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")), ape::getMRCA returns the
parent node of the corresponding taxon -- rather than the tip index. I
didn't know that, but now I do.
You can switch to using phytools::fastMRCA. fastMRCA takes two tip label
arguments instead of one -- so in your case the function call would be
fastMRCA(tree,"Cricetomys_emini","Cricetomys_emini").
You can also just use the base R function which. In this case, you would
do which(tree$tip.label=="Cricetomys_emini"). This should have the same
effect.
You do seem to be using the arguments 'where' and 'position' correctly
in phytools::bind.tip. 'where' should point to the node immediately
*above* (i.e., tipward) of the place you want to attach the new tip;
while 'position' should be the depth *below* that node.
Here's an update to your mapply call using fastMRCA instead of getMRCA.
newtree<-mapply(bind.tip,tree=tree,where=lapply(tree,fastMRCA,
sp1="Cercopithecus_mitis",sp2="Cercopithecus_mitis"),
MoreArgs=list(tip.label="Cercopithecus_albogularis",
position=0.59,edge.length=0.59),SIMPLIFY=FALSE)
class(newtree)<-"multiPhylo"
Please let me (& the list) know if this solution works as expected.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
http://faculty.umb.edu/liam.revell/, http://www.phytools.org,
http://blog.phytools.org
Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile
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https://covid19-explorer.org/
On 6/4/2021 1:17 AM, Russell Engelman wrote:
EXTERNAL SENDER
Dear Everyone,
I think these are all really good suggestions. I tried this with my data
(specifically the mapply with getMRCA) and it sort of worked. Sort of in
that the mapply did apply the transformation to all 100 trees, but I
noticed that after I applied it I got some funky results. Here is
another example with /Cricetomys ansorgei /and some associated code...
hbltree <-read.nexus(file=" hbltree .nex")
class(hbltree)<-"multiPhylo"
newtrees<-mapply(bind.tip,tree=hbltree,where=lapply(hbltree,getMRCA,
tip=c("Cricetomys_emini","Cricetomys_emini")),
MoreArgs=list(tip.label="Cricetomys_ansorgei",
position=3.282,edge.length=3.282),SIMPLIFY=FALSE)
However I noticed that when I printed the phylogeny the function for
some reason does not place /C. ansorgei /as the sister taxon to /C.
emini/, instead it places it as sister to /C. emini/ + /C. gambianus.
/That part I am not sure why this is because getMRCA should find the
terminal tip of /C. emini/, given that it is finding the MRCA of the
same taxon.
It also does not place /C. ansorgei /at the tip of the tree. This might
be a side effect of the function selecting the wrong node to insert the
taxon on, but I think part of it as well is that I'm not familiar with
how to handle the position and edge.length arguments in this case. I
know from consulting the primary literature that /C. ansorgei /is
recoded to have diverged from its nearest sister taxon, /C. emini/,
about 3.282 Ma. So I know the 'edge.length' argument should be set to
3.282. I've often struggled a lot with how to efficiently set the
'position' argument afterwards.
Is it possible I am calling the wrong node or something to insert the
taxon at?
Sincerely,
Russell
On Thu, Jun 3, 2021 at 10:47 AM Liam J. Revell <liamjrev...@gmail.com
<mailto:liamjrev...@gmail.com>> wrote:
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 'applying' over (tree) also
appears among the arguments!
If you want to use apply-family functions instead of a for loop (just,
say, for fun) then you have two basic options: you can write a custom
function; or you can use mapply.
Here's some (untested) code to do it.
## first, using a custom function & lapply:
foo<-function(tree) bind.tip(tree,
tip.label="Cercopithecus_albogularis",
position=0.59,edge.length=0.59,
where=getMRCA(tree,tip=c("Cercopithecus_mitis",
"Cercopithecus_mitis")))
newtree<-lapply(tree,foo)
class(newtree)<-"multiPhylo"
## now, using mapply:
newtree<-mapply(bind.tip,tree=tree,where=lapply(tree,getMRCA,
tip=c("Cercopithecus_mitis","Cercopithecus_mitis")),
MoreArgs=list(tip.label="Cercopithecus_albogularis",
position=0.59,edge.length=0.59),SIMPLIFY=FALSE)
class(newtree)<-"multiPhylo"
(Code is not guaranteed! I don't have the data file, so I didn't
actually test it -- but something like this ought to work.)
Regardless, I recommend using ape::getMRCA (or phytools::fastMRCA)
because otherwise you're computing an N x N matrix in each iteration of
your function call just to get one node index.
Good luck! All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
Web & phytools:
http://faculty.umb.edu/liam.revell/
<http://faculty.umb.edu/liam.revell/>, http://www.phytools.org
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On 6/2/2021 8:18 PM, Nathan Upham wrote:
> 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 of 28 Bayesian patch clades.
>
> Adding additional species described since the 2015 cutoff of that
VertLife taxonomy makes sense (e.g., up to ~6,500 species on
mammaldiversity.org
<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmammaldiversity.org%2F&data=04%7C01%7Cliam.revell%40umb.edu%7C31aef1ba99c742b14f6b08d927182bbc%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637583807154183969%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=1Ua4UnPAguLQi%2BRv7AOP00PBg3Hbuzovhqk%2FGow6uAI%3D&reserved=0>).
However, keep in mind that they will not have birth-death estimated
branch lengths, but rather more likely be added as a polygamy to
given clade and then randomly resolved.
