[Phylobase-devl] path between two tips

[Brian O'Meara]

The MRCA error may relate to this bug (<http://r-forge.r-project.org/ 
tracker/index.php?func=detail&aid=177&group_id=111&atid=488>) which  
Francois has a patch for, but I haven't checked to see if it's  
committed.

Brian

On Nov 20, 2008, at 2:54 PM, Thibaut Jombart wrote:

> Peter Cowan wrote:
>> There is a function for calculating the MRCA.  Line 101 of the
>> treewalk.R file.  Perhaps this is helpful.
>>
>> Peter
> Yes, it is. I used it in the function:
>
> shortestPath <- function(x, node1, node2){
>     if(!require(phylobase)) stop("phylobase package is not installed")
>
>     ## conversion from phylo, phylo4 and phylo4d
>     x <- as(x, "phylo4")
>
>     ## check phylo4 object
>     if (is.character(checkval <- check_phylo4(x))) stop(checkval)
>
>     ## main computations
>     t1 <- getnodes(x, node1)
>     t2 <- getnodes(x, node2)
>
>     comAnc <- MRCA(x, t1, t2) # common ancestor
>     desComAnc <- descendants(x, comAnc, which="all")
>     ancT1 <- ancestors(x, t1, which="all")
>     path1 <- intersect(desComAnc, ancT1) # path: common anc -> t1
>
>     ancT2 <- ancestors(x, t2, which="all")
>     path2 <- intersect(desComAnc, ancT2) # path: common anc -> t2
>
>     res <- union(path1, path2) # union of the path
>     res <- c(comAnc,res) # add the common ancestor
>     res <- getnodes(x, res)
>
>     return(res)
> } # end shortestPath
>
> Example:
> ##
> tr=as(rtree(20),"phylo4")
> plot(tr, show.node=T)
> shortestPath(tr,"t1","t2")
> ##
>
> It works for tips, but some pb occur with internal nodes.
> The pb seems to come from MRCA. For instance:
> ##
> data(geospiza)
> plot(as(geospiza,"phylo4"), show.node=T)
> shortestPath(geospiza, "N02","N05")
> MRCA(geospiza, "N02","N05")
> ##
>
> MRCA returns N01 (the root) instead of N02.
>
>
> Best,
>
> Thibaut.
>
> -- 
> ######################################
> Dr Thibaut JOMBART
> CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
> Universite Lyon 1
> 43 bd du 11 novembre 1918
> 69622 Villeurbanne Cedex
> Tél. : 04.72.43.29.35
> Fax : 04.72.43.13.88
> jombart at biomserv.univ-lyon1.fr
> http://biomserv.univ-lyon1.fr/%7Ejombart/
> http://adegenet.r-forge.r-project.org/
>
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________________________________
Brian O'Meara
NESCent
Durham, NC
http://www.brianomeara.info
________________________________