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' is larger than the branch length"
I know that usually this means the new node position is usually further
back in time than the point where the branch diverges from its nearest
neighbor. However when I went to check how long the terminal branch leading
to *C. ansorgei*'s sister taxon that I am trying to bind it to is, *C.
emini*, it said that the branch length to this taxon is much, much greater
than the branch length of the new taxon I am trying to set (3.28 Ma), so it
is not clear why it is returning this error message. Here is some code that
shows this with the data set I attached.
```
nodes<-sapply(hbltree$tree_3084$tip.label,function(x,y)
which(y==x),y=hbltree$tree_3084$tip.label)
edge.lengths<-setNames(hbltree$tree_3084$edge.length[sapply(nodes,
function(x,y)
which(y==x),y=hbltree$tree_3084$edge[,2])],names(nodes))
edge.lengths[c("Cricetomys_emini","Cercopithecus_mitis")]
```
When I do this with my own dataset I get an edge length of 8.588. I tried
this with another tree (tree_7180) to see if things were varying between
trees and I got a branch length of 7.760.
The only thing I can think of is this is a result of the divergence time
varying among the trees, but in that case I am not sure of how to bind a
tip to these trees given I have the divergence data from the literature but
the Upham et al. dataset may not be calibrated to account for it. I.e., the
Upham et al. supertree is estimating divergence time in *Cricetomys *spp.
based on the available data for the species included: *C. emini *and *C.
gambianus*, and when additional constraining data from *C. ansorgei *is
included it might produce a different estimate of branch lengths.
Additionally, is there a way to do this if there is no branch length known?
I have a number of taxa for which divergence times have not been published,
but for whom their phylogenetic position is known. I am trying to just
stick them in the tree as close as possible. I thought it should be
possible if I just delete the `position` and `edge.length` arguments, as I
thought it said in the `ape` documentation that doing so just create a
polytomy or something like that at the split, but when I tried that with my
data I got the message...
"Error in while (currnode != rt) { : missing value where TRUE/FALSE needed"
Which suggests I am missing a key parameter somewhere or misusing the
bind.tip function somehow.
Sincerely,
Russell
On Fri, Jun 4, 2021 at 11:39 AM Mike Collyer <mlcoll...@gmail.com> wrote:
> 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
> >>>>
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo__%3B!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQqcmU5jCQ%24&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9qGpfdSpUHFbwBSiKL9t962V%2FRbNXrD1wl0QtZRoMao%3D&reserved=0
> >>>> Searchable archive at
> >>>>
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F__%3B!!IKRxdwAv5BmarQ!OZj7-dFRbxvUothKjSj6hr9B0eXscAO6LVWi1-a0w3J_PxlDqvsFDNb0lQq_N5pSwg%24&data=04%7C01%7Cliam.revell%40umb.edu%7C1174c283b881427e2df508d926253e2a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mRFMrjsvvxLFqUgUpVEog3jySUxoY2uY%2FhzRUEMJZd0%3D&reserved=0
> >>>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> >>>
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