search for: mcmcpvalue

Displaying 7 results from an estimated 7 matches for "mcmcpvalue".

2009 Feb 24
2
lmer, estimation of p-values and mcmcsamp
...er 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.matr...
2007 Feb 12
1
lmer and estimation of p-values: error with mcmcpvalue()
...llow the suggestions for a correct estimation of p-values as discusssed at R-Wiki (http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-tests&s=lme%20and%20aov). However, I have the problem that my model only consists of parameters with just 1 d.f. (intercepts, slopes), so that the "mcmcpvalue" function defined below obviously produces error messages. How can I proceed in estimating the p-values, then? I very much acknowledge any suggestions. Best regards Christoph. ## mcmcpvalue <- function(samp) { std <- backsolve(chol(var(samp)), cbind(0, t(samp)...
2007 Mar 12
2
Lmer Mcmc Summary and p values
...7.666 1.77e-14**** Treatment 2 3.7970 0.505 7.516 5.51e-14**** Treatment 3 0.2409 9.6704 0.359 0.719 Treatment 4 -0.2483 0.8661 -0.287 0.774 Correlation of fixed effects Intra T2 T3 T2 -0.989 T3 -0.745 0.737 T4 -0.577 0.570 0.430 > The p-values from mcmc are: > 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) } fitSI<-mcmcsamp(fit,50000) library(coda) HPDinterval(fitSI) lower upper Intercept -4.0778905...
2007 Feb 13
1
lme4/lmer: P-Values from mcmc samples or chi2-tests?
...lower upper (Intercept) -1.394287660 0.6023229 logpatch 0.031154910 0.1906861 loghab 0.002961281 0.2165285 landscape_diversity 0.245623183 1.6442544 log(site.(In)) -41.156007604 -1.6993996 attr(,"Probability") [1] 0.95 ## mcmcpvalue(as.matrix(markov1[,1])) #i.e. the p value for the intercept [1] 0.3668 > mcmcpvalue(as.matrix(markov1[,2])) #i.e. the p-value for logpatch [1] 0.004 > mcmcpvalue(as.matrix(markov1[,3])) #i.e. the p-value for loghab [1] 0.0598 > mcmcpvalue(as.matrix(markov1[,4])) #i.e. the p-value for la...
2007 Mar 12
0
Pvalues and lme
...arkov1) > lower upper > (Intercept) -1.394287660 0.6023229 > logpatch 0.031154910 0.1906861 > loghab 0.002961281 0.2165285 > landscape_diversity 0.245623183 1.6442544 > log(site.(In)) -41.156007604 -1.6993996 > attr(,"Probability") > [1] 0.95 > > ## > > mcmcpvalue(as.matrix(markov1[,1])) #i.e. the p value for the intercept > [1] 0.3668 > > mcmcpvalue(as.matrix(markov1[,2])) #i.e. the p-value for logpatch > [1] 0.004 > > mcmcpvalue(as.matrix(markov1[,3])) #i.e. the p-value for loghab > [1] 0.0598 > > mcmcpvalue(as.matrix(markov1[,4]...
2007 Mar 13
1
lme4 and mcmcamp
...4995 -7.666 1.77e-14**** Treatment 2 3.7970 0.505 7.516 5.51e-14**** Treatment 3 0.2409 9.6704 0.359 0.719 Treatment 4 -0.2483 0.8661 -0.287 0.774 Correlation of fixed effects Intra T2 T3 T2 -0.989 T3 -0.745 0.737 T4 -0.577 0.570 0.430 > The p-values from mcmc are: > 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) } fitSI<-mcmcsamp(fit,50000) library(coda) HPDinterval(fitSI) lower upper Intercept -4.0778905...
2008 Aug 29
1
significance of random effects in poisson lmer
...ength) as a function of fixed effects Shrub (%shrub cover) and Width (width of road), and random effect Site (nested within Site Cluster). >From reading answers to previous posts, it seems that the consensus is to derive p-values using the neat little piece of code posted by Doug Bates as "mcmcpvalue". This code calls the merMCMC object created by the function mcmcsamp, but I can't even get as far as using this function without running into difficulty. Basically, I get an error message saying "Error in .local(object, n, verbose, ...) : Update not yet written" - see below for...