Hi Simon and others,
I ran into the same problems a few days ago and I suspect it's
related to changes associated with R 3.4.0. Re-installing ape solved
the issue for me.
Cheers,
-- François
On Wed, Apr 26, 2017 at 11:01 PM, Simon Blomberg wrote:
> False alarm. I cleared my workspace and
False alarm. I cleared my workspace and re-started R and the problem has
gone away. I'm curious to know how it occurred but I'm happy that it has
been resolved. We now return you to your scheduled R programming...
Cheers,
Simon.
On 27/04/17 12:44, Simon Blomberg wrote:
Hi Emmanuel and other
Hi Emannuel (and list),
Just wanted to let you know that after some testing with my own cases,
the new drop.tip appears to fix the error, so the issue is closed from
my perspective.
Cheers,
-Dave
On Tue, Jul 28, 2015 at 12:25 PM, Emmanuel Paradis
wrote:
> Hi David,
>
> I've conducted more tests
Hi David,
I've conducted more tests and the bug was really in drop.tip and
sometimes apparent without calling ladderize. The fix seems to work
well. I have built ape 3.3-0.6 which is available on ape-package.ird.fr
as source package.
Best,
Emmanuel
Le 25/07/2015 19:33, Emmanuel Paradis a é
David,
I was thinking about some simple tests to check that the function still
works correctly in other situations. It can happen that when fixing a
bug which occurs in a special situation in a piece of code, the code
then fails in other (possibly simpler) situations. In the present case,
the
Hi Emmanuel,
Thank you for the fix! And, yes, I realize, its probably one of ape's
most widely used functions. Perhaps what we need is a function that
tests whether there is a mismatch in the node.labels, across trees
that might have different sets of taxa, which will help in the future
to alert u
Hi David,
Here is a fix for drop.tip (line numbers refer to the source file
drop.tip.R):
229,231c229,230
< ## executed from right to left, so newNb is modified before phy$edge:
< phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]] <-
< (n + 2):(n + phy$Nnode)
---
> newNb[sort
