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 <[EMAIL PROTECTED]>.
Uwe Ligges
Juli
______________________________________________
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
