[Phylobase-devl] Root node number should be one plus number of tips?

[Ben Bolker]

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Ben Bolker wrote:
|   Sang Chul,
|
|   sorry no-one has responded yet -- I hope to look into all this
| stuff tomorrow ... (but if any other developers want to poke
| around in the meantime, feel free!)
|
|   cheers
|     Ben
|
|
| Sang Chul Choi wrote:
|> Hi,
|>
|> getAncest and getDescend seem to work under "any" circumstances (from
|> my perspective). Since nodeRoot does not work I may use getDescend
|> function to find root node.
|>
|> Thank you,
|>
|> Sang Chul
|>
|> On Apr 12, 2008, at 5:17 PM, Sang Chul Choi wrote:
|>> Hi,
|>>
|>> Continued from the previous message, getLabelByNode() function behaves
|>> not quite right. I think that trees seem to be handled assuming
|>> somthing in phylobase package not exactly based on user's input of
|>> tree structure matrix. In the example of tree1, node 1 is labelled
|>> "T5" but it prints "T1," and node 8 is labelled "N2", but it prints
|>> "N3." Root node 9 is is labelled "N1," and it prints error message.
|>>
|>> Thank you,
|>>
|>> Sang Chul
|>>
|>>
|>>   m <- rbind(c(6,8),c(8,7),c(9,6),c(6,5),c(8,4),c(9,3),c(7,2),c(7,1))
|>>   m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
|>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
|>>   tree1 <- phylo4(edge=m, edge.length=m.l)
|>>   rootNode(tree1)
|>>   print(tree1)
|>>   getLabelByNode(tree1, 1)
|>>   getLabelByNode(tree1, 8)
|>>   getLabelByNode(tree1, 9)
|>>
|>> On Apr 12, 2008, at 4:37 PM, Sang Chul Choi wrote:
|>>> Hi,
|>>>
|>>> In my previous message, the first tree's root is 9 but, using
|>>> rootNode() function it returns 6, so it may returns one plus number  of
|>>> tips.
|>>>
|>>> Thank you,
|>>>
|>>> Sang Chul
|>>>
|>>>  m <- rbind(c(6,8),c(8,7),c(9,6),c(6,5),c(8,4),c(9,3),c(7,2),c(7,1))
|>>>  m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
|>>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
|>>>  tree1 <- phylo4(edge=m, edge.length=m.l)
|>>>  rootNode(tree1)
|>>>
|>>> On Apr 11, 2008, at 12:56 PM, Sang Chul Choi wrote:
|>>>> Hi,
|>>>>
|>>>> I made trees using phylo4 object with time. I tested if it is
|>>>> ultrametric using is.ultrametric, and I also write it to a tree  file.
|>>>> It seems that the if root node number is not one plus number of  tips,
|>>>> then ultrametric and write.tree does not seem to work. Maybe there  is
|>>>> help document how to create a tree in APE or phylobase package,  but I
|>>>> could not see any requirement except that matrix first column is for
|>>>> ancestors, and second column is for descendants.
|>>>>
|>>>> Is there any further requirement for making trees other than this
|>>>> (that matrix first column is for ancestors, and second column is for
|>>>> descendants)?
|>>>>
|>>>> I am trying to update trees or subtree pruning and regrafting kind  of
|>>>> work. I take edge information using edges() function and change it.
|>>>> Using the changed edge matrix table, I recreate phylo4 object. This
|>>>> would change root node numbers and changed trees are behave
|>>>> "awkwardly" (I guess only) to me. By the way, I found a "nice"
|>>>> function in APE, "reorder", which does somehow help me to change  tree
|>>>> internal information so that tree can properly manipulated by APE
|>>>> function. Is there a function in phylobase that change tree internal
|>>>> structure so that tree internal information is corrected?
|>>>>
|>>>> I do not think that this is a bug, but it is something that is not
|>>>> that I expected.
|>>>>
|>>>> Thank you,
|>>>>
|>>>> Sang Chul
|>>>>
|>>>> Just if anybody is interested in (I guess not) what I am doing?
|>>>> CODE start:
|>>>> All trees are 5 tips binary ultrametric tree.
