Tuesday, May 3, 2011

Comment on evol.rate.mcmc()

Yesterday a user reported that when he tried to reproduce my example analysis for the function evol.rate.mcmc() here, he encountered the following error when pre-processing the posterior sample:

> mcmc<-posterior.evolrate(tree,minsplit,result$mcmc[201:1001,], result$tips[201:1001])
Error in if (where == 0 || where == "root") where <- ROOTx :
missing value where TRUE/FALSE needed

Today I suggested he try updating {ape} - he did, and the problem went away.

I'm not sure what the compatibility issue is here, but I suspect it has something to do with one of drop.tip(), extract.clade(), or bind.tree(), as these are all called extensively in this function. Take home message - update {ape}!

To find out what version of {ape} (or any other package) you are working with, simply type:

> packageDescription("ape")["Version"]
[1] "2.7-1"

(FYI 2.7-1 is in fact the version I have installed on this machine.)

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