smith_cc <smith_cc <at> yahoo.com> writes:
>
>
> The object is a mcmc sample from lmer. I am using R v2.7.1. Please let me
> know what additional information I can provide, hopefully I am just making a
> simple mistake. Thanks in advance!
>
> > data(ratdrink, package = 'faraway')
> > rd.er <- lmer(wt ~ weeks*treat + (1 | subject), data = ratdrink)
> > rd.mc <- mcmcsamp(rd.er, 10000)
> > library(coda)
> Loading required package: lattice
> > summary(rd.mc)
> Length Class Mode
> 1 merMCMC S4
> > HPDinterval(rd.mc)
> Error in UseMethod("HPDinterval") :
> no applicable method for "HPDinterval"
I don't think it should necessarily have been obvious,
but help("merMCMC-class") suggests that lme4 contains
its own methods for doing HPDinterval calcs. Furthermore,
loading coda after lme4 gives the following warning
The following object(s) are masked from package:lme4 :
HPDinterval
If you really want HPDintervals from coda, it looks like
you can do
HPDinterval(as.mcmc(as.matrix(rd.mc)))
or if you want to use lme4's HPDinterval while
coda is loaded, do
lme4::HPDinterval(rd.mc)
(I don't quite know why lme4 is including its own
calculations rather than just allowing conversion to
coda objects -- maybe they don't want the dependency)
If you have further questions it might make sense
to send them to r-sig-mixed ...
Ben Bolker
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
