[R-sig-ME] lmer formula syntax?

[Dominick Samperi]

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

>
>
>
>
>> Apparently it is available on something called an SVN
>> respository. Im getting into language I am unfamiliar with. If you can
>> provide some advice to aid my ignorance in installing this package I could
>> likely get a lot more out of the book draft.
>>
>> Thank for you time and assistance.
>>
>> On Tue, Feb 1, 2011 at 6:34 PM, George Wang <pseudotelphusa at gmail.com>wrote:
>>
>>> I am also quite new to lme4 myself, so I'll just add one thing to Toby's
>>> earlier answer.
>>>
>>> On Tue, Feb 1, 2011 at 5:14 PM, Colin Wahl <biowahl at gmail.com> wrote:
>>>
>>>> Dear r-sig-mixed-models List,
>>>>
>>>> [snip]
>>>
>>>
>>>
>>>> Secondarily: I have read a few times that "wshed/stream" is
>>>> interchangeable
>>>> with  "wshed:stream" which is a meaningless interaction. Also I've seen
>>>> that
>>>> random effects are specified as (a|b) where a is a covariate and b is a
>>>> grouping factor. Does having 1 as a covariate simply specifying an
>>>> intercept
>>>> of 1? What is the purpose of placing a factor in the place of 1 as a
>>>> covariate? OR is there a nice complete summary tutorial that I've missed.
>>>>
>>> A specification of (1|b) means that the model is fit with a random effect
>>> for each level of b (simple scalar random effect). The "a" in (a|b) is a
>>> correlated random effect along with "b", with both an intercept and slope.
>>> You can also make them uncorrelated, with slope only for a.
>>>
>>> The draft of Prof. Doug Bate's book covers many useful basics on lmer, and
>>> is where I learned most of mine.
>>> http://lme4.r-forge.r-project.org/book/
>>>
>>>
>>
>>
>>> HTH
>>> George
>>>
>>>
>>>>
>>>> I'm looking forward to hearing any comments.
>>>>
>>>> Thank you,
>>>> --
>>>> Colin Wahl
>>>> Department of Biology
>>>> Western Washington University
>>>> Bellingham, WA 98225
>>>> ph: 360-391-9881
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>>
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>>>>
>>>>
>>>
>>
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>>
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