Dear all
It seems there is a name conflict between the reorder.factor() function
from the package "gdata" and the reorder.factor() from the package "stats" .
After loading the library "gdata", dotplot(ranef( model_object.lmer) )
- which seems using internally by default reorder.factor() from the
package "stats" -
does not plot the random terms sorted any more .
The regular behavior can be recovered with:
detach("package:gdata",unload=T)
but is there an easier or a more convenient way ?
Thank you for your help
R. Espesser
CNRS - Universit? de Provence
Laboratoire Parole & Langage
5 avenue Pasteur
BP 80975
13604 Aix en Provence Cedex 1 (France)
web : www.lpl-aix.fr/~espesser
possible side effect of gdata library on dotplot of random terms
4 messages · espesser, Douglas Bates, Kevin Wright
My suggestion would be not to use gdata. :-) More seriously, as I understand it you are saying that gdata provides a method for reorder that is not upwardly compatible with the method in the stats package. If so, I would regard this as a flaw in the design of the gdata package. One should not willfully change the behavior of functions in required packages. Having said that, I am a bit confused by your saying that dotplot seems to be using the method from the stats package but it does not provide the desired reordering when gdata is attached in the search path before stats. The first part (continuing to use the method from stats) is what I would expect to happen. This is exactly what namespaces are for - to seal the set of functions and methods that are seen inside the lme4 package. What I don't understand is why the plot does not then work as before. Could you provide us with a reproducible example and the output of sessionInfo() please?
On Tue, Dec 8, 2009 at 3:43 AM, espesser <robert.espesser at lpl-aix.fr> wrote:
Dear all
It seems there is a name conflict between the reorder.factor() function
from the package "gdata" and the reorder.factor() from the package "stats" .
After loading the ?library "gdata", dotplot(ranef( model_object.lmer) ?)
- which seems using internally ?by default reorder.factor() ?from the
package "stats" ?-
does not plot the random terms sorted any more .
The regular behavior can be recovered with:
detach("package:gdata",unload=T)
but is there an easier or a more convenient way ?
Thank you for your help
R. Espesser
CNRS - Universit? de Provence
Laboratoire Parole & Langage
5 avenue Pasteur
BP 80975
13604 Aix en Provence Cedex 1 (France)
web : www.lpl-aix.fr/~espesser
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
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Here is a reproducible example: # begin of a new session of R > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] grid_2.8.1 lattice_0.17-17 lme4_0.999375-28 Matrix_0.999375-21 ##### REM: I got same results with a scratch install of R 2.10.0 > library(lme4) > data(sleepstudy) > fm2 <- lmer(Reaction ~ Days + (1|Subject),data=sleepstudy) > dotplot(ranef(fm2)) # dotplot OK > library(gdata) > dotplot(ranef(fm2)) # dotplot not in order # the suggestion of Kevin Wright seems OK : >Maybe just copy the correct version of the function into .GlobalEnv >so that it is first on the search path: reorder.factor=stats:::reorder.factor dotplot(ranef(fm2)) # OK Douglas Bates a ?crit :
My suggestion would be not to use gdata. :-) More seriously, as I understand it you are saying that gdata provides a method for reorder that is not upwardly compatible with the method in the stats package. If so, I would regard this as a flaw in the design of the gdata package. One should not willfully change the behavior of functions in required packages. Having said that, I am a bit confused by your saying that dotplot seems to be using the method from the stats package but it does not provide the desired reordering when gdata is attached in the search path before stats. The first part (continuing to use the method from stats) is what I would expect to happen. This is exactly what namespaces are for - to seal the set of functions and methods that are seen inside the lme4 package. What I don't understand is why the plot does not then work as before. Could you provide us with a reproducible example and the output of sessionInfo() please? On Tue, Dec 8, 2009 at 3:43 AM, espesser <robert.espesser at lpl-aix.fr> wrote:
Dear all
It seems there is a name conflict between the reorder.factor() function
from the package "gdata" and the reorder.factor() from the package "stats" .
After loading the library "gdata", dotplot(ranef( model_object.lmer) )
- which seems using internally by default reorder.factor() from the
package "stats" -
does not plot the random terms sorted any more .
The regular behavior can be recovered with:
detach("package:gdata",unload=T)
but is there an easier or a more convenient way ?
Thank you for your help
R. Espesser
CNRS - Universit? de Provence
Laboratoire Parole & Langage
5 avenue Pasteur
BP 80975
13604 Aix en Provence Cedex 1 (France)
web : www.lpl-aix.fr/~espesser
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models