Klaus-
Oh, that worked rather splendid! Thanks for letting me know.
> system.time(desc<-Descendants(res_tree,edge_end))
user system elapsed
1.56 0.00 1.56
-Dave
On Sun, Mar 6, 2011 at 3:22 PM, Klaus Schliep <klaus.schl...@gmail.com> wrote:
> Hi David,
>
> you can supply Descendents (from phangorn) with a vector instead of
> using sapply. I should have mentioned this in the help file.
> If your vector (edge_end) is long enough (I don't have a exact number
> here) this can be much faster than using sapply as some results are
> reused.
> Here are some timings:
>
>> set.seed(123)
>> res_tree = rtree(1700)
>> edge_end = unique(res_tree$edge[,1])
>> system.time(desc1<-sapply(edge_end,function(x) Descendants(res_tree,x)))
> user system elapsed
> 54.51 0.00 54.87
>> system.time(desc2<-Descendants(res_tree,edge_end))
> user system elapsed
> 0.75 0.00 0.75
>> system.time(desc3<-sapply(edge_end,function(x) node.tips(res_tree,x)))
> user system elapsed
> 4.07 0.00 4.07
>
>
> Cheers,
> Klaus
>
>
>
> On 3/6/11, David Bapst <dwba...@uchicago.edu> wrote:
>> Hello all,
>> I'm currently trying to measure a parameter over a large number of
>> large trees (>1700 tips), and part of this calculation requires
>> knowing the tip taxa descended from each node (I must compare the
>> difference in tip values among taxa descended from a node). Because I
>> must do this many times, I decided to compare the efficiency of
>> several methods for doing this in various R libraries with
>> system.time() (as Liam did recently with some BM simulation functions
>> in some recent blog posts). As I feel that others may benefit from
>> this comparison of methods, I am posting the results to this list.
>>
>> Geiger's node.leaves() is much faster than the alternatives, although
>> at ~13s a run, it is still not a particularly speedy process. I didn't
>> need the actual tip.labels, so I took node.leaves() and made it as
>> lean as possible, to produce node.tips(), below. That cut the run time
>> down to ~9 sec.
>>
>> node.tips<-function (phy, node){
>> n <- length(phy$tip.label)
>> if (node <= n){node}else{
>> l<- numeric()
>> d<- phy$edge[which(phy$edge[,1]==node),2]
>> for(j in d){if(j <= n){l <- c(l, j)}else{l<-c(l,
>> node.tips(phy,j))}}
>> l}}
>>
>> If anyone knows of another alternative that might be faster, I would
>> greatly appreciate any suggestions.
>> -Dave Bapst, UChicago Geosci
>>
>> Using the modified node.leaves() function from geiger, node.tips()
>>
>>> system.time(desc<-sapply(edge_end,function(x) node.tips(res_tree,x)))
>> user system elapsed
>> 9.39 0.00 9.44
>>
>> Using node.leaves() in geiger
>>
>>> system.time(desc<-sapply(edge_end,function(x) node.leaves(res_tree,x)))
>> user system elapsed
>> 13.29 0.02 13.34
>>
>> Using Descendants() in phangorn
>>
>>> system.time(desc<-sapply(edge_end,function(x) Descendants(res_tree,x)))
>> user system elapsed
>> 75.60 0.10 76.83
>>
>> Using listTips() in adephylo
>>
>>> system.time(desc_list<-c(as.list(1:Ntip(res_tree)),listTips(res_tree)))
>> user system elapsed
>> 75.27 2.93 87.28
>>
>> Using descendants() in phylobase
>>
>>> system.time(desc<-sapply(edge_end,function(x)
>>> descendants(res_tree4,x,type="tips")))
>> user system elapsed
>> 149.56 0.67 155.15
>>
>> Using nodeDecendants() in maticce (note that translating the tree
>> into ouchtree format was prohibitively very lengthy)
>>
>>> system.time(res_tree_ou<-ape2ouch(res_tree))
>> user system elapsed
>> 84.01 0.13 85.34
>>> system.time(desc<-sapply(edge_end,function(x)
>>> nodeDescendents(res_tree_ou,x)))
>> user system elapsed
>> 65.91 0.23 68.47
>>
>> --
>> David Bapst
>> Dept of Geophysical Sciences
>> University of Chicago
>> 5734 S. Ellis
>> Chicago, IL 60637
>> http://home.uchicago.edu/~dwbapst/
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>
>
>
> --
> Klaus Schliep
> Université Paris 6 (Pierre et Marie Curie)
> 9, Quai Saint-Bernard, 75005 Paris
>
--
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
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