[Phylobase-devl] path between two tips

[Hilmar Lapp]

Isn't it easy enough for the caller to prepend (or append, depending  
on the order in which ancestors() returns nodes, assuming that it does  
return them ordered) the node to the array?

I.e., does having to do

	ALLancestors <- c(t1, ancestors(x, t1, which="all"))

really warrant an extra option to ancestors()?

I'm probably missing something obvious here, so feel free to set me  
straight if I'm off track.

	-hilmar

On Nov 20, 2008, at 5:35 PM, François Michonneau wrote:

> The modification of MRCA I committed a couple of month ago indeed  
> fixes
> the bug reported by Brian.
>
> However, what Thibault describes in the email below is another bug.
> Oddly enough, fixing it is easy if the other idea I suggested in my
> first email today is implemented. Indeed, if the function 'ancestors'
> also returns the node originally called, then MRCA returns the correct
> ancestors in the case described by Thibault.
>
> I am not sure how to call this option. I chose "ALL" but if someone  
> has
> a better idea, please let me know.
>
> Cheers,
>  - François
>
>
>
> On Thu, 2008-11-20 at 20:54 +0100, 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.
>>
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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