Hi folks, I've been tinkering with a model selection script for codon models (attached), based heavily on the syntax for phymltest from ape. When I try running it, I get that the files a, c, and t cannot be found. I know that the a and c have to do with gamma rate classes, and the t has to do with specifying the optimization strategy for the tstv rate, but I do not see where the syntax I specified went wrong. I'm assuming there is a rep(), c(), or combination error.
Any suggestions would be greatly appreciated! Best, ~John John S. S. Denton Ph.D. Candidate Department of Ichthyology and Richard Gilder Graduate School American Museum of Natural History www.johnssdenton.com
codonphymltest.R
Description: codonphymltest.R
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