juli g. pausas wrote:
> 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 ape 1.2-1 is the recent version.
>
>
> Note that the results are different.
> Am I doing something wrong? Which is the correct answer?
> Thanks for any help
I guess that one with the data argument:
Are you sure there is no object called "alt" or "R" in your
workspace
before attaching the data frame (it will mask the attached object)?
You might want to check that:
identical(R, mydata$R)
identical(alt, mydata$alt)
If those objects are identical, you might want to ask the maintainer of
ape, Emmanuel Paradis <paradis at isem.univ-montp2.fr>.
Uwe Ligges
> Juli
>
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