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, has a few arguments to vary, or
might require several steps. As a way to deal with this kind of issue, I often
define a new list for lapply and avoid using the list I want to work as the
target. Here is an attempt to show how that can be done (but I think Liam’s
suggestion is actually better)
n <- length(tree)
newTree <- lapply(1:n, function(j){
tree.j <- tree[[j]]
bind.tip(tree.j, bind.tip, tip.label="Cercopithecus_albogularis",
position=0.59, edge.length = 0.59,
where=mrca(tree.j)["Cercopithecus_mitis","Cercopithecus_mitis"])
})
Another way this could be done is to make multiple lists and use the Map
function, which is basically a modification of the mapply example Liam used.
(This example also uses Liam’s suggestion to use fastMRCA.)
tip.label <- lapply(1:n, function(.) "Cercopithecus_albogularis")
MRCA <- lapply(1:n, function(j) fastMRCA(tree[[j]],
"Cercopithecus_albogularis", "Cercopithecus_albogularis"))
newTree <- Map(function(tr, tl, m) bind.tip(tr, tl,
position=0.59, edge.length = 0.59,
where = m),
tree,
tip.label,
MRCA
)
Finally, the do.call function can be helpful when repeating a function that has
only one or few arguments among several changing over a list. Building on
previous set up, one could do this
bind.args <- list(tree = tree[[1]], tip.label = “Cercopithecus_albogularis”,
position=0.59, edge.length = 0.59, where = MRCA[[1]],
interactive = FALSE)
newTree <- lapply(1:n, function(j){
bind.args$tree <- tree[[j]]
bind.args$where <- MRCA[[j]]
do.call(bind.tip, bind.args)
})
I also suggest these without verification with real data.
Cheers!
Mike
> On Jun 2, 2021, at 9:11 PM, Liam J. Revell <liam.rev...@umb.edu> wrote:
>
> 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 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 [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
>
> U.S. COVID-19 explorer web application:
> https://covid19-explorer.org/
>
> On 6/2/2021 8:18 PM, Nathan Upham wrote:
>> EXTERNAL SENDER
>> 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).
>> 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://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%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674838188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=KeZWNETOkPBekL3j5AIr2hygW49PbdSKImMV39QTXtE%3D&reserved=0
>> And here is the code file:
>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fn8upham%2FCaribbeanExtinctions-WTWTW%2Fblob%2Fmaster%2FmamPhy_pruningCode%2FpruningCode_MamPhy-to-CaribbeanTaxa.R&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674838188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=10u8o7U8dqC1pyK6GteNycoSACTOXAO2VaHNJmTeddk%3D&reserved=0
>> 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
>> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvertlife.org%2Fdata%2Fmammals%2F&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674838188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DbfdSFyjoCtDqUWuVoRs%2BC8Toe3v2BuFHgIpBTim9M0%3D&reserved=0>
>> and the Mammal Diversity Database
>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmammaldiversity.org%2F&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674838188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=sYqcCTEhWozvCAIC1vdxbBf5qeJq%2FBsV54zDRuOKABE%3D&reserved=0>
>> 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 | Google Scholar
>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fhl%3Den%26user%3DzIn4NoUAAAAJ%26view_op%3Dlist_works%26gmla%3DAJsN-F6ybkfthmTdjTpow6sgMhWKn1EKcfNtmIF_wzZcev7yeHuEu5_aolFS85rWiVRHpiQgbwg43i6eS6kArrabLdFL4bntzUSRmlRP2CW4lbZqeEcColw&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674838188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=sa9VBUNzHzzPUecVRmknFoa36gEQA7hySS7uFuxXh9o%3D&reserved=0>
>> | ASU profile
>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fisearch.asu.edu%2Fprofile%2F3682356&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674838188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=D9p3TXN7AdorpSqBqnydAvKNoPXOGZ0wR7ESw8bB4H0%3D&reserved=0>
>> e: nathan.up...@asu.edu | Skype: nate_upham | Twitter: @n8_upham
>> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2Fn8_upham&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=OM3Q8KIzJ%2BpAvHy6Z5B74%2FD%2Bsy7LkDGVCSAotBNwjnU%3D&reserved=0>
>> ========================================================================
>>> On Jun 2, 2021, at 4:19 PM, Eliot Miller <eliot.is...@gmail.com> wrote:
>>>
>>> Hi Russell,
>>>
>>> A package I wrote a while back should be able to do that fairly easily.
>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Feliotmiller%2FaddTaxa__%3B!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQrzxl2aIw%24&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=kgDYJXKFXRFIM8mv1x8fViY6QDiEjTQ8qP5mQ0SUq3k%3D&reserved=0
>>> The only paper it's described in
>>> remains
>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbsapubs.onlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.3732%2Fajb.1500195__%3B!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQp7PnRRHg%24&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DmHEuwIvxP0uiRhdBPZ%2BuUWUoVpIQ5PW8Xfrjyv9Nyg%3D&reserved=0
>>> 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>
>>> wrote:
>>>
>>>> Dear R-sig-phylo,
>>>>
>>>> I have been working with a mammalian phylogeny I recently downloaded from
>>>> VertLife
>>>> (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fvertlife.org%2Fphylosubsets%2F__%3B!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQoEdEnMAg%24&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=j6H0DVJ0hHT3CgQa6N3ySbpkOj%2FmSifnMnSuZlFOEEE%3D&reserved=0
>>>> ). 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]]
>>>>
>>>> _______________________________________________
>>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
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>>>> Searchable archive at
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>>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
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>> [[alternative HTML version deleted]]
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