Maybe
methods(class=class(myobjetc))
for example:
library(ape)
data(bird.families)
class(bird.families)
[1] phylo
methods(class=class(bird.families))
[1] +.phyloall.equal.phylo
[3] as.hclust.phyloas.matching.phylo
[5] c.phylo
Emmanuel, all-
That's pretty fast, even on my cheap laptop!
system.time(desc1-c(as.list(1:Ntip(res_tree)),prop.part(res_tree)))
user system elapsed
0.650.000.66
As far as why I didn't try prop.part, to be honest, I had no idea that
prop.part() did that. The help file says:
Hi All,
On the issue of visibility of functions in R, I definitely find it a
struggle to 'discover' things that I could do with a particular object.
Python has this worked out in a really nice way - if I have an object I can
simply put a full-stop after it and hit tab, and I get a list of all
Hi Rob,
this is partly also possible in R. You can find all generic functions
specificly written for an (S3) object using:
methods(class=phylo)
This will miss functions, which are not generic and generic function
which use the default mechanism, e.g. class pml has a specific
logLik.pml method,
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
Hi Dave.
It seems like one way to get these values faster would be to count the
number of descendants as the tree is read in to R. This is possible
because when the ) character is reached by the Newick parser, all
descendant nodes (and tips) have already been created in memory.
This was
Klaus-
Oh, that worked rather splendid! Thanks for letting me know.
system.time(desc-Descendants(res_tree,edge_end))
user system elapsed
1.560.001.56
-Dave
On Sun, Mar 6, 2011 at 3:22 PM, Klaus Schliep klaus.schl...@gmail.com wrote:
Hi David,
you can supply Descendents (from
Hi David and others,
prop.part() with a single tree does what you want:
set.seed(123)
res_tree - rtree(1700)
system.time(desc2 - prop.part(res_tree))
user system elapsed
0.050 0.000 0.053
edge_end - unique(res_tree$edge[,1])
system.time(desc1 - Descendants(res_tree,edge_end))