|>>>> tree1: root number is 9 -> tree file has a tree with 4 tips, not
|>>>> ultrametric
|>>>> tree2: root number is 6 (6 and 9 are reversed from tree1) -> tree
|>>>> file has the right tree
|>>>> tree3: root number is 6, and change two internal node numbers (8 <-
|>>>>> 9) -> tree file has the right tree.
|>>>> m <- rbind(c(6,8),c(8,7),c(9,6),c(6,5),c(8,4),c(9,3),c(7,2),c(7,1))
|>>>> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
|>>>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
|>>>> tree1 <- phylo4(edge=m, edge.length=m.l)
|>>>> tree1 <- reorder(as(tree1, "phylo"))
|>>>> print(tree1)
|>>>> print(paste("Is tree1 ultametric?", is.ultrametric(tree1)))
|>>>> print("Coal. Intervals")
|>>>> print(coalescent.intervals(tree1)$interval.length)
|>>>> write.tree(tree1, "1.tre")
|>>>>
|>>>> m <- rbind(c(9,8),c(8,7),c(6,9),c(9,5),c(8,4),c(6,3),c(7,2),c(7,1))
|>>>> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
|>>>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
|>>>> tree2 <- phylo4(edge=m, edge.length=m.l)
|>>>> tree2 <- reorder(as(tree2, "phylo"))
|>>>> print(tree2)
|>>>> print(paste("Is tree2 ultametric?", is.ultrametric(tree2)))
|>>>> print("Coal. Intervals")
|>>>> print(coalescent.intervals(tree2)$interval.length)
|>>>> write.tree(tree2, "2.tre")
|>>>>
|>>>> m <- rbind(c(8,9),c(9,7),c(6,8),c(8,5),c(9,4),c(6,3),c(7,2),c(7,1))
|>>>> m.l <- c(0.13979526, 0.04856891, 1.51140412, 0.46082282,
|>>>> 0.32102756, 1.97222694, 0.27245865, 0.27245865)
|>>>> tree3 <- phylo4(edge=m, edge.length=m.l)
|>>>> tree3 <- reorder(as(tree3, "phylo"))
|>>>> print(tree3)
|>>>> print(paste("Is tree3 ultametric?", is.ultrametric(tree3)))
|>>>> print("Coal. Intervals")
|>>>> print(coalescent.intervals(tree3)$interval.length)
|>>>> write.tree(tree3, "3.tre")
|>>>>
|>>>> hylogenetic tree with 5 tips and 4 internal nodes.
|>>>>
|>>>> Tip labels:
|>>>> [1] "T1" "T2" "T3" "T4" "T5"
|>>>>      Node labels:
|>>>> [1] "N1" "N2" "N3" "N4"
|>>>>
|>>>> Rooted; includes branch lengths.
|>>>> [1] "Is tree1 ultametric? FALSE"
|>>>> [1] "Coal. Intervals"
|>>>> [1] 0.46082282 1.32303995 0.04856891 0.13979526
|>>>>
|>>>> Phylogenetic tree with 5 tips and 4 internal nodes.
|>>>>
|>>>> Tip labels:
|>>>> [1] "T1" "T2" "T3" "T4" "T5"
|>>>>      Node labels:
|>>>> [1] "N1" "N2" "N3" "N4"
|>>>>
|>>>> Rooted; includes branch lengths.
|>>>> [1] "Is tree2 ultametric? TRUE"
|>>>> [1] "Coal. Intervals"
|>>>> [1] 0.27245865 0.04856891 0.13979526 1.51140412
|>>>>
|>>>> Phylogenetic tree with 5 tips and 4 internal nodes.
|>>>>
|>>>> Tip labels:
|>>>> [1] "T1" "T2" "T3" "T4" "T5"
|>>>>      Node labels:
|>>>> [1] "N1" "N2" "N3" "N4"
|>>>>
|>>>> Rooted; includes branch lengths.
|>>>> [1] "Is tree3 ultametric? TRUE"
|>>>> [1] "Coal. Intervals"
|>>>> [1] 0.27245865 0.04856891 0.13979526 1.51140412
|>>>>
|>>>>
|>>>> _______________________________________________
|>>>> Phylobase-devl mailing list
|>>>> Phylobase-devl at lists.r-forge.r-project.org
|>>>>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
|>>>>
|>
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