First of all, thank you for helping :)
Well, this didn't work out, although it should work perfectly. When I type
in nc - name.check(tree, data) and then nc I get all tree species (over
3000 species) in the $Tree.not.data part. In the $Data.not tree part I see
281 numbers from 1 to 281, this
Hi Eugen,
Did you try my suggestion?
In your case, if the species you want to keep are in a row separated
text file, with a header (species), first read them in:
species.to.keep-read.table(file=species.list.file,header=T)
Now, for phylo object tree, type:
Yes, name.check() will only work with a named vector of data or data frame, so
Liam's code should work for you. it also looks like your names in the vector
species are different from those of the tip labels, as you say that
nc$Tree.not.data gives you a bunch of numbers but your vector is made
Well, Liams suggestion produced an error message only zeros are allowed to
be mixed with negative indices. I just tried a bunch of command lines from
various internet sites and came up with what seems to be a solution. Here
the skript:
tree-read.tree(tree.tre)
data-read.csv(data.csv)
Hi Eugen.
name.check() uses the row names of your data matrix, so that's why it
works now.
The error message that was returned by the -match() method suggests that
you have species in your to include file that are not actually in the
tree (thus match() returns one or multiple NAs). I did
All-
As far as I understand it, the vast majority of continuous character
analyses assume that the trait is distributed normally and without
bounds. Is there an appropriate transformation to for measurements of
a trait that does have one or more bounds and where some taxa actually
are at that
