[Phylobase-devl] phylo4: tabulate() requires nbins argument
Aaron Mackey
ajmackey at gmail.com
Wed May 21 17:41:58 CEST 2008
err, wait, sorry. it's not nrows() we want, but max(edge) ...
-Aaron
On Wed, May 21, 2008 at 11:35 AM, Ben Bolker <bolker at zoology.ufl.edu> wrote:
>
>
>
> Aaron Mackey wrote:
>
>> I don't have functional SVN access at the moment, otherwise I'd do this
>> myself. But essentially, calls to "tabulate()" need to define the number
>> of
>> bins explicitly, otherwise problems occur. For example:
>>
>> edge
>>>
>> [1,] 1 3
>> [2,] 1 2
>> [3,] 3 4
>> [4,] 3 7
>> [5,] 4 5
>> [6,] 4 6
>> [7,] 7 8
>> [8,] 7 9
>>
>>> tabulate(edge[,1])
>>>
>> [1] 2 0 2 2 0 0 2
>>
>>> tabulate(edge[,1], nbins=dim(edge)[1])
>>>
>> [1] 2 0 2 2 0 0 2 0
>>
>> -Aaron
>>
>>
> I grepped for "tabulate". Are you recommending that
> we change all of these usages as above?
> (Is it worth defining a "tabedge" function
>
> tabedge <- function(object,i) {
> tabulate(edges(object[,i]), nbins=nrow(edges(object)))
> }
>
> to replace most of these, or is that just too complicated?
>
> Ben
>
>
> 1 checkdata.R: nAncest <- tabulate(edges(object)[, 2])
> 2 class-phylo4.R: ntips <- sum(tabulate(edge[, 1]) == 0)
> 3 class-phylo4.R: nnodes <- sum(tabulate(edge[, 1]) > 0)
> 4 methods-phylo4.R: tabulate(edges(x)[, 1])[nTips(x) + 1] <= 2
> 5 methods-phylo4.R: temp <- tabulate(E[,1])
> 6 treestruc.R: degree <- tabulate(edges(object)[, 1])
> 7 treestruc.R: degree <- tabulate(edges(object)[, 1])
> 8 treestruc.R:# isTips <- (tabulate(x at edge[,1]) == 0)
> 9 treestruc.R:# res <- (tabulate(x at edge[,1]) > 2)
>
>
>
>
>
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