Hi, all.
I'm working on a script that iteratively removes taxa from an initial
total tree and re-searches for optimal (pruned) topologies after
outputting a pruned alignment.
I'm trying to get a few things to happen:
First, the script iteratively checks to make sure that the taxon names
match in the alignments and trees, and terminates if they do not. I can
get it to print that the matches are okay as it checks each taxon:
for (i in totaltr$tip.label) {
if (all(totaltr$tip.label %in% rownames(alig)) && all(rownames(alig)
%in%
totaltr$tip.label)) cat("OK: Taxon labels match in tree and alignment")
else stop("Taxon labels do not match. Script terminates.")
}
But I want each line of "OK: Taxon labels match...." and "Taxon labels do
not match" to print the name of the taxon being checked, or the taxon for
which a match does not occur, something like
"Taxon labels match in tree and alignment FOR TAXON i." and
"Taxon labels do not match FOR TAXON i. Script terminates."
Suggestions?
Second, I want the script to store a list of the tree lengths it
calculates as it goes. I can calculate tree lengths via
sum(tree.name$edge.length), but I am having trouble, it seems,
initializing and storing the list. The code I have is
ts.values <- list()
length(ts.values) <- length(row.names(alig))
for (i in totaltr$tip.label) {
if (all(totaltr$tip.label %in% rownames(alig)) && all(rownames(alig)
%in%
totaltr$tip.label)) cat("OK: Taxon labels match in tree and alignment")
else stop("Taxon labels do not match. Script terminates.")
}
Sys.sleep(3)
for (i in totaltr$tip.label) {
write.tree(drop.tip(totaltr, i), file = paste("minus_", i, ".tre", sep =
"") )
ts.values[[i]] <- {sum(drop.tip(totaltr, i)$edge.length)}
}
So ts.values is the list I am trying to store the tree lengths in. After
the script finishes, though, I try to call ts.values via print(ts.values),
but it says the object does not exist.
I am tinkering with these two problems using a modified version of the
phymltest routine in the ape package, so the tree/alignment filenames
written are for phyml output.
Suggestions?
Thanks a lot.
~John
--
"ORGANIC LIFE beneath the shoreless waves
Was born and nurs'd in ocean's pearly caves;
First forms minute, unseen by spheric glass,
Move on the mud, or pierce the watery mass;
These, as successive generations bloom,
New powers acquire and larger limbs assume;
Whence countless groups of vegetation spring,
And breathing realms of fin and feet and wing."
~Erasmus Darwin, The Temple of Nature Canto I.V
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