Hello all,
I have a workflow which involves getting some phylogenetic trees from
program A, doing some processing (including scaling down the branch
lengths) with ape, and then using the resulting trees as input to program
B. The scaling sometimes results in scientific notation in the branch
lengths (eg. 2.789e-05) which program B doesn't accept. I have tried to get
rid of these by using the scipen option in R, but it doesn't affect the
output of write.tree.
options(scipen=999)
t <- read.tree("test.nwk")
t$edge.length <- t$edge.length/100000.
t$edge.length # shows "correct" format, eg. 0.00002789
write.tree(t) # still has scientific notation, eg. 2.789e-05
Right now I am using a short bash script after the fact to find and replace
the scientific notation. I also realize there is probably a way to do this
within R, using grep and so forth. I was just wondering if there is a
better way within ape itself.
Thanks a lot,
Rosemary McCloskey
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