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 bound
Dear Emmanuel, List,
Thank you for the reply, I hadn't realized that rTraitCont simulates
the trait evolution numerically from the SDE. I believe it would be
more efficient and accurate to use the analytic solution, which is
what sim.char and simulate in geiger and ouch do. Since both BM and
OU
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
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"
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
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:
> pruned.tree<-drop.tip(tr
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