[R] Coda not providing summary on mcmc object

From: smith_cc <smith_cc_at_yahoo.com>
Date: Mon, 30 Jun 2008 14:24:36 -0700 (PDT)

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"
> str(rd.mc)

Formal class 'merMCMC' [package "lme4"] with 9 slots

  ..@ Gp      : int [1:2] 0 27
  ..@ ST      : num [1, 1:10000] 1.179 0.878 0.864 0.760 0.614 ...
  ..@ call    : language lmer(formula = wt ~ weeks * treat + (1 | subject),
data = ratdrink)
  ..@ deviance: num [1:10000] 964 964 966 966 969 ...
  ..@ dims    : Named int [1:14] 1 135 6 27 1 1 1 2 5 1 ...
  .. ..- attr(*, "names")= chr [1:14] "nf" "n" "p" "q" ...
  ..@ fixef   : num [1:6, 1:10000] 52.880 26.480  4.780 -0.794 -9.370 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:6] "(Intercept)" "weeks" "treatthiouracil"
"treatthyroxine" ...
  .. .. ..$ : NULL
  ..@ nc      : int 1
  ..@ ranef   : num[1:27, 0 ] 
  ..@ sigma   : num [1, 1:10000] 7.16 6.68 6.60 7.14 7.96 ...

> search()
[1] ".GlobalEnv" "package:lme4" "package:Matrix" "package:coda" "package:lattice" "package:datasets" "package:grDevices" [8] "package:graphics" "package:stats" "package:utils" "package:methods" "Autoloads" "package:base"

>

Cheers,
Chad

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