[R] Coda not providing summary on mcmc object

[Ben Bolker]

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