Wrong list! This does not concern R programming. Post on the r-sig-mixed-models list instead in **PLAIN TEXT** rather than html.
Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Thu, May 22, 2014 at 6:52 AM, Claire <c.word...@live.com> wrote: > Dear all, > > I am quite new to R so apologies if I fail to ask properly. I have done a > test comparing bat species richness in five habitats as assessed by three > methods. I used a linear mixed model in lme4 and got habitat, method and the > interaction between the two as significant, with the random effects > explaining little variation. > > I then ran Tukey's post hoc tests as pairwise comparisons in three ways: > > Firstly in lsmeans: > lsmeans(LMM.richness, pairwise~Habitat*Method, adjust="tukey") > > Then in ‘agricolae’: > > tx <- with(diversity, interaction(Method, Habitat)) > amod <- aov(Richness ~ tx, data=diversity) > library(agricolae) > interaction <-HSD.test(amod, "tx", group=TRUE) > interaction > > Then in ghlt 'multcomp': > summary(glht(LMM.richness, linfct=mcp(Habitat="Tukey"))) > > summary(glht(LMM.richness, linfct=mcp(Method="Tukey"))) > > tuk <- glht(amod, linfct = mcp(tx = "Tukey")) > summary(tuk) # standard display > tuk.cld <- cld(tuk) # letter-based display > opar <- par(mai=c(1,1,1.5,1)) > par(mfrow=c(1,1)) > plot(tuk.cld) > par(opar) > > I got somewhat different levels of significance from each method, with ghlt > giving me the greatest number of significant results and lsmeans the least. > All the results from all packages make sense based on the graphs of the data. > > Can anyone tell me if there are underlying reasons why these tests might be > more or less conservative, whether in any case I have failed to specify > anything correctly or whether any of these post-hoc tests are not suitable > for linear mixed models? > > Thankyou for your time, > Claire > > [[alternative HTML version deleted]] > > > ______________________________________________ > R-help@r-project.org 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. > ______________________________________________ R-help@r-project.org 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.
