Hi,
I'm attempting a comparative analysis using the function compare.gee,
package (ape), which uses phylogeny as a correlation matrix in gee
(package gee), in R version 2.2.0 on a Windows XP PC. I'm looking to
model the relationship between a continuous explanatory variable and a
binary response variable for 600 species, taking into account the
phylogeny of those species.
Here's an example of the code used:
model.range<compar.gee(DS2$thr.vs.non.thr~DS2$log.range,family="binomial
",phy=pruned.di.tree,scale.fix=FALSE)
(where "DS2$thr.non.thr" is a binary response variable, and
"DS2$log.range" is a continuous explanatory variable).
When I run the function, a model summary is produced, but so is
following message:
[1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27"
[1] "running glm to get initial regression estimate"
[1] 5.069447 -1.220802
Warning message:
Note: Cgee had an error (code= 1 ). Results suspect. in:
gee(DS2$thr.vs.non.thr ~ DS2$log.range, c(1, 1, 1, 1, 1, 1, 1,
I looked into code of compare.gee and gee (which is called in
compare.gee), and it appears that the error state is an "Unknown
error".
I wondered if anyone has experienced similar problems, or may be aware
of the most likely reasons for this error message. If more info is
required in order to give any advice, please let me know and I can
forward you details of the dataset or the tree used in the analysis
Many thanks for any help that can be offered.
Cheers, Jon.
<http://www.zoo.cam.ac.uk/ioz/people/bielby.htm>
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