[R-sig-ME] LME and TukeyHSD

[Christoph Scherber]

Dear Sibylle,

The reason for the error message may be that you transform your response
variable inside the model formula. This frequently causes errors when
working with components of lme models. In addition, you should try "ML"
instead of "REML" (when working with the fixed effects).

You may want to try:

##

mydata<-subset(Kaltenborn,ADDspecies!=1)
mydata$sinmortality<-asin(sqrt(Kaltenborn$PropMortality))
mydata<-mydata[!is.na(mydata$sinmortality),]

modelF<-lme(sinmortality~Diversity+Management+Species
+Height+Year+Diversity*Year, data=mydata, random=~1|Plot/SubPlot,
weights=varPower(form=~Diversity), method="ML")

summary(glht(modelF,linfct=mcp(Species="Tukey")))

##

Be reminded that it may not be sensible to test for Species main effects
when interactions are present; have you tested for interactions between
Species and other terms in the model?

Best wishes,
Christoph





> Dear R users
>
> I used lme to fit a linear mixed model inlcuding weights=varPower()
> and subset. Additionally I wanted to use glht to calculate Tukey-
> Kramer multiple comparisions.
>
> I think that the error in glht() is probably caused by the subset and
> varPower function within the lme model? I would very much appreciate
> an input.
>
> Thanks
> Sibylle
>
> LME MODEL
>  > modelF<-lme(asin(sqrt(PropMortality))~Diversity+Management+Species
> +Height+Year+Diversity*Year, data=Kaltenborn, random=~1|Plot/SubPlot,
> na.action=na.omit, weights=varPower(form=~Diversity), subset=Kaltenborn
> $ADDspecies!=1, method="REML")
>
>  > anova(modelF, type="marginal")
>                 numDF denDF  F-value p-value
> (Intercept)        1   162  7.12789  0.0084
> Diversity          1    14 12.89284  0.0030
> Management         2    30  5.52544  0.0091
> Species            3   162 41.81003  <.0001
> Height             1   162  2.59134  0.1094
> Year               1   162  7.07660  0.0086
> Diversity:Year     1   162 12.88095  0.0004
>
> TukeyHSD
>  > library(multcomp)
> Loading required package: mvtnorm
> Warning messages:
> 1: package 'multcomp' was built under R version 2.7.2
> 2: package 'mvtnorm' was built under R version 2.7.2
>  > summary(glht(modelF,linfct=mcp(Species="Tukey")))
>
> error
> Error in glht.matrix(model = list(modelStruct = list(reStruct =
> list(SubPlot = -0.305856275920955,  :
>    ‘ncol(linfct)’ is not equal to ‘length(coef(model))’
>  >
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