How to resolve error message: could not find function "gls"

Question

I am using the "ape" package to run a phylogenetic gls, but I am stumped by an error message: could not find function "gls". Does anyone please know how to resolve this? Thank you.

tree <- tree.primates 
bm.prim <- corBrownian(phy=tree) 
XY <- data.frame(Y, X) 
summary(gls(Y ~ X, correlation=corBrownian(phy=tree), data=XY))

It would help dramatically to see the code that actually produced this error... — nrussell, Oct 09 '15 at 19:48
it's a shot in the dark, but try `library(ape)` before you call the function :) — maRtin, Oct 09 '15 at 19:52
Here is the code that I am working with. Not sure how much to include, but thank you for looking: — GTC, Oct 09 '15 at 19:55
> tree bm.prim XY summary(gls(Y ~ X, correlation=corBrownian(phy=tree), data=XY)) — GTC, Oct 09 '15 at 19:56
Thank you RHertel for your help. That resolved this issue. Thanks to all. — GTC, Oct 09 '15 at 20:00
@RHertel can you elaborate why the nlme package is needed here? — maRtin, Oct 09 '15 at 20:01
https://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html — RHertel, Oct 09 '15 at 20:03

score 0 · Answer 1 · answered Oct 09 '15 at 20:02

ape does not have a gls function. You'll need to load a package that has the implementation you want, probably nlme, though apparently a package called QTLRel has one as well.

Here are my search results on rdocumentation.org which is where I found the packages that have gls functions.

How to resolve error message: could not find function "gls"

1 Answers1