Carl,
was the other machine this was working on a Linux box? I just ran into
this exact problem two days ago, and it seems to have something to do
with the tolerance level in Linux, as it came up in a course and I was
surrounded by non-Linux computers that seemed to have no problem with
the
Hi Matt, all,
The other machine is also linux, but 64 bit. I've also tested it on a third
linux machine, which is running R-2.10 instead of R2.13, (but is 64 bit),
and it works fine there too. Only on my 32 bit linux have I observed the
error. I don't seem to have another 32 bit machine lying
Hi Carl Matt,
ape has drop.fossil() with a tol option set to 1e-8 by default. I wonder
whether it gives different outputs than geiger's function.
Best,
Emmanuel
-Original Message-
From: Carl Boettiger cboet...@gmail.com
Sender: r-sig-phylo-boun...@r-project.org
Date: Wed, 18 May 2011
drop.fossil drops all tips as well.
drop.fossil(p2)
Phylogenetic tree with 0 tips and 35 internal nodes.
drop.fossil(p2, tol=.01)
Phylogenetic tree with 0 tips and 35 internal nodes.
not sure why it still has internal nodes (note also that trying to plot the
result hangs).I've tried
Hi Tanja,list
Yes, everything is going extinct, but as you say, that shouldn't happen when
mu = 0.
sim.bd.age(age=2,numbsim=3,lambda=2,mu=0,frac,mrca=FALSE,complete=FALSE)
[[1]]
[1] 0
[[2]]
[1] 0
[[3]]
[1] 0
It's a rather malicious error in that, as you point out, it's a possible
outcome
As a general approach, when this sort of thing happens, I'll modify and load
a copy of the function that has been changed to produce a lot of debugging
info (lots of dput and print statements, for example). Then what happens at
each simulation step to identify where the problem occurs. [Better
Hi,
I have a question for phyml.
When I run phymltest under R, it returned in R as a vector with the
log-likelihood value of each model.
I am wondering if I can obtain rate(transition/transversion ratio)
matrix using R too ?
I know that I can have the *.txt_phyml_stats output file after I do
Hi Annemarie,
