[R-sig-ME] New mcmcpvalue?

Hank Stevens HStevens at MUOhio.edu
Tue Jul 8 18:33:46 CEST 2008

Hi folks,
It seems that with lme4_0.999375-21, and -20, lmer objects (mer class)  
require a new mcmcpvalue function, because of the values created. This  
(I think) works properly, because it converts the rows of the output  
to columns used by the original mcmcpvalue.

mcmcpvalue <- function(X) {
    ##From Bates pers comm. September 14, 2006 2:59:23 PM EDT
    ## elementary version that creates an empirical p-value for the
    ## hypothesis that the columns of samp have mean zero versus a
    ## general multivariate distribution with elliptical contours.
# samp <- rnorm(10000, m=3)
    ## differences from the mean standardized by the observed
    ## variance-covariance factor

if(class(X) == "numeric") samp <- as.matrix(X) else{
   samp <- t( X ) }
## END new part

std <- backsolve(chol(var(samp)),
                     cbind(0, t(samp)) - colMeans(samp),
                     transpose = TRUE)
    sqdist <- colSums(std * std)
    sum(sqdist[-1] > sqdist[1])/nrow(samp)

Dr. Hank Stevens, Associate Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056

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believe and adore." -Ralph Waldo Emerson, writer and philosopher  

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