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/
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