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Dear all,<br>
<br>
I'm a bit confused about last comments from Ben Bolker. <br>
I read Bolker et al., 2009 TREE and what I remembered is that it was
advised to use Wald tests instead of LRT whent testing for fixed
effects (and the contrary when testing for random effects). Hence,
I'm surprised that Ben just said the contrary: is it just true for
glmmADMB or for any packages ?<br>
<br>
If we want to use more accurate approaches, but if possible not MCMC
techniques, are there any possibilities with glmmADMB ?<br>
<br>
I tried to install glmmADMB_0.7.2.10 from bolker-mcmaster
repository, but I got the following error message: <br>
<br>
Installation d(es) package(s) dans ‘C:/Users/thomas
merkling/Documents/R/win-library/2.14’<br>
(car ‘lib’ n'est pas spécifié)<br>
* installing *source* package 'glmmADMB' ...<br>
** R<br>
** data<br>
** moving datasets to lazyload DB<br>
<br>
Error : l'objet 'dat_write' n'est pas exporté par 'namespace:R2admb'<br>
ERROR: lazydata failed for package 'glmmADMB'<br>
<br>
* removing 'C:/Users/thomas
merkling/Documents/R/win-library/2.14/glmmADMB'<br>
* restoring previous 'C:/Users/thomas
merkling/Documents/R/win-library/2.14/glmmADMB'<br>
<br>
<br>
Thanks in advance !<br>
Thomas<br>
<br>
<br>
Le 26/03/2012 18:12, Ben Bolker a écrit :
<blockquote cite="mid:%3C4F70956C.1050009@gmail.com%3E" type="cite">
<pre wrap="">On 12-03-26 10:37 AM, Paula Rosewarne wrote:
</pre>
<blockquote type="cite">
<pre wrap="">
Dear All,
I came across this posting (below) on a different list- how to get an
Anova table from glmm.admb model objects- but I cannot get the
car::Anova function to work for my model, or for the owl example I
worked through from the glmmadmb package help notes, so I am guessing
my code is wrong
When I tried it with the owl example I get the following message, the
same as when I try for my model:
</pre>
<blockquote type="cite">
<pre wrap="">car::Anova(fit_zipoiss)
</pre>
</blockquote>
<pre wrap="">Error in data.frame(df, teststat, p) : arguments imply differing
number of rows: 5, 6 In addition: Warning message: In Ops.factor(1,
Nest) : | not meaningful for factors
(I am using glmm.admb v0.7.2.4)
Please could you advise, many thanks,
Paula
</pre>
</blockquote>
<pre wrap="">
[cross-posted to ADMB users and r-sig-mixed because I didn't want to
write it twice]
Before I answer the question I want to strongly caution people about
using the Anova() (Wald) tests on glmmADMB output. I am generally of the
"give people the tools, let them do what they want" [in other words
"give them enough rope"] philosophy (which is why I tweaked glmmADMB to
allow car::Anova() to work), but Wald tests are the most approximate
approach to model comparison and inference. For vanilla (non-mixed)
linear models they are identical to standard marginal F tests, but for
mixed/generalized/zero-inflated models they are sometimes very poor
approximations. Using anova() on alternative models instead gives a
likelihood ratio test, which is still approximate but is generally much
better (it relies on the normality of the likelihood itself, rather than
on the normality of the sampling distribution of the parameters). It is
a bit tedious to use in glmmADMB at the moment because I haven't got the
drop1() functionality working yet, but it should be much more reliable.
Even that is not perfect, though, because it does depend on the
approximate normality of the likelihood estimate; MCMC and parametric
bootstrap approaches are more accurate.
You need at least version 0.7.2.9. I am currently struggling to get
the newest version to build properly on r-forge; in the meantime, below
is a helper function to check which versions are available where. You
may want to use the optional argument type="source" (as documented at
<a class="moz-txt-link-freetext" href="http://glmmadmb.r-forge.r-project.org">http://glmmadmb.r-forge.r-project.org</a>) ...
In the meantime I've put 0.7.2.10 (source only, use type="source") at
the bolker-mcmaster repository and on the alternative r-forge location
(where it should show up within 24 hours).
## helper function to check availability
favail <- function(repos="r-forge.r-project.org",
pkg="glmmADMB",
...) {
hdr <- <a class="moz-txt-link-rfc2396E" href="http://">"http://"</a>
if (!substr(repos,1,8)==hdr) repos <- paste(hdr,repos,sep="")
a <- available.packages(contriburl=contrib.url(repos),...)
if (length(grep(pkg,rownames(a)))==0)
stop(sprintf("%s unavailable at repos %s",pkg,repos))
a[pkg,"Version"]
}
favail() ## unavailable
favail("<a class="moz-txt-link-abbreviated" href="http://www.math.mcmaster.ca/bolker/R">www.math.mcmaster.ca/bolker/R</a>") ## 0.7.2.10
favail("glmmadmb.r-forge.r-project.org/repos") ## 0.6.4
</pre>
<blockquote type="cite">
<pre wrap="">
>From the r-sig-mixed-models list: Le 20/03/2012 22:43, Ben Bolker a
écrit : On 12-03-20 02:32 PM,
</pre>
<blockquote type="cite">
<pre wrap="">Thomas Merkling wrote:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Dear Ben and other list members,
- Is there any way to produce a Anova/deviance table for a
model fitted with glmmADMB ? I used the Anova() function
from the car library for glmer models, but it does not seem
to work with glmmadmb (I'm using glmmADMB 0.7) and I would
like only one p-value for each term and interaction and NOT
one p-value for each level of the interaction.
</pre>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">Ben's reply:
</pre>
<blockquote type="cite">
<pre wrap="">car::Anova() should work now -- I had to add a model.frame() and a
df.residual() method for glmmadmb objects. (The df.residual number
may be a little dodgy -- I'm not sure I counted the parameters
right -- but I don't think it's actually used for much by default,
cause you get Wald chi-square tests)
</pre>
</blockquote>
<pre wrap="">
Paula Rosewarne, PhD researcher, Faculty of Biological Sciences
Manton Building 8.17 Clarendon Way University of Leeds LS2 9JT UK
Email: <a class="moz-txt-link-abbreviated" href="mailto:bspjr@leeds.ac.uk">bspjr@leeds.ac.uk</a><a class="moz-txt-link-rfc2396E" href="mailto:bspjr@leeds.ac.uk"><mailto:bspjr@leeds.ac.uk></a>
_______________________________________________ Users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Users@admb-project.org">Users@admb-project.org</a>
<a class="moz-txt-link-freetext" href="http://lists.admb-project.org/mailman/listinfo/users">http://lists.admb-project.org/mailman/listinfo/users</a>
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<br>
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<br>
Thomas Merkling, Doctorant (PhD Student) <br>
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Page </a> <br>
<br>
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<br>
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