hello, i found it most convenient to use package contrast for planned comparisons on mixed models. for instance i have a model with 2 fixed factors, one with 4 levels (stage) and one with 2 levels (gap) and a nested random factor (site) and i tested gap within level A of factor stage:
library(contrast) library(nlme) m1<-lme(rich ~ stage*gap, random=~1|site,data=richness) contrast(m1, a = list(stage="A",gap="0"), b = list(stage="A",gap="1")) ..this works fine. now i wont to do the same with lmer() because the response is a count - but this doesn't work with contrast(): library(lme4) detach(package:nlme) m2<-lmer(rich ~ stage*gap+(1|site),family=poisson,data=richness) contrast(m2, a = list(stage="A",gap="0"), b = list(stage="A",gap="1")) Error in UseMethod("contrast") : no applicable method for 'contrast' applied to an object of class "mer" i tried with glht() from multcomp, but was not able to set it up right - could anyone please help me with how this sort of contrast is produced with glht()? thanks for any help, kay my data: richness<-data.frame(list(structure(list(stage = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("A", "B", "C", "D" ), class = "factor"), site = structure(c(2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 18L, 18L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 25L, 25L, 25L, 25L, 26L, 26L, 26L, 26L, 27L, 27L, 27L, 27L, 28L, 28L, 28L, 28L, 29L, 29L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 32L, 32L, 32L, 32L, 33L, 33L, 33L, 33L, 34L, 34L, 34L, 34L, 35L, 35L, 35L, 35L, 36L, 36L, 36L, 36L, 37L, 37L, 38L, 38L, 38L, 38L, 39L, 39L, 39L, 39L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 18L, 18L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 25L, 25L, 25L, 25L, 26L, 26L, 26L, 26L, 27L, 27L, 27L, 27L, 28L, 28L, 28L, 28L, 29L, 29L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 32L, 32L, 32L, 32L, 33L, 33L, 33L, 33L, 34L, 34L, 34L, 34L, 35L, 35L, 35L, 35L, 36L, 36L, 36L, 36L, 37L, 37L, 38L, 38L, 38L, 38L, 39L, 39L, 39L, 39L), .Label = c("A11", "A12", "A14", "A15", "A16", "A17", "A18", "A19", "A20", "A5", "A7", "A8", "B1", "B12", "B13", "B14", "B15", "B17", "B18", "B2", "B4", "B7", "B8", "B9", "C1", "C10", "C11", "C15", "C17", "C18", "C19", "C2", "C20", "C3", "C4", "C6", "D1", "D4", "D7"), class = "factor"), gap = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("0", "1"), class = "factor"), rich = c(0L, 2L, 3L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 0L, 1L, 3L, 3L, 3L, 1L, 2L, 3L, 7L, 4L, 2L, 1L, 3L, 2L, 2L, 2L, 2L, 3L, 4L, 1L, 1L, 2L, 1L, 3L, 1L, 1L, 2L, 0L, 0L, 3L, 1L, 0L, 1L, 3L, 2L, 3L, 5L, 6L, 7L, 2L, 5L, 8L, 10L, 10L, 9L, 3L, 9L, 6L, 2L, 5L, 1L, 6L, 8L, 7L, 7L, 2L, 6L, 7L, 5L, 3L, 2L, 3L, 9L, 9L, 9L, 9L, 5L, 7L, 4L, 2L, 8L, 4L, 8L, 5L, 8L, 5L, 3L, 7L, 6L, 7L, 8L, 6L, 7L, 5L, 6L, 10L, 10L, 15L, 10L, 11L, 5L, 10L, 6L, 7L, 7L, 10L, 7L, 11L, 6L, 4L, 4L, 6L, 5L, 6L, 5L, 5L, 8L, 5L, 5L, 7L, 5L, 9L, 8L, 6L, 9L, 3L, 4L, 8L, 9L, 7L, 10L, 9L, 9L, 12L, 10L, 12L, 12L, 13L, 11L, 9L, 9L, 9L, 0L, 2L, 1L, 4L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 3L, 1L, 7L, 4L, 2L, 4L, 2L, 2L, 3L, 1L, 3L, 1L, 1L, 1L, 2L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 0L, 3L, 2L, 2L, 3L, 1L, 2L, 2L, 4L, 5L, 4L, 5L, 7L, 6L, 4L, 9L, 5L, 2L, 2L, 0L, 3L, 6L, 1L, 4L, 3L, 3L, 4L, 2L, 5L, 7L, 4L, 2L, 1L, 1L, 5L, 4L, 4L, 4L, 1L, 2L, 1L, 2L, 6L, 5L, 10L, 1L, 4L, 4L, 1L, 3L, 5L, 4L, 4L, 4L, 4L, 4L, 3L, 3L, 5L, 9L, 4L, 5L, 6L, 7L, 4L, 5L, 4L, 7L, 4L, 6L, 5L, 2L, 3L, 2L, 6L, 1L, 4L, 5L, 6L, 3L, 5L, 4L, 4L, 3L, 2L, 4L, 1L, 4L, 3L, 4L, 3L, 6L, 2L, 9L, 8L, 10L, 5L, 7L, 10L, 7L, 7L, 4L, 5L, 5L)), .Names = c("stage", "site", "gap", "rich"), class = "data.frame", row.names = c(NA, -286L)))) ----- ------------------------ Kay Cichini Postgraduate student Institute of Botany Univ. of Innsbruck ------------------------ -- View this message in context: http://r.789695.n4.nabble.com/contrasts-for-lmer-model-tp2222682p2222682.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.