[R] Problem with lme4

[Douglas Bates]

On 8/12/05, Peter Ho <peter at fe.up.pt> wrote:
> Hi,
> 
> I cannot seem to get lme4 to work. I have installed the lme4 and Matrix
> package with apt-get. and both can be found in /usr/lib/R/site-library.
> When I tried an example for lmer, R could not find the function lmer(),

Try using

install.packages("Matrix")
install.packages("lme4")

in R instead.  I have not created and uploaded new Debian packages of
the lme4 and Matrix R packages for several weeks.  The versions on
CRAN are more recent than the versions on the Debian archives.

> 
>  > library(lme4)
> 
> Attaching package: 'lme4'
> 
> 
>         The following object(s) are masked from package:nlme :
> 
>          getCovariateFormula getResponseFormula groupedData
> 
> Error in autoloader(name = "confint", package = "MASS") :
>         autoloader did not find 'confint' in 'MASS'

Try not to have the nlme and the lme4 packages loaded simultaneously. 
It appears that you may have had Rcmdr loaded causing many of the
other packages to be loaded.  It would be better to use --vanilla in
the call to R and keep the number of loaded packages to a minimum
until you can work out the problem of where lmer can be found.

It is a bit confusing.  The lmer function was in the lme4 package but
now is in the Matrix package.
>  > (fm1 <- lmer(decrease ~ treatment + (1|rowpos) + (1|colpos),
> +              OrchardSprays))
> Error: couldn't find function "lmer"
>  >
> 
> Is this a bug with the lme4 package for Debian (r-cran-lme4)?
> 
> 
> Peter
> 
> 
> 
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> 
> Loading Tcl/Tk interface ... done
> Loading required package: tcltk
> Loading required package: rgl
> Loading required package: zoo
> Loading required package: strucchange
> Loading required package: sandwich
> Loading required package: relimp
> Loading required package: nnet
> Loading required package: graphics
> Loading required package: grDevices
> Loading required package: stats
> Loading required package: nlme
> 
> Attaching package: 'nlme'
> 
> 
>         The following object(s) are masked from package:stats :
> 
>          contr.SAS
> 
> Loading required package: mvtnorm
> Loading required package: multcomp
> Loading required package: mgcv
> This is mgcv 1.2-4
> Loading required package: MASS
> Loading required package: lmtest
> Loading required package: lattice
> Loading required package: grid
> Loading required package: foreign
> Loading required package: effects
> Loading required package: car
> Loading required package: abind
> [Previously saved workspace restored]
> 
>  > library(Matrix)
>  > library(lme4)
> 
> Attaching package: 'lme4'
> 
> 
>         The following object(s) are masked from package:nlme :
> 
>          getCovariateFormula getResponseFormula groupedData
> 
> Error in autoloader(name = "confint", package = "MASS") :
>         autoloader did not find 'confint' in 'MASS'
>  > (fm1 <- lmer(decrease ~ treatment + (1|rowpos) + (1|colpos),
> +              OrchardSprays))
> Error: couldn't find function "lmer"
>  >
> 
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