François,
François Michonneau wrote on 12/02/2010 19:08:
Hi Dave,
Maybe this example will help you:
foo <- vector("list", 2) #create an empty list of 2 elements
class(foo) <- "multiPhylo" #make this list a multiPhylo object
foo[[1]] <- rtree(10) #put a random tree with 10 tips in the first slot of the
list
foo[[2]] <- rtree(10) #put another random tree in the second slot
foo[[3]] <- rtree(10) #here you add another tree to your mutlPhylo object
foo
3 phylogenetic trees
That's a solution indeed. You could even add several trees at once:
foo[4:5] <- list(rtree(10), rtree(10))
A problem may occur though because some "multiPhylo" objects have a
unique vector of tip labels for all the trees (eg, if read from a NEXUS
file with a translate block), so this kind of manipulation may lead to
problems.
The advantage of having a unique vector of tip labels is to save memory
and speed-up some computations (eg, in prop.part). But there's a problem
here that needs to be solved. There are solutions at the R level of
course, but they depend on what we want to have in practice. Any
feed-back will be welcome.
Best,
Emmanuel
PS: technical details may be found here:
http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf
Cheers,
-- François
On Fri, Feb 12, 2010 at 12:43, David Williams
<david.2.willi...@uconn.edu> wrote:
Hi
How can separate phylo objects be combined or added to an already existing
multiPhylo object? Using 'c()' loses attributes and various attempts with
as.list() failed as well. I resorted to writing to a tree file with
'append=T' then reading from that file into a multiPhylo object but
presumably there is a quicker way.
thanks
DaveW
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--
Emmanuel Paradis
IRD, Montpellier, France
ph: +33 (0)4 67 16 64 47
fax: +33 (0)4 67 16 64 40
http://ape.mpl.ird.fr/
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