Hi everyone,
I have been running PGLS with gls from NLME and phyl.resid from PHYTOOLS.
Most of my analyses are running well with no problems and give the same
results in both packages. With just a few of my dependent variables, which
happen to be evolutionary rates extracted from the program BAMM and the
associated package BAMMtools, I get lambda values greater than 1 when using
both gls and phyl.resid.
I have read an older post that says that lambda can theoretically be >1,
but I am wondering whether it is safe to interpret results from such PGLS
analyses? If I constrain lambda to be 1 (instead of 1.0015, which gls and
phyl.resid return when letting them optimize lambda) the results and
p-values change considerably. Any advice or experience with how to proceed
or interpret results in light of lambda greater than 1 would be greatly
appreciated! Thanks for your time!
Regards,
Zach
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