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

[Sang Chul Choi]

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
>>>
>>>
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>>
>