1. Did you try "anova(f1)"? The documentation for
"glmmPQL" says it
produces an object of class lme, and "anova.glm" might not work
properly
for it. Also, did you try "summary(f1)", as suggested in the example
in
"?glmmPQL"?
2. Have you considered using "lmer" in the "lme4"
package? As far
as I know, this is the most up-to-date and state-of-the art function for
this kind of analysis. For documentation on "lmer", I'd start
with Doug
Bates, "Fitting linear mixed models in R", R News, 5(1): 27-30, May
2005, and "Linear mixed model implementation in lmer", July 26, 2005,
distributed with lme4 and stored on my hard drive under
"~\R\R-2.2.0\library\lme4\doc\Implementation.pdf". I might also
consult
Pinheiro and Bates (2000) Mixed-Effects Models in S and S-PLUS
(Springer), which is my primary source for mixed models generally.
3. If you'd like more help with this, I suggest you PLEASE do read
the posting guide! "www.R-project.org/posting-guide.html", especially
the bit about supplying a simple, reproducible example that someone like
me can copy from your email into R to see if they get the same error
message. I and others are much more likely to have the time to test a
simple, self-contained example than to try to replicate your problem
from scratch.
hope this helps.
spencer graves
jmgreyes at ugr.es wrote:
> Hi,
>
> My name is Jos?? Mar??a G??mez, and I am pretty new in R. Thus, I apologize
> deeply if my questions are extremmely na??ve.I have checked several
> available books and URL's, without finding any answer.
>
> I'm trying to fit Generalized Linear Mixed Models via PQL. Below I
provide
> the structure of my data set. Year and Plot are random variables. Fate is
> the binomial dependent. I have severe problems after calling glmmPQL:
>
> 1) I would like to nest Plot within Year, but I don't know how to
argument
> it.
>
> 2) I'm not sure the analysis I fit (see below) is actually considering
> Year and Plot as random.
>
> 3) No way to obtain an analysis of deviance for the GLMM fit.
>
> 4) Year appears without degrees of freedom.
>
> As you see, too many problems. Thank you very much for any help.
> JM
> _____________________________________________
>
>
>>summary (Ifate)
>
> Year Plot Fate Hab Peso Dist
> A:664 A:359 cache : 91 Oak :621 Min. :0.1903 Min. :1.362
> B:574 B:427 comida:1147 Open : 94 1st Qu.:0.5515 1st Qu.:1.847
> C:135 Pine :159 Median :0.6670 Median :2.137
> D: 97 Rock : 23 Mean :0.6674 Mean :2.200
> E:220 Shrub:341 3rd Qu.:0.7597 3rd Qu.:2.476
> Max. :1.1386 Max. :3.872
>
>>library (MASS)
>>library (nlme)
>>f1<-glmmPQL(Fate~Year+Plot+Hab+Peso+Dist, random=~1|Year/Plot,
>
> family=binomial, data=Ifate)
>
>
>>anova.glm(f1)
>
> Error in eval(expr, envir, enclos) : Object "Fate" not found
>
>
>>anova(f1)
>
> numDF denDF F-value p-value
> (Intercept) 1 1223 124.10634 <.0001
> Year 1 0 0.00271 NaN
> Plot 4 3 0.96230 0.5343
> Hab 4 1223 6.03162 0.0001
> Peso 1 1223 4.34225 0.0374
> Dist 1 1223 5.97248 0.0147
> Warning messages:
> 1: NaNs produced in: pf(q, df1, df2, lower.tail, log.p)
> 2: NAs introduced by coercion
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
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spencer.graves at pdf.com
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