Dear Everyone,
Sorry for the late reply. I had a crunch with several manuscripts that had
a looming due date, and am coming back to trying to fix the issue I am
having with the phylogeny I emailed about before. I've been trying
several things but I've still been unable to resolve the issue with
Dear Everyone,
So this is really strange. I tried what Dr. Revell suggested, and for the
two examples I gave it worked for *Cercopithecus albogularis*, but when I
applied it to *Cricetomys ansorgei *I got the message...
"Error in bind.tree(tree, tip, where = where, position = pp) :
'position'
Dear Russell.
For some reason, my emails don't seem to be getting through to the whole
list -- so my apologies if this ends up being redundant with another reply.
In short, if you supply a vector of tip labels that are identical (e.g.,
c("Cricetomys_emini","Cricetomys_emini")),
Hello Everyone,
Just to stack onto Liam’s “fun with apply family of functions”, I often use
lapply, which works well by having a function that only applies to the objects
in a list, but often — and for difficult to decipher reasons — breaks down if
the function is not predefined, is complex,
Dear Everyone,
So this is really strange. I tried what Dr. Revell suggested, and for the
two examples I gave it worked for *Cercopithecus albogularis*, but when I
applied it to *Cricetomys ansorgei *I got the message...
"Error in bind.tree(tree, tip, where = where, position = pp) :
'position'
Russell,
If you're trying to do this across a lot of species, you're going to bump
into a lot of complexities like this. I got the impression you were trying
to do this for many species. For example, there's no reason that the taxon
you're adding is, even if we assume monophyly of the clade
Dear Russell et al. (sorry if this is a re-send: my message yesterday
seems to have been blocked by the listserv)
Using a for loop is a great idea! Highly underrated in R, IMO.
However, for future reference, the reason that your code didn't work
with lapply is because the list you're
Dear Russell et al.
Using a for loop is a great idea! Highly underrated in R, IMO. ;)
However, for future reference, the reason that your code didn't work
with lapply is because the list you're 'applying' over (tree) also
appears among the arguments!
If you want to use apply-family
Dear Russell et al. (sorry if this is a re-send: my message yesterday
seems to have been blocked by the listserv)
Using a for loop is a great idea! Highly underrated in R, IMO.
However, for future reference, the reason that your code didn't work
with lapply is because the list you're
Dear Russell,
there is also a function getMRCA() in ape, which is more appropriate to use
for your problem, as it only computes the MRCA for a set of tips. This
should be much more efficient than using mrca().
Kind regards,
Klaus
On Thu, Jun 3, 2021 at 1:05 AM Russell Engelman
wrote:
> Dear
Hi Russell:
Glad to hear you’re using the VertLife mammal trees — they are built on a
taxonomy of 5,911 species of which only 4,098 are sampled for DNA, so there is
already a ~30% chunk that is placed using taxonomic constraints and birth-death
branch lengths as sampled during the estimation
Hi Russell,
A package I wrote a while back should be able to do that fairly easily.
https://github.com/eliotmiller/addTaxa The only paper it's described in
remains https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1500195
It's a wrapper for bind.tip, with some additional stuff. You
Dear R-sig-phylo,
I have been working with a mammalian phylogeny I recently downloaded from
VertLife (http://vertlife.org/phylosubsets/). Unfortunately, the phylogeny
is missing a large number of species, so I am trying to manually add these
taxa to the phylogeny. I have a series of 100 trees
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