In developing an exercise recently, I discovered a small bug that was
introduced into the function
phenogram
when I changed (in the latest phytools) version the optional argument
spread.labels
to default from FALSE
to
TRUE
. This bug causes the function to crash if labels are
turned off using ftype="off"
under the default conditions.
Here's how it manifests using simulated tree & data:
library(phytools)
packageVersion("phytools")
## [1] '0.4.56'
tree<-pbtree(n=26,tip.label=LETTERS)
x<-fastBM(tree)
phenogram(tree,x) ## works
phenogram(tree,x,ftype="off") ## doesn't work
## Error in optim(zz, ff, yy = yy, mo = mo, ms = ms, cost = cost, method = "L-BFGS-B", : L-BFGS-B needs finite values of 'fn'
phenogram(tree,x,ftype="off",spread.labels=FALSE) ## works
The fix is pretty easy - I just check if ftype="off"
and
set spread.labels=FALSE
if it is. I will put this in the
next version of phytools. Here's how it works:
source("http://www.phytools.org/phenogram/v1.4/phenogram.R")
phenogram(tree,x)
phenogram(tree,x,ftype="off") ## now works
OK, that's it for now.
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