Dear R users, I have developed a model I have compared several options of obtaining p-values for poisson lmer model including Marlov chain monty carlo methods, single term deletions and summary. > > However, I encountered several problems that can be classified as > (1) the p values from the summary command are total different from those derived from Marlov chain monty carlo methods
> How can I proceed, left with these uncertainties in the estimations of > the p-values? > > Below is the corresponding R code with some output so that you can see: > > ## > fit<-lmer(End~Treatment+offset(log(Area)+(1|Site/Treatment), family=poisson) > Summary Intercept > The p-values from mcmc are: > > ## > markov1=mcmcsamp(m2,5000) > > HPDinterval(markov1) > 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 landscape.div > [1] 0.0074 > > If one runs the mcmcsamp function for, say, 50,000 runs, the p-values > are slightly different (not shown here). > > ##here are the p-values summarized in tabular form: <snip> [MCMC] > logpatch 0.004 > loghab 0.0598 > landscape_diversity 0.0074 <snip> [single-term deletions] > logpatch 0.007106 > loghab 0.1704 > landscape_diversity 0.01276 <snip> > To summarize, at least for quasipoisson models, the p-values obtained > from mcmcpvalue() are quite different from those obtained using > single-term deletions followed by a chisquare test. > > Especially in the case of "loghab", the difference is so huge that one > could tend to interpret one of the p-values as "marginally significant". ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
