Thank you both for your kind and helpful answers that have solved my problem!
It is very much appreciated :)
Best,
Liam
> On 17 Oct 2018, at 5:01 am, Liam J. Revell wrote:
>
> Hi Liam.
>
> First of all, great choice of names!
>
> Secondly, add.species.to.genus is a very old function & I
Hi there,
If I read this right, you're also wanting to loop this over multiple
genera. If so, it might save some time to try this with the addTaxa package
(https://github.com/eliotmiller/addTaxa/blob/master/DESCRIPTION). I haven't
worked on this project in a while, and I left the documentation in
In the interests of furthering appalling hackery of the worst kind, on the
assumption you want to replace *all* generic nodes with their descendants (or
you don�t care about ultrametricity), you can do this easily with a good text
editor and the genus tree in one of the parenthetical notation
Hi Liam.
First of all, great choice of names!
Secondly, add.species.to.genus is a very old function & I wouldn't be
surprised to find that it had some bugs. Be forewarned!
Thirdly, I used Will's suggestion & got the function to work in the
script you sent to me off-list, but with one
This might be somewhat of a hacky solution, but could you just add "sp." to
all of your genus names? The phytools function is looking for "Genus
species" in your tree tip names, but none of your tips have binomials, so
it's not finding the correct genus. By adding "sp." to all of your original
tip
I thought this course might be of interest to some page members...
Phylogenetic comparative methods for studying diversification and
phenotypic evolution (PCME01)
https://www.prstatistics.com/course/phylogenetic-comparative-methods-for-studying-diversification-and-phenotypic-evolution-pcme01/
Hi members,
I am struggling with what I think is a relatively simple problem. I have a
genera tree (i.e. genera are the branch tips) that I need to add 390 species to
as polytomies with equal branch lengths below the genera tips/nodes.
Can anyone help me do this in R? I have tried a for loop
