [[alternative HTML version deleted]]
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