Dear Tania, Shouldn't that be varIdent(form = ~species.group) instead of varIdent(form = ~1|species.group)?
Notice that this is untested as you did not provide a self-contained example (as de posting guide asked you to do). HTH, Thierry PS Next time try the mixed-models mailing list with questions about nlme. ------------------------------------------------------------------------ ---- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [email protected] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: [email protected] [mailto:[email protected]] Namens Tania BrenesArguedas Verzonden: dinsdag 24 februari 2009 16:23 Aan: [email protected] Onderwerp: [R] Initialize varFunc in R Hi, I am running R2.8.1 under Linux, and I am having trouble using the variance functions in nlme My basic model was something like: model0 <- lme( log(growth) ~ light * species.group , data=data, random=~light|species ) # with 20 odd species divided in 2 groups Following the methods in Pinheiro&Bates I tried to put a variance function in the model: model1 <- update(model0, weights=varIdent(form = ~1|species.group) ) I got no error message or note but when I printed model1 the output did not print any variance structure. It just didn't add any weights or variance structure and model1 = model0 If instead I ran the varFunc sepparately: varf1 <- varIdent(form = ~1|species.group) varf.init <- Initialize(varf1, data) model1 <- update(model0, weights=varf.init ) it works just fine, and I get an output with "Variance function: Structure: Different standard deviations per stratum" and a change in the diagnostic plots. So, this one works Digging a little bit I noticed that the "initialize" in Pinheiro&Bates is not capitalized. And "initialize" in R is used by some other package, such that each time I would try to follow the book I would get an error message: " c("\"varIdent\" is not a defined class", "\"varFunc\" is not a defined class")" When I figured out that in R I had to use "Initialize" with uppercase, I was able to make the above work. Is this an bug with the R varFunc or am I doing something wrong? Tania ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
