Hi David Brian,
Yes, I'll put this function in the next release.
Cheers,
Emmanuel
Le 15/06/2015 18:27, David Bapst a écrit :
Whoops, I meant a 'function in ape?'
-Dave
On Mon, Jun 15, 2015 at 10:26 AM, David Bapst dwba...@gmail.com wrote:
Hi Brian,
I was already aware of the
A kludgy solution to achieve Dave's original use case of fixing
not-quite-right phylo objects is to do:
phy - read.tree(text=write.tree(phy))
It converts the tree to Newick and reads it back in.
It's not as good a solution as using a validator (great addition, Emanuel!)
to find and fix the
Hi Brian,
I was already aware of the read.tree(write.tree()) fix, however I've
run into (corner?) cases where a particular sorting of edges or
whatever can lead to a loss of tip taxa using the
read.tree(write.tree()) approach; plus, read.tree(write.tree()) gets
completely flabbergasted by
Whoops, I meant a 'function in ape?'
-Dave
On Mon, Jun 15, 2015 at 10:26 AM, David Bapst dwba...@gmail.com wrote:
Hi Brian,
I was already aware of the read.tree(write.tree()) fix, however I've
run into (corner?) cases where a particular sorting of edges or
whatever can lead to a loss of tip
Hi David.
I'm not sure about this, but changing to:
tree-read.newick(text=write.tree(tree))
tree-collapse.singles(tree)
may work. I believe that write.tree will write trees with singletons
read.newick in phytools should be able to read them.
All the best, Liam
Liam J. Revell, Assistant
Hi David,
I found the bug. Somehow ape assumes on the one hand that the root is
number of tips + 1.
On the other hand the root of an phylo object is the node which is in
tree$edge[,1], but not in tree$edge[,2],
this is the case even in an unrooted tree. This annoys me for a long time.
The root
Hi Klaus (and others),
Ah, I see! The real bug then appears to be in collapse.singles, as it
does not reorder the ID numbers in $edge. Here's a quick function to
return the root ID:
getRootID-function(tree){
uniqueNode-unique(tree$edge[,1])
whichRoot-sapply(uniqueNode,function(x)
Hello all,
As those of you who directly manipulate the guts of phylo objects in
your code (or construct new phylo objects whole cloth from
un-phylo-like data structures) have probably experienced, it is
sometimes easy to create $edge matrices that aren't accepted by ape
functions (I often use