>
> Given the sample code you provided, the key thing you’ll want to
do is run a *loop* rather than using lapply, so that you can specify
a given tree each time, e.g.:
>
> newtrees<-vector(“list”,length(trees))
> for(j in 1:length(trees)){
> newtrees[[j]] <- bind.tip(tree=trees[[j]],
tip.label="Cercopithecus_albogularis”, position=0.59,edge.length =
0.59,
where=mrca(tree[[j]])["Cercopithecus_mitis","Cercopithecus_mitis"])
> }
>
> I also wrote some code to prune mammal trees and add extinct
Caribbean species, which uses a similar approach of making
polytomies and randomly resolving them — here is the repo:
>
https://github.com/n8upham/CaribbeanExtinctions-WTWTW/tree/master/mamPhy_pruningCode
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fn8upham%2FCaribbeanExtinctions-WTWTW%2Ftree%2Fmaster%2FmamPhy_pruningCode&data=04%7C01%7Cliam.revell%40umb.edu%7C31aef1ba99c742b14f6b08d927182bbc%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637583807154193960%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=tbsBqp83Ylw6Icw9%2FIo4FH6gb7YwF8wU%2FdDTsSHGgCg%3D&reserved=0>
> And here is the code file:
>
https://github.com/n8upham/CaribbeanExtinctions-WTWTW/blob/master/mamPhy_pruningCode/pruningCode_MamPhy-to-CaribbeanTaxa.R
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>
> Hope that helps,
> —nate
>
>
>
>
========================================================================
> Nathan S. Upham, Ph.D. (he/him)
> Assistant Research Professor & Associate Curator of Mammals
> Arizona State University, School of Life Sciences
> ~> Check out the new Mammal Tree of Life
<http://vertlife.org/data/mammals/
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and the Mammal Diversity Database <https://mammaldiversity.org/
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>
> Research Associate, Yale University (Ecology and Evolutionary
Biology)
> Research Associate, Field Museum of Natural History (Negaunee
Integrative Research Center)
> Chair, Biodiversity Committee, American Society of Mammalogists
> Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group
>
> personal web: n8u.org
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> e: nathan.up...@asu.edu <mailto:nathan.up...@asu.edu> | Skype:
nate_upham | Twitter: @n8_upham <https://twitter.com/n8_upham
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>
========================================================================
>
>
>
>> On Jun 2, 2021, at 4:19 PM, Eliot Miller <eliot.is...@gmail.com
<mailto:eliot.is...@gmail.com>> wrote:
>>
>> Hi Russell,
>>
>> A package I wrote a while back should be able to do that fairly
easily.
>>
https://urldefense.com/v3/__https://github.com/eliotmiller/addTaxa__;!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQrzxl2aIw$
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The only paper it's described in
>> remains
https://urldefense.com/v3/__https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1500195__;!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQp7PnRRHg$
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>> It's a wrapper for bind.tip, with some additional stuff. You
basically
>> would give it a taxonomic file where you identify the clades you're
>> interested in (e.g. both of those Cercopithecus species could be
named some
>> unique clade name and off you go, it'd add the missing one to
the other),
>> then lapply that whole addTaxa command over the list of trees in
>> multiPhylo. At some point I made laser a dependency, and it's
possible I
>> left it in that state. If that's the case, you can still get
laser from old
>> CRAN mirrors I believe. Let me know if you want more help.
>>
>> Best,
>> Eliot
>>
>> On Wed, Jun 2, 2021 at 7:05 PM Russell Engelman
<neovenatori...@gmail.com <mailto:neovenatori...@gmail.com>>
>> wrote:
>>
>>> Dear R-sig-phylo,
>>>
>>> I have been working with a mammalian phylogeny I recently
downloaded from
>>> VertLife
(https://urldefense.com/v3/__http://vertlife.org/phylosubsets/__;!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQoEdEnMAg$
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). 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 that I am
using to do
>>> things such as test for phylogenetic signal. I know how to use
bind.tip to
>>> add new taxa to a single tree, but I am having more trouble with a
>>> multiPhylo object. I am primarily adding these taxa by placing
them as
>>> sister to their nearest included relative (since most of them
are elevated
>>> former subspecies), but the issue here is that in the 100 trees
in the
>>> multiPhylo object the node representing the taxon to bind these
taxa to is
>>> not the same across all trees due to shifting topologies.
>>>
>>> This is an example of the code I have been using, in which
"tree" is the
>>> tree object. This works for a single 'phylo' tree but not
'multiphylo'.
>>>
>>> ```
>>>
newtree<-lapply(tree,bind.tip,tip.label="Cercopithecus_albogularis",
>>> position=0.59,edge.length = 0.59,
>>>
>>> where=mrca(tree)["Cercopithecus_mitis","Cercopithecus_mitis"])
>>> ```
>>>
>>> Now, this code will not work, but I know exactly why: 'tree' is a
>>> multiPhylo object and so the 'where' argument cannot find the
node for the
>>> terminal taxon. However, the issue is how can I tell R to
repeat this
>>> 'where' argument for each of the 100 trees, since the node in
question is
>>> not identical across these trees? Is there an easier way to do
this than
>>> using the 'mrca' call for each terminal taxon? I've noticed
adding a 'mrca'
>>> argument also increases computation time and if I am
reinventing the wheel
>>> it would be nice to know if I am overthinking things.
>>>
>>> Sincerely,
>>> Russell
>>>
>>> [[alternative HTML version deleted]]
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