Wendy Qiao
2013-Jan-10 16:08 UTC
[R] Questions about the glht function for planned comparison
Hi all, I've posted this question before, but did not get any reply. I post it again here and see if anybody can help. Thank you. I have a nested model with the following effects fixed: treatments random: experiment_date I used lme() to model the data mod1 <- lme(N_cells ~treatments-1, random=~1|experiment_date, method='ML') Then I want to compare all the other treatments to the control (included in the "treatments" in mod1). After a fair amount of searching around, I decided to use glht() from the multcomp package (any other suggestions?). lvl.treatments=table(treatments) K = contrMat(lvl.treatments,type='Dunnett',base=1) mc<-glht(mod1, linfct=mcp(treatments=K),alternative='greater') But I got the following error: Error in contr.treatment(n = 0L) : not enough degrees of freedom to define contrasts I tried to extract the df parameter using "modelparm()", but the function couldn't be applied to lme: Error in UseMethod("modelparm") : no applicable method for 'modelparm' applied to an object of class "lme" The degree of freedom of the fixed effect was 194. I tried to specify the number in glht, but got the same error as "not enough degrees of freedom to define contrasts". Does anyone know what's happening and how I could possibly solve the problem? Thank you so much. Best, Wendy [[alternative HTML version deleted]]