This new code works perfectly for me.
Thanks so much everyone for helping me to solve this issue in record time!
Kamila
> On Jan 6, 2017, at 6:39 AM, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote:
>
> I paste below the new code of extract.clade for those who want to try it.
>
> Best,
>
> Emmanuel
>
> ########################################################################
> extract.clade <- function(phy, node, root.edge = 0, interactive = FALSE)
> {
> n <- length(phy$tip.label)
> if (interactive) {
> cat("Click close to the node...\n")
> node <- identify(phy)$nodes
> } else {
> if (length(node) > 1) {
> node <- node[1]
> warning("only the first value of 'node' has been considered")
> }
> if (is.character(node)) {
> if (is.null(phy$node.label))
> stop("the tree has no node labels")
> node <- match(node, phy$node.label) + n
> if (is.na(node)) stop("'node' not among the node labels.")
> }
> if (node <= n)
> stop("node number must be greater than the number of tips")
> }
> if (node == n + 1L) return(phy)
> keep <- prop.part(phy)[[node - n]]
> drop.tip(phy, (1:n)[-keep], root.edge = root.edge, rooted = TRUE)
> }
> ########################################################################
>
> Le 06/01/2017 à 10:17, Emmanuel Paradis a écrit :
>> Hi,
>>
>> Klaus is right: extract.clade() fails if the tree has been rooted with
>> resolve.root = TRUE before. I'm going to rewrite the function calling
>> drop.tip (which will be safer). In the meantime, Klaus's function should
>> work for Kamila.
>>
>> Best,
>>
>> Emmanuel
>>
>> Le 06/01/2017 à 05:17, Klaus Schliep a écrit :
>>> I had a look at the tree. There seems a bug in extract.clades, when the
>>> tree was rooted before with the root() function. extract.clade() seem to
>>> expect some ordering of nodes which seems not satisfied (and it looks as
>>> it was written a long time ago).
>>>
>>> I just wrote a small function (easier than to debug the old one) which
>>> should do the same and it seems to work:
>>>
>>> library(phangorn)
>>>
>>> extract.clade2 <- function(phy, node){
>>> if(!(node %in% phy$edge[,1])) stop("node number must be greater than
>>> the number of tips")
>>> drop.tip(phy, setdiff(1:Ntip(phy), Descendants(phy, node)[[1]]))
>>> }
>>>
>>> Klaus
>>>
>>>
>>>
>>> On Jan 5, 2017 10:25 PM, "Joseph W. Brown" <josep...@umich.edu
>>> <mailto:josep...@umich.edu>> wrote:
>>>
>>> Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree
>>> and tried things out:
>>>
>>> phy <- rtree(17);
>>> rootID <- length(phy$tip.label) + 1;
>>> counter <- 1;
>>> for (i in rootID:max(phy$edge[,1])) {
>>> clade <- extract.clade(phy, i);
>>> # do something. just printing clade properties here
>>> print(paste0("clade ", counter, " (node ", i, ") has ",
>>> length(clade$tip.label), " tips."));
>>> counter <- counter + 1;
>>> }
>>>
>>> [1] "clade 1 (node 18) has 17 tips."
>>> [1] "clade 2 (node 19) has 11 tips."
>>> [1] "clade 3 (node 20) has 10 tips."
>>> [1] "clade 4 (node 21) has 4 tips."
>>> [1] "clade 5 (node 22) has 3 tips."
>>> [1] "clade 6 (node 23) has 2 tips."
>>> [1] "clade 7 (node 24) has 6 tips."
>>> [1] "clade 8 (node 25) has 5 tips."
>>> [1] "clade 9 (node 26) has 3 tips."
>>> [1] "clade 10 (node 27) has 2 tips."
>>> [1] "clade 11 (node 28) has 2 tips."
>>> [1] "clade 12 (node 29) has 6 tips."
>>> [1] "clade 13 (node 30) has 2 tips."
>>> [1] "clade 14 (node 31) has 4 tips."
>>> [1] "clade 15 (node 32) has 3 tips."
>>> [1] "clade 16 (node 33) has 2 tips."
>>>
>>> and had no problem. Maybe post your tree here?
>>>
>>> JWB
>>> ________________________________________
>>> Joseph W. Brown
>>> Post-doctoral Researcher, Smith Laboratory
>>> University of Michigan
>>> Department of Ecology & Evolutionary Biology
>>> Room 2071, Kraus Natural Sciences Building
>>> Ann Arbor MI 48109-1079
>>> josep...@umich.edu <mailto:josep...@umich.edu>
>>>
>>>
>>>
>>> > On 5 Jan, 2017, at 17:18, Kamila Naxerova <knaxer...@partners.org
>>> <mailto:knaxer...@partners.org>> wrote:
>>> >
>>> > Dear Joseph,
>>> >
>>> > thanks so much. This is exactly what I need!
>>> >
>>> > I am running into some problems that I don’t understand though. In
>>> my case, rootID is 18, and max(phy$edge[,1]) is 33. When I try to
>>> execute your loop, this happens:
>>> >
>>> > > extract.clade(phy, 18)
>>> >
>>> > Phylogenetic tree with 17 tips and 16 internal nodes.
>>> >
>>> > Tip labels:
>>> > X1, X8, X9, X10 ...
>>> >
>>> > Rooted; includes branch lengths.
>>> >
>>> > So far so good… but then I keep getting these errors:
>>> >
>>> > > extract.clade(phy, 19)
>>> > Error in phy$edge[, 2] : incorrect number of dimensions
>>> > > extract.clade(phy, 20)
>>> > Error in phy$edge[, 2] : incorrect number of dimensions
>>> >
>>> > Not sure why extract.clade produces these errors. 19-23 don’t
>>> work, 24-26 work, 27 produces the error again, 28 works etc.
>>> >
>>> > Thanks again.
>>> >
>>> > Kamila
>>> >
>>> >
>>> >> On Jan 5, 2017, at 4:12 PM, Joseph W. Brown <josep...@umich.edu
>>> <mailto:josep...@umich.edu> <mailto:josep...@umich.edu
>>> <mailto:josep...@umich.edu>>> wrote:
>>> >>
>>> >> Not sure if I understand the problem completely, but this should
>>> allow you to examine all of the clades (and should work if
>>> polytomies are involved):
>>> >>
>>> >> # for tree phy
>>> >> rootID <- length(phy$tip.label) + 1;
>>> >> for (i in rootID:max(phy$edge[,1])) {
>>> >> clade <- extract.clade(phy, i);
>>> >> # do something
>>> >> }
>>> >>
>>> >> This includes the root node (i.e. whole tree), but that can be
>>> changed. This can be rewritten as an lapply if necessary.
>>> >>
>>> >> HTH.
>>> >> JWB
>>> >> ________________________________________
>>> >> Joseph W. Brown
>>> >> Post-doctoral Researcher, Smith Laboratory
>>> >> University of Michigan
>>> >> Department of Ecology & Evolutionary Biology
>>> >> Room 2071, Kraus Natural Sciences Building
>>> >> Ann Arbor MI 48109-1079
>>> >> josep...@umich.edu <mailto:josep...@umich.edu>
>>> <mailto:josep...@umich.edu <mailto:josep...@umich.edu>>
>>> >>
>>> >>
>>> >>
>>> >>> On 5 Jan, 2017, at 15:50, Kamila Naxerova
>>> <knaxer...@partners.org <mailto:knaxer...@partners.org>
>>> <mailto:knaxer...@partners.org <mailto:knaxer...@partners.org>>>
>>> wrote:
>>> >>>
>>> >>> Hi all,
>>> >>>
>>> >>> I would like to break a phylogenetic tree into all possible
>>> clades and then examine each one of them for certain characteristics.
>>> >>>
>>> >>> I am writing some code to do this from scratch, but it’s getting
>>> pretty cumbersome quickly.
>>> >>>
>>> >>> I was wondering whether there are some functions out there
>>> already that could help me with this task?
>>> >>>
>>> >>> Thanks so much for any help.
>>> >>>
>>> >>> Cheers,
>>> >>> Kamila
>>> >>>
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