rjswift <rosejswift <at> gmail.com> writes: > > I'm trying to select a model under PCA using independent contrasts. Since > PICs need to be forced through the origin I've been using lmorigin for the > original regression, but it doesn't appear that stepAIC recognizes it. I > keep receiving an error message - "Error in na.fail.default(list(Phenology = > c(NA_integer_, NA_integer_, : > missing values in object" > > I'm having trouble navigating around this error message, and any suggestions > would be appreciated. >
Do you mean "select a model under PIC"? I think you'll be better off posting this to the r-sig-ph...@r-project.org mailing list. lmorigin() [which is in the ape package] is a special-purpose function; the tricky part about fitting regressions through the origin is not fitting them (adding a -1 or a +0 to a model formula does that easily)] but making inferences about the resulting model. Depending on how you want to proceed, you can: 1. examine the permutation p-values produced by lmorigin() and do your stepwise procedure by hand; 2. fit through the origin using lm(y~...-1,...) and use stepAIC as usual However, I'm not sure which of this will be *correct* -- you're likely to get wiser comments on r-sig-phylo. In any case, beware stepwise fitting approaches! ______________________________________________ R-help@r-project.org 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.
