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
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