[Phylobase-devl] [R-sig-phylo] phylobase::descendants issue

[François Michonneau]

Hi all,

  I just submitted to R-forge a patch to fix this issue. It came from a
recent change to ape. If you notice something weird or have any question,
let us know.

  Cheers,
  -- François


On Sat, Apr 27, 2013 at 5:10 PM, Ben Bolker <bbolker at gmail.com> wrote:

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>   Thanks for the heads-up.  I or one of the other phylobase developers
> will try to take a look ...
>
>   cheers
>     Ben Bolker
>
>
> On 13-04-26 06:50 PM, Nick Matzke wrote:
> > Hi all,
> >
> > Not sure if this is a bug, but I noticed weird behavior when
> > loading a tree with APE and then converting to phylo4 to do
> > descendants() -- not all the tips are produced.
> >
> > Example:
> >
> >
> > library(ape) library(phylobase)
> >
> > trstr =
> >
> "((((((((P_hawaiiensis_WaikamoiL1:0.9656850499,P_mauiensis_Eke:0.9656850499):0.7086257935,(P_fauriei2:1.230218511,P_hathewayi_1:1.230218511):0.4440923324):0.1767115552,(P_kaduana_PuuKukuiAS:1.851022399,P_mauiensis_PepeAS:1.851022399):0.0008897862802):0.3347375986,P_kaduana_HawaiiLoa:2.185759997):0.302349378,(P_greenwelliae07:1.131363255,P_greenwelliae907:1.131363255):1.35674612):1.689170274,((((P_mariniana_MauiNui:1.994011054,P_hawaiiensis_Makaopuhi:1.994011054):0.7328279804,P_mariniana_Oahu:2.726839034):0.2574151709,P_mariniana_Kokee2:2.984254205):0.4601084855,P_wawraeDL7428:3.444362691):0.732916959):0.7345185743,(P_grandiflora_Kal2:2.479300491,P_hobdyi_Kuia:2.479300491):2.432497733):0.2873119899,((P_hexandra_K1:2.363984189,P_hexandra_M:2.363984189):0.4630447802,P_hexandra_Oahu:2.826939991):2.372081244);"
> >
> >
> >
> > # Load tree tr = read.tree(file="", text=trstr) tr
> >
> > # Convert to phylo4 tr4 = as(tr, "phylo4")
> >
> > # Find root (node 20) rootnode = nodeId(tr4, type="root") rootnode
> >
> > # Only 3 tips! (there should be 19) tipnames = descendants(phy=tr4,
> > node=rootnode, type="tips") tipnames
> >
> >
> >
> >
> > The problem is here in descendants():
> >
> > if (phy at order == "preorder") { edge <- phy at edge } else { edge <-
> > reorder(phy, order = "preorder")@edge } ancestor <-
> > as.integer(edge[, 1]) descendant <- as.integer(edge[, 2]) isDes <-
> > .Call("descendants", node, ancestor, descendant)
> >
> > ...it works if I force phy at order to "cladewise" or "unknown"
> >
> >
> > library(ape) library(phylobase)
> >
> > trstr =
> >
> "((((((((P_hawaiiensis_WaikamoiL1:0.9656850499,P_mauiensis_Eke:0.9656850499):0.7086257935,(P_fauriei2:1.230218511,P_hathewayi_1:1.230218511):0.4440923324):0.1767115552,(P_kaduana_PuuKukuiAS:1.851022399,P_mauiensis_PepeAS:1.851022399):0.0008897862802):0.3347375986,P_kaduana_HawaiiLoa:2.185759997):0.302349378,(P_greenwelliae07:1.131363255,P_greenwelliae907:1.131363255):1.35674612):1.689170274,((((P_mariniana_MauiNui:1.994011054,P_hawaiiensis_Makaopuhi:1.994011054):0.7328279804,P_mariniana_Oahu:2.726839034):0.2574151709,P_mariniana_Kokee2:2.984254205):0.4601084855,P_wawraeDL7428:3.444362691):0.732916959):0.7345185743,(P_grandiflora_Kal2:2.479300491,P_hobdyi_Kuia:2.479300491):2.432497733):0.2873119899,((P_hexandra_K1:2.363984189,P_hexandra_M:2.363984189):0.4630447802,P_hexandra_Oahu:2.826939991):2.372081244);"
> >
> >
> >
> > # Load tree tr = read.tree(file="", text=trstr) tr
> >
> > # Convert to phylo4 tr4 = as(tr, "phylo4")
> >
> > # Looks like by default the tree is called "preorder" tr4 at order
> >
> > # It works if I do this: tr4 at order = "cladewise"
> >
> > # Find root (node 20) rootnode = nodeId(tr4, type="root") rootnode
> >
> > # Now this works tipnames = descendants(phy=tr4, node=rootnode,
> > type="tips") tipnames
> >
> >
> >
> >
> > # This also works:
> >
> > # Load tree tr = read.tree(file="", text=trstr) tr
> >
> > # Convert to phylo4 tr4 = as(tr, "phylo4")
> >
> > # Looks like by default the tree is called "preorder" tr4 at order
> >
> > # It works if I do this: tr4 at order = "unknown"
> >
> > # Find root (node 20) rootnode = nodeId(tr4, type="root") rootnode
> >
> > # Now this works tipnames = descendants(phy=tr4, node=rootnode,
> > type="tips") tipnames
> >
> >
> > ...so at least there's a workaround...
> >
> > Cheers, Nick
> >
> >
> >
> ph
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