All,
I would first like to say that I'm a relative novice with R so please take
that into consideration with your responses. Basically, give me the
totally dumbed down version of answers when you can.
I have a biological data set with count data that I'm currently
analyzing. Namely, I'm interested in looking at the effects of animal age,
bodysize, and antler size on annual male reproductive success (i.e. number
of fawns produced). I would also like to see how the relationships are
influenced by changes in population demographics. I have been using a GLMM
to evaluate the following global model:
repro =
glmer(Fawn~Age+I(Age^2)+BodySize+SSCM+AvgAge+Age*AvgAge+I(Age^2)*AvgAge+BodySize*AvgAge+SSCM*AvgAge+(1|Sire),data=datum,family=poisson)
where:
Age, BodySize, SSCM are measured characteristics
Fawn = number of fawns produced in a given year
AvgAge = Population demographic factor
(1|Sire) = Random effect for each sampled male ID
I first used the following to evaluate potential overdispersion of my data
from the global model:
overdisp_fun <- function(model) {
## number of variance parameters in
## an n-by-n variance-covariance matrix
vpars <- function(m) {
nrow(m)*(nrow(m)+1)/2
}
model.df <- sum(sapply(VarCorr(model),vpars))+length(fixef(model))
rdf <- nrow(model.frame(model))-model.df
rp <- residuals(model,type="pearson")
Pearson.chisq <- sum(rp^2)
prat <- Pearson.chisq/rdf
pval <- pchisq(Pearson.chisq, df=rdf, lower.tail=FALSE)
c(chisq=Pearson.chisq,ratio=prat,rdf=rdf,p=pval)
}
With the following result
repro =
glmer(Fawn~Age+I(Age^2)+BodySize+SSCM+AvgAge+Age*AvgAge+I(Age^2)*AvgAge+BodySize*AvgAge+SSCM*AvgAge+(1|Sire),data=datum,family=poisson)
overdisp_fun(repro)
chisq ratio rdf
p
1.698574e+02 1.681756e+00 1.010000e+02 2.169243e-05
Since the ratio of Pearson-statistic to rdf is 1.68 I assume that I need
to take this overdispersion into account
My first inclination was to use quasipoisson distribution to account for
overdispersion; however, I see that in no longer available in lme4. I used
glmmPQL in the MASS package with quasipoisson but do not receive AICc
information. I had planned on using AICc to evaluate competitive models.
My specific question is: 1) is there a way to generate the necessary
information (AICc or something like) to compare competitive models from
overdispersed data in a current R environment? I have read
https://cran.r-project.org/web/packages/bbmle/vignettes/quasi.pdf but I'm
having a difficult time understanding exactly how to implement from a
technical perspective. I'm on the path of trying to use a negative
binomial (I'm not locked into this method so please provide insight if
appropriate) with package glmmADMB: however, I have been unable to get this
package to load successfully. I've followed the instructions to the best
of my understanding and abilities but cannot figure out where I'm going
wrong. Any advice is much appreciated as I'm totally stumped right now on
many fronts. I'm running windows 7 on 64-bit machine. Here is what I have
attempted with output:
install.packages("glmmADMB",
+ repos=c("http://glmmadmb.r-forge.r-project.org/repos",
+ getOption("repos")),
+ type="source")
Installing package into ?C:/Users/newboch/Documents/R/win-library/3.3?
(as ?lib? is unspecified)
trying URL '
http://glmmadmb.r-forge.r-project.org/repos/src/contrib/glmmADMB_0.8.3.3.tar.gz
'
Content type 'application/x-gzip' length 9391177 bytes (9.0 MB)
downloaded 9.0 MB
* installing *source* package 'glmmADMB' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
:
there is no package called 'stringi'
ERROR: lazy loading failed for package 'glmmADMB'
* removing 'C:/Users/newboch/Documents/R/win-library/3.3/glmmADMB'
The downloaded source packages are in
?C:\Users\newboch\AppData\Local\Temp\RtmpK23VOM\downloaded_packages?
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l
"C:\Users\newboch\Documents\R\win-library\3.3"
C:\Users\newboch\AppData\Local\Temp\RtmpK23VOM/downloaded_packages/glmmADMB_0.8.3.3.tar.gz'
had status 1
2: In install.packages("glmmADMB", repos = c("
http://glmmadmb.r-forge.r-project.org/repos", :
installation of package ?glmmADMB? had non-zero exit status
Error in loadNamespace(name) : there is no package called ?glmmADMB?
library("R2admb")
glmmADMB:::get_bin_loc()
Error in loadNamespace(name) : there is no package called ?glmmADMB?
install.packages("glmmADMB")
Installing package into ?C:/Users/newboch/Documents/R/win-library/3.3?
(as ?lib? is unspecified)
Warning message:
package ?glmmADMB? is not available (for R version 3.3.1)
Thanks,
Chad
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