Dear Jurriaan and Emmanuel,
thank you for your responses! I solved it the mrca() function.
Many thanks for your help and Jurriaan, I hope Emmanuel's solution
solves your question as well!
Best,
Annemarie
Emmanuel Paradis wrote:
Hi Annemarie,
Annemarie Verkerk wrote on 16/02/2012 09:57:
Hello,
I keep getting the following error when trying to calculate independent
contrasts:
pic.log_repertoire_data - pic(log_repertoire_data, t.100species)
Warning message:
In pic(log_repertoire_data, t.100species) :
the names of argument 'x' and the tip labels of the tree did not match: the
Hi Tom,
have you tried running
name.check(t.100species, log_repertoire_data)
to confirm that the names perfectly match in both? If there is even a slight
mismatch, then pic will ignore all the names in the data and assume that they
are in the same order as the tip labels in the tree. Thus
Graham is absolutely right. If you did this you would find that
Chlorocebus pygerythrus has an underscore separating genus specific
epithet in your tree, but not in your data vector:
require(geiger)
name.check(tree,x)
$Tree.not.data
[1] Chlorocebus_pygerythrus
$Data.not.tree
[1]
Nice! Thanks Graham and Liam,
-Tom
On Feb 20, 2012, at 9:07 PM, Liam J. Revell wrote:
Graham is absolutely right. If you did this you would find that Chlorocebus
pygerythrus has an underscore separating genus specific epithet in your
tree, but not in your data vector:
require(geiger)
