[R-sig-ME] Chapter 4 script hack [was Re: lmer formula syntax?]

[Douglas Bates]

Actually I think I should update the files on the book site rather
than patching the code.  I'll do that later today.

On Wed, Feb 16, 2011 at 7:18 AM, Ben Bolker <bbolker at gmail.com> wrote:
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>   While it is probably still worth posting reference versions of lme4a
> + dependencies to the lme4 repository when I get a chance, I don't think
> the problems people have been having with Chap4.R (or other chapters)
> are caused by package problems.
>
>  The function env() is used in every chapter, and I can't find a
> definition for it anywhere.  Its purpose seems to be to extract the
> random effects slot from a 'mer' object as an environment.
>
>  I added this helper function to the beginning of Chap4.R
>
> ## chunk 0: BMB hack
> env <- function(x) {
>  z <- list()
>  for (i in slotNames(x at re))
>    z[[i]] <- slot(x at re,i)
>  as.environment(z)
> }
>
> and got it to run fine with current versions of minqa, MatrixModels,
> lme4a.  I was running with a bleeding-edge SVN release, but I think it
> should work with a range of options (lme4 repos, r-forge, etc.)
>
>  Doug, is this a helper function you defined elsewhere in your working
> environment, or one that was defined in a long-lost previous version of
> lme4?
>
>  cheers
>    Ben Bolker
>
>
>
>
> ===============
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i486-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] lme4a_0.999375-63  MatrixModels_0.2-1 minqa_1.1.13
> [4] Rcpp_0.9.1         Matrix_0.999375-47 lattice_0.19-19
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-7 grid_2.12.1     nlme_3.1-97     stats4_2.12.1
> [5] tools_2.12.1
>
> On 11-02-15 10:36 PM, Dominick Samperi wrote:
>> On Tue, Feb 15, 2011 at 10:28 PM, Ben Bolker <bbolker at gmail.com> wrote:
>> On 11-02-15 10:24 PM, Dominick Samperi wrote:
>>>>> On Wed, Feb 2, 2011 at 4:55 PM, Douglas Bates <bates at stat.wisc.edu> wrote:
>>>>>> On Wed, Feb 2, 2011 at 3:43 PM, Colin Wahl <biowahl at gmail.com> wrote:
>>>>>>> I too have found the Bate's book draft helpful, but I have not been able to
>>>>>>> get the lme4a package installed. The best description I have found to do so
>>>>>>> is:
>>>>>>> http://kmyu.wordpress.com/2010/12/04/installing-lme4a-in-r-mac-osx-10-6-4/
>>>>>>
>>>>>>> I'm understanding that the lme4a package is dependent on a number of
>>>>>>> packages: RcppArmadillo, minqa and MatrixModels (available on CRAN
>>>>>>> respositories) and Rcpp version 0.8.8.1 or later (which is not; version
>>>>>>> 0.8.6 is).
>>>>>>
>>>>>> (Actually it doesn't depend on RcppArmadillo).
>>>>>>
>>>>>> You must be using Mac OS X.  If you check at
>>>>>> cran.r-project.org/web/packages/Rcpp you will see that the Windows
>>>>>> binary and the source code packages are at version 0.9.0 but the Mac
>>>>>> OS X version is only at 0.8.6, which is rather old.  I'm not sure what
>>>>>> the problem is as Romain develops on a Mac OS X system and he can't
>>>>>> reproduce the error.
>>>>>>
>>>>>> However, you don't really need lme4a for most of the examples in the
>>>>>> book.  The lme4 package can't handle the profile-related material, but
>>>>>> the rest of the examples should be okay.  The output looks slightly
>>>>>> different but the parameter estimates should be essentially the same.
>>>>>>
>>>>>
>>>>> FYI, I just tried the current R-Forge version of lme4a using Rcpp 0.9.0
>>>>> and there is a problem in the print function when the first argument x
>>>>> is an image() call. This happens while trying the script Ch4.R.
>>>>>
>>>>> I realize this is work in progress, and I tried to use lme4 first, but there
>>>>> was a problem with that.
>>>>>
>>>>> Is there a recommended snapshot/version set for minqa, MatrixModels,
>>>>> lme4a, etc. that will run the chapter scripts?
>>>>>
>>>>> Thanks,
>>>>> Dominick
>>>>>
>>
>>  Have you tried the lme4a version posted at
>> <http://lme4.r-forge.r-project.org> (see the last paragraph on that
>> page)?  If that doesn't work, please let me know and I will try to fix
>> it / resolve dependencies by making them available.
>>
>>> Yes, that is where I fetched lme4a from, but there are dependencies
>>> on Rcpp, minqa, MatrixModels, etc., and I downloaded those from CRAN.
>>> I'm not sure if this combination will work.
>>
>>> I tried the Linux source. I will try again using the Windows binaries...
>>
>>
>>  Ben Bolker
>
>
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