[R] APE: compar.gee( )
juli g. pausas
juli at ceam.es
Sun Feb 8 18:38:40 CET 2004
Dear all,
I don't understand the following behaviour: Running compar.gee (in
library ape ) with and without the option 'data', it give me different
results
Example:
.... Start R ....
> load("eiber.RData")
> ls()
[1] "gee.na" "mydata" "mytree"
> library(ape)
> # runnig with the option data= mydata
> compar.gee(alt ~ R, family="gaussian", data=mydata, phy=mytree)
Loading required package: gee
[1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27"
[1] "running glm to get initial regression estimate"
[1] 7.9500000 0.5155172
Call:
formula: alt ~ R
Number of observations: 37
Model:
Link: identity
Variance to Mean Relation: gaussian
Summary of Residuals:
Min 1Q Median 3Q Max
-12.1267954 -9.4267954 -7.4267954 -0.4267954 20.7903982
Coefficients:
Estimate S.E. t Pr(T > |t|)
(Intercept) 9.209602 4.760274 1.934679 0.08798892
R1 3.217194 2.548273 1.262500 0.24130121
Estimated Scale Parameter: 86.39367
"Phylogenetic" df (dfP): 10.24615
> # Second way, without the option data (so attaching the dataframe)
> attach(mydata)
> compar.gee(alt ~ R, family="gaussian", phy=mytree)
[1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27"
[1] "running glm to get initial regression estimate"
[1] 7.9500000 0.5155172
Call:
formula: alt ~ R
Number of observations: 37
Model:
Link: identity
Variance to Mean Relation: gaussian
Summary of Residuals:
Min 1Q Median 3Q Max
-14.123399 -11.423399 -8.856398 -1.856398 20.143602
Coefficients:
Estimate S.E. t Pr(T > |t|)
(Intercept) 9.856398 5.137029 1.918696 0.09020828
R1 4.567001 2.351966 1.941781 0.08701965
Estimated Scale Parameter: 103.2713
"Phylogenetic" df (dfP): 10.24615
> search()
[1] ".GlobalEnv" "mydata" "package:gee" "package:ape"
[5] "package:methods" "package:ctest" "package:mva" "package:modreg"
[9] "package:nls" "package:ts" "Autoloads" "package:base"
>
(R 1.8.1 for Windows
ape 1.2)
Note that the results are different.
Am I doing something wrong? Which is the correct answer?
Thanks for any help
Juli
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