Hi:

2010/11/19 Niccolò Bassani <biostatistica@gmail.com>

> Dear R-users,
> from Douglas Bates lme4 book I'm trying to run profile() on a quite large
> dataset, in order to have some confidence intervals on random effects
> parameter in mixed models. When I run it in lme4 however I'm faced with the
> following error:
>
> Errore in UseMethod("profile") :
>  no applicable method for 'profile' applied to an object of class "mer"
>
> Surfing on R-help mailing lists I understood that this has to do with some
> compatibility problems which are undergoing development for next version of
> the lme4 package, right? Also, I found that this function is active in the
> development packages lme4a and lme4b, available from R-forge...
>

If you were surfing on R-mixed-models, you should have discovered somewhere
along the way that the release version of lme4 on CRAN does not have (m?)any
of the experimental functions in the first draft of Prof. Bates' book. The
code/functions corresponding to the book in progress reside in package lme4a
on R-forge and much, if not all, of it is in active development and subject
to change (both in the book and the code). lme4b is not intended for general
use, if I've read Prof. Bates' meaning from past posts correctly.

I don't know what you infer by 'compatibility problems', but my
understanding is that the eventual goal is to have an integrated
computational platform that provides a unified way of modeling [non]linear
[generalized] mixed effects problems. Considering that the theory itself is
in quite active development, this project is very ambitious in scope.
Because it's bleeding edge methodology, I understand why Prof. Bates is
loath to add new features to the release version lme4 until they meet his
performance standards on the computational side and whatever issues exist on
the methodological side are more or less resolved, since his name is on it.
I trust his judgment in these matters.

Moreover, Prof. Bates does his development work in Linux, so binaries for
Windows and Macs are not always completely up to date. He has also mentioned
several times this term that his teaching schedule gives him little
opportunity to make substantial progress re development and maintenance of
lme4(a). Such is life on the bleeding edge.

The operative word here is patience. I'm certain that when he has the time
to do so, the binaries for non-Linux platforms will be updated and reported
here and/or R-mixed-models.

With thanks to Prof. Bates for all the great work he's done on this project
and many others,

Dennis

>
> I was trying to install these packages, at least to have profile() running.
> I've tried different ways for doing this but I'm stuck in a blind
> alley...I've tried the following (all suggestions from R users found on the
> Internet):
>
> - install.packages("lme4a", repos="http://R-Forge.R-project.org")
>
> returning  "Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘lme4a’ is not available"
>
> - installing binary file directly in the .libpaths directory, but: lme4a
> binary for MAC can not be retrieved on the web (page not found), and lme4b
> gives similar problem.
>
> Now only installing package from source files remain, but this does not
> seem
> so easy...at least not for me!
> I have a Macbook Pro (running Mac OS/X 10.6.4 with Leopard)...
>
> Any help is appreciated, since previous talks on R mailing list kind of
> confused me much!!
>
> thanx in advance
> niccolò
>
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>
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