[R] [R-sig-ME] Post hoc tests with lme

[Robert Kushler]

At the risk of annoying Doug Bates, I'll point out that "glht" in
the multcomp package works with lmer objects.  In fact, you can
supply your own degrees of freedom value via the "df" argument
(a fact which is not immediately obvious in the glht help page).
If you don't supply a df value, it will use "Inf" (i.e., normal
instead of t).

Regards,   Rob Kushler


Gang Chen wrote:
> Using the "ergoStool" data cited in Mixed-Effects Models in S and
> S-PLUS by Pinheiro and Bates as an example, we have
> 
> ========
>> library(nlme)
>> fm <- lme(effort~Type-1, data=ergoStool, random=~1|Subject)
>> summary(fm)
> 
> Linear mixed-effects model fit by REML
>   Data: ergoStool
>        AIC      BIC   logLik
>   133.1308 141.9252 -60.5654
> 
> Random effects:
>  Formula: ~1 | Subject
>         (Intercept) Residual
> StdDev:    1.332465 1.100295
> 
> Fixed effects: effort ~ Type - 1
>            Value Std.Error DF  t-value p-value
> TypeT1  8.555556 0.5760123 24 14.85308       0
> TypeT2 12.444444 0.5760123 24 21.60448       0
> TypeT3 10.777778 0.5760123 24 18.71102       0
> TypeT4  9.222222 0.5760123 24 16.01046       0
>  Correlation:
>        TypeT1 TypeT2 TypeT3
> TypeT2 0.595
> TypeT3 0.595  0.595
> TypeT4 0.595  0.595  0.595
> 
> Standardized Within-Group Residuals:
>         Min          Q1         Med          Q3         Max
> -1.80200345 -0.64316591  0.05783115  0.70099706  1.63142054
> 
> Number of Observations: 36
> Number of Groups: 9
> 
> ========
> 
> Now suppose I want to test the following hypothesis
> 
> H0: TypeT1 =0 and TypeT2 = 0
> 
> I've tried estimable() and glh.test() in package gmodels, esticon() in
> package boBy, and linear.hypothesis() in package car, but it seems
> none of them would work with objects from lme:
> 
> ========
>> library(gmodels)
>> estimable(fm, rbind(c("TypeT1"=1), c("TypeT2"=1)))
> Error in FUN(newX[, i], ...) :
>   `param' has no names and does not match number of coefficients of
> model. Unable to construct coefficient vector
>> glh.test(fm, rbind(c("TypeT1"=1), c("TypeT2"=1)))
> Error in glh.test(fm, rbind(c(TypeT1 = 1), c(TypeT2 = 1))) :
>   Only defined for lm,glm objects
> 
>> library(doBy)
>> esticon(fm, rbind(c("TypeT1"=1), c("TypeT2"=1)))
> Error in t(abs(t(tmp) * obj$fixDF$X)) :
>   dims [product 2] do not match the length of object [4]
> In addition: Warning message:
> In esticon.lme(fm, rbind(c(TypeT1 = 1), c(TypeT2 = 1))) :
>   The esticon function has not been thoroughly teste on 'lme' objects
> 
>> library(car)
>> linear.hypothesis(fm, rbind(c("TypeT1"=1), c("TypeT2"=1)))
> Error in L %*% b : requires numeric matrix/vector arguments
> ========
> 
> So is there any other package with which I can run this kind of tests?
> 
> Thanks,
> Gang
> 
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