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 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
