[R-sig-ME] Fwd: same old question - lme4 and p-values

Kevin E. Thorpe kevin.thorpe at utoronto.ca
Tue Apr 15 14:53:45 CEST 2008

Thanks for this pointer Ben.  Too bad the wiki is still down. :-(

I was able to retrieve a cached page from a Google search.
I think (hope) this will do the trick.

One more question.  Would there be an "official" citation to
this information appropriate as a reference in the manuscript?

Ben Bolker wrote:
>   Also note that in the long thread on the R wiki
> (wiki.r-project.org, search for "bates mixed" or some such --
> I can't get through to it right now) DB suggests an
> test for a composite hypothesis a_1=a_2=...=a_n=0
> along with R code to do it ...
> Andrew Robinson wrote:
>> On Sat, Apr 12, 2008 at 02:02:09PM +0200, Reinhold Kliegl wrote:
>>> On Fri, Apr 11, 2008 at 3:10 PM, Kevin E. Thorpe
>>> <kevin.thorpe at utoronto.ca> wrote:
>>>> This has been a very interesting thread.  However, I'm still
>>>>  wrestling with what to do for a fixed-effect that has more than
>>>>  one degree of freedom.
>>>>  In the data I'm analyzing, I have three groups to compare.
>>>>  So, I can get CIs for the two parameters, but that is a bit
>>>>  problematic for assessing an overall difference.
>>>>  Is it valid to do the following?  Estimate the parameters using both
>>>>  ML and REML.  If the estimates show good agreement, is that sufficient
>>>>  evidence to conclude the ML procedure is converging and that I can
>>>>  use a likelihood ratio test for the fixed effect?
>>> I assume you refer to using anova(fm1, fm2) with fm1 fitting the model
>>> without the fixed effect. This a comparison of nested models, so a
>>> likelihood ratio test can be defined for ML fits only. Note, however,
>>> that Pinheiro & Bates (2000, p. 87, 2.4.2) "do not recommend using
>>> such tests"; "not" is set in bold face. They show that such tests tend
>>> to be anti-conservative, especially if the number of parameters
>>> removed is large relative to the number of observations. Assuming you
>>> have a decent number of total observations, you may be fine.
>>> Alternatively, you may want to run a simulation for your situation;
>>> you will also find R-code examples in the P&B section.
>> I agree with Reinhold's position, here.  I also note in passing that
>> Doug uses this strategy to test the fixed effects in the cake data
>> (see ?cake).  Doug, does the cake data analysis represent a softening
>> on your position or a place-filler?
>>> My first reaction to your email was: Why is he only interested in the
>>> overall effect of a fixed factor and not in specific comparisons
>>> between its levels? After Andrew's comment to an earlier post, I
>>> understand that there are such situations where you just want to
>>> control for an aspect of the design that is not in the focus of your
>>> theoretical concerns (e.g., in ecology you may have three sites that
>>> could be characterized as levels of a fixed factor or as a sample from
>>> a random factor). Perhaps  your fixed factor may also be better
>>> conceptualized as a random factor. In a way, you just want to control
>>> for the variance contributed by this factor. If this applies to your
>>> data, then you may be better off to specify your fixed factor as a
>>> random factor. Then, your anova(fm1, fm2) compares nested models that
>>> differ only in the random-effects part. In this case the likelihood
>>> ratio test can be used with models fit by REML. These tests tend to be
>>> conservative (Pinheiro & Bates, 2000, p. 2.4.1; following up on Stram
>>> & Lee, 1994). So if your ANOVA statistic is significant, you are on
>>> the save side; if not, you do not know. Also keep in mind, that random
>>> effects with few units may generate problems for model convergence.
>> That's an interesting idea, even if the interpretation is intended to
>> be a fixed factor.  It might work to a certain order of approximation,
>> but I'm not clear how the math would play out.  Some simulations might
>> provide a measure of comfort in individual situations.
>> Best wishes,
>> Andrew

Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: kevin.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.6057

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