Thanks Peter for the advice and quick response. I just want to clarify what you suggest. I should average values within a site then do a one-way anova to test for differnces between sites based on the 2 to 3 new samples per stand type -- and not use random effects for site? Or, because I've reduced the data I've 'corrected' the problem with the glht multiple comparisons and can use the p-values from that summary if I include site as a random effect? Thanks again for your advice.
> lba...@montana.edu wrote: >> Hello, >> I have some conflicting output from an aov summary and tukey contrasts with a mixed effects model I was hoping someone could clarify. I am comparing the abundance of a species across three willow stand types. Since I have 2 or 3 sites within a habitat I have included site as a random effect in the lme model. My confusion is that the F test given by >> aov(model) indicates there is no difference between habitats, but the tukey contrasts using the multcomp package shows that one pair of habits >> is significantly different from each other. Why is there a discrepancy? >> Have I specified my model correctly? I included the code and output below. Thank you. > > Looks like glht() is ignoring degrees of freedom. So what it does is wrong but it is not easy to do it right (whatever "right" is in these cases). If I understand correctly, what you have is that "stand" is strictly coarser than "site", presumably the stands representing each 2, 2, and 3 sites, with a varying number of replications within each site. Since the between-site variation is considered random, you end up with a comparison of stands based on essentially only 7 pieces of information. (The latter statement requires some qualification, but let's not go there to day.) > > If you have roughly equal replications within each site, I'd be strongly tempted to reduce the analysis to a simple 1-way ANOVA of the site averages. > >>> co.lme=lme(coye~stand,data=t,random=~1|site) >>> summary (co.lme) >> Linear mixed-effects model fit by REML >> Data: R >> AIC BIC logLik >> 53.76606 64.56047 -21.88303 >> Random effects: >> Formula: ~1 | site >> (Intercept) Residual >> StdDev: 0.3122146 0.2944667 >> Fixed effects: coye ~ stand >> Value Std.Error DF t-value p-value >> (Intercept) 0.4936837 0.2305072 60 2.1417277 0.0363 >> stand2 0.4853222 0.3003745 4 1.6157240 0.1815 >> stand3 -0.3159230 0.3251201 4 -0.9717117 0.3862 >> Correlation: >> (Intr) stand2 >> stand2 -0.767 >> stand3 -0.709 0.544 >> Standardized Within-Group Residuals: >> Min Q1 Med Q3 Max >> -2.4545673 -0.5495609 -0.3148274 0.7527378 2.5151476 >> Number of Observations: 67 >> Number of Groups: 7 >>> anova(co.lme) >> numDF denDF F-value p-value >> (Intercept) 1 60 23.552098 <.0001 >> stand 2 4 3.738199 0.1215 >>> summary(glht(co.lme,linfct=mcp(stand="Tukey"))) >> Simultaneous Tests for General Linear Hypotheses >> Multiple Comparisons of Means: Tukey Contrasts >> Fit: lme.formula(fixed = coye ~ stand, data = R, random = ~1 | site) Linear Hypotheses: >> Estimate Std. Error z value Pr(>|z|) >> 2 - 1 == 0 0.4853 0.3004 1.616 0.2385 >> 3 - 1 == 0 -0.3159 0.3251 -0.972 0.5943 >> 3 - 2 == 0 -0.8012 0.2994 -2.676 0.0202 * >> --- >> Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 >> (Adjusted p values reported -- single-step method) >> Lisa Baril >> Masters Candidate >> Department of Ecology >> Montana State University - Bozeman >> 406.994.2670 >> ______________________________________________ >> 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. > > > -- > O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > ~~~~~~~~~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 > > ______________________________________________ > 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. > > > Lisa Baril Masters Candidate Department of Ecology Montana State University - Bozeman 406.994.2670 ______________________________________________ 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.
