[R] incorrect MCMC CIs in pvals.fnc (languageR) ?

From: Mike Allerhand <michael.allerhand_at_ed.ac.uk>
Date: Fri, 11 May 2007 14:16:25 +0100

library(lme4)
library(coda)
library(languageR)

fit = lmer(Reaction~Days + (1|Subject) + (0+Days|Subject), data=sleepstudy)

pvals.fnc(fit)$random

# compare with...

samp = mcmcsamp(fit, n=10000, trans=FALSE) HPDinterval(samp)
densityplot(samp, plot=F)

# 'pvals.fnc' reports sigma instead of sigma^2, but it looks like the
# Sbjc.(In) and Sbjc.Days are also sqrt compared with the corresponding
# results from HPDinterval and densityplot. Is that intended?

best wishes, Mike Allerhand



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