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

From: Robert Kushler <kushler_at_oakland.edu>
Date: Wed, 16 Apr 2008 14:45:33 -0400

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
>
> _______________________________________________
> R-sig-mixed-models_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>

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