lmer p-value extraction: LanguageR S4 object error

Hey All,

I'm using the package languageR to extract p-values from a lmer model using
the syntax and data at the end of this post. Within language R,  when I try
and use the pvals.fnc function I get the following error:

Error in pvals.fnc(lmer.seeded, nsim = 10000) :
  trying to get slot "coefs" from an object (class "summaryDefault") that is
not an S4 object

Any help in figuring this out would be appreciated.

The background on this analysis is that I have two treatments (C and UC)
within five blocks, within two sites (M and CF). With data collected over
three consecutive years. In this analysis I would like to set year, and
block (nested within site) as random effects, with treatment as the fixed
effect to determine if there are differences in vegetation density between
treatments.

It's a little dodgy to use year (with only 3 levels) as a random
effect -- you might try with a fixed effect and see whether you get
different results.

  I don't understand why you're using aovlmer.fnc with
which=c("TreatC","TreatUC") -- it looks to me as though this function is
intended to be used to test hypotheses involving multiple parameters
simultaneously equalling zero.  Testing both levels of the treatment in
this way doesn't really make sense (to me).  Furthermore, I think you'd
need "Treat-1" rather than "Treat" as your fixed effect to do this.

  If you just want to test for differences between the two treatment
levels, what's wrong with the results of 'mcmc0' below?

lmer.seeded=lmer(Seeded~Treat+(1|Fire/Block)+(1|Year),data=cover)
mcmc0=pvals.fnc(lmer.seeded,nsim=10000)
mcmc=pvals.fnc(lmer.seeded,nsim=10000,withMCMC=TRUE)
xyplot(as.mcmc(mcmc$mcmc),layout=c(2,3))

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Daniel,

This has happened to me before, and Harald Baayen explained the issue:
It appears that recent versions of the languageR package are not
compatible with the newest version of R.

Please try to use R version 2.11 or 2.12 and see if this solves the problem.

If you can't go back to the older version of R, use R version 2.13
with languageR version 1.2 (which is on CRAN)

http://cran.r-project.org/web/packages/languageR/index.html

Let me know if that fixes things,

Cyrus
http://www.ualberta.ca/~cshaoul/

I tried the code that you included in your response and it came up with the
same error that I've been getting all along:

Error in pvals.fnc(lmer.seeded, nsim = 10000) :
?trying to get slot "coefs" from an object (class "summaryDefault")
that is not an S4 object

Were you able to get results using this code? Any ideas on why I'm getting
this error when I try the pvals.fnc function?

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