[R] Simplification of Generalised Linear mixed effects models using glmmPQL

[T.C. Cameron]

Dear R users I have built several glmm models using glmmPQL in the
following structure:
 
m1<-glmmPQL(dev~env*har*treat+dens, random = ~1|pop/rep,  family =
Gamma)
 
(full script below, data attached)
 
I have tried all the methods I can find to obtain some sort of model fit
score or to compare between models using following the deletion of terms
(i.e. AIC, logLik, anova.lme(m1,m2)), but I cannot get any of them to
work.
Yet I see on several R help pages that others have with similar models?
 
I have tried the functions in lme4 as well and lmer or lmer2 will not
accept my random terms of "rep" (replicate) nested within "pop"
population.
 
I have read the appropriate sections of the available books and R help
pages but I am at a loss of where to move from here
 
 

data<-read.table("D:\\bgytcc\\MITES\\Data\\Analysis\\test.txt",header=T)
attach(data)
names(data)
 
 
 
m1<-glmmPQL(dev~env*har*treat+dens, random = ~1|pop/rep, family = Gamma)
summary(m1)
anova.lme(m1)
m2<-update(m1,~.-env:har:treat)
anova.lme(m1,m2)###this does not work
AIC(m1)##this does not work
logLik(m1)##this does not work?
 
 
 
##################this does not work
class(m1) <- "lme"
class(m2) <- "lme"
anova.lme(m1,m2)
#################################
 
m3<-lmer(dev~env*har*treat+dens + (1|pop/rep), family = Gamma)
 
## this generates an error
Error in lmerFactorList(formula, mf, fltype) : 
        number of levels in grouping factor(s) 'rep:pop', 'pop' is too
large
In addition: Warning messages:
1: numerical expression has 1851 elements: only the first used in:
rep:pop 
2: numerical expression has 1851 elements: only the first used in:
rep:pop 
 

m4<-lmer(dev~env*har*treat + dens + (1|rep) +(1|pop), family = Gamma,
method = "Laplace")
## this works but it does not give me an anova output with p values
anova(m4)
Analysis of Variance Table
              Df  Sum Sq Mean Sq
env            1   17858   17858
har            2     879     439
treat          2    2613    1306
dens           1 1016476 1016476
env:har        2     870     435
env:treat      2    1188     594
har:treat      4     313      78
env:har:treat  4    1188     297

 

........................................................................
............
Dr Tom C Cameron
Genetics, Ecology and Evolution
IICB, University of Leeds
Leeds, UK
Office: +44 (0)113 343 2837
Lab:    +44 (0)113 343 2854
Fax:    +44 (0)113 343 2835


Email: t.c.cameron at leeds.ac.uk
Webpage: click here
<http://www.fbs.leeds.ac.uk/staff/profile.php?tag=Cameron_TC> 

 
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