[R] lmer, estimation of p-values and mcmcsamp

[levyofi]

For getting the p-values from a lmer object you need to use the pvals.fnc()
function. do the following:

library(lme4)
library(languageR)
lnmass <- lmer(log.mass ~ treatment + (1|block), data=exp1)
pvals.fnc(lnmass, nsim=10000)

See the documentation for futher details.

Best regards,
Ofir. 


Maureen Ryan wrote:
> 
> (To the list moderator: I just subscribed to the list.  Apologies for not
> having done so longer before trying to post.)
> 
> Hi all,
>      I am currently using lmer to analyze data from an experiment with a
> single fixed factor (treatment, 6 levels) and a single random factor
> (block). I've been trying to follow the online guidance for estimating
> p-values for parameter estimates on these and other help threads:
> 
> https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html
> http://pidgin.ucsd.edu/pipermail/r-lang/2007-August/000057.html
> 
> but have not yet been successful. This is my code:
> 
> lnmass <- lmer(log.mass ~ treatment + (1|block), data=exp1)
> summary(lnmass)
> 
> samp <- rnorm(n=10000)
> mcmcpvalue <- function(samp)
>      {std <- backsolve(chol(var(samp)),
>           cbind(0,t(samp)) - colMeans(samp),
>           transpose = TRUE)
>      sqdist <- colSums(std*std)
>      sum(sqdist[-1] > sqdist[1]/nrow(samp) }
> 
> markov1 <- mcmcsamp(lnmass, 10000)
> HPDinterval(markov1)
> 
> mcmcpvalue(as.matrix(markov1[,1]))
> mcmcpvalue(as.matrix(markov1[,2]))
> mcmcpvalue(as.matrix(markov1[,3]))
> mcmcpvalue(as.matrix(markov1[,4]))
> mcmcpvalue(as.matrix(markov1[,5]))
> mcmcpvalue(as.matrix(markov1[,6]))
> 
> The first time I tried it HPDinterval generated CIs for each treatment
> level, etc. but after each of the last 6 lines of code I received the
> following error messages:
> 
> Error in markov[,1] : object is not subsettable
> Error in as.matrix(markov1[,1]) : error in evaluating the argument 'x' in
> selecting a method for function  'as.matrix'
> Error in chol(val(samp)) : error in evaluating the argument 'x' in
> selecting
> a method for function 'chol'
> 
> When I came back to it today HPDinterval(markov1) also no longer worked
> and
> gave me the following error message:
> 
> Error in UseMethod("HPDinterval"): no applicable method for "HPDinterval"
> 
> I imagine at least some of this has to do with the fact that I don't fully
> understand what exactly the mcmcpvalue function is doing.  Any help on
> either problem would be very much appreciated.
> 
> Thanks, Maureen
> 
> *****
> Maureen Ryan
> Department of Evolution and Ecology
> University of California Davis
> One Shields Avenue
> Davis, CA 95616
> (530)304-2266
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
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> 
> 

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