Dear Sibylle,

Have you tried to create a new variable?

ME$fDiversity <- factor(ME$Diversity)

H08_lme <- lme(
log(Height2008_mean) ~ fDiversity,
data = ME,
random = ~ 1|Plot/SubPlot,
weights = varPower(form = ~Diversity),
na.action = na.omit,
subset = ME$Species == "Ace_pse",
method = "ML"
)
summary(H08_lme)
anova(H08_lme)
g_H08_lme <- glht(H08_lme, linfct = mcp(fDiversity = "Tukey"))

Please note that I’ve added (a lot of) whitespace to your code to make it easier to read.

Best regards,

Thierry

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx@inbo.be<mailto:Thierry.Onkelinx@inbo.be>
www.inbo.be<http://www.inbo.be/>

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

Van: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org] Namens Sibylle Stöckli
Verzonden: donderdag 25 juli 2013 12:16
Aan: r-help@r-project.org
Onderwerp: [R] lme (weights) and glht

Dear R members,

I tried to fit an lme model and to use the glht function of multcomp.
However, the glht function gives me some errors when using
weights=varPower().
The glht error makes sense as glht needs factor levels and the model
works fine without weights=. Does anyone know a solution so I do not
have to change the lme model?

Thanks
Sibylle

--> works fine
ME$Diversity=factor(ME$Diversity)
H08_lme<-lme(log(Height2005_mean)~Diversity, data=ME, random=~1|Plot/
SubPlot, na.action=na.omit, subset=ME$Species=="Pse_men", method="ML")
summary(H08_lme)
anova(H08_lme)
g_H08_lme<-glht(H08_lme, linfct=mcp(Diversity="Tukey"))
print(summary(g_H08_lme))

--> using lme with weights I changed the order of factor() and
introduced as.factor in the model

H08_lme<-lme(log(Height2008_mean)~as.factor(Diversity), data=ME,
random=~1|Plot/SubPlot, weights=varPower(form=~Diversity),
na.action=na.omit, subset=ME$Species=="Ace_pse", method="ML")
summary(H08_lme)
anova(H08_lme)
ME$Diversity=factor(ME$Diversity)
g_H08_lme<-glht(H08_lme, linfct=mcp(Diversity="Tukey"))

Error in mcp2matrix(model, linfct = linfct) :
   Variable(s) �Diversity� have been specified in �linfct� but cannot
be found in �model�!
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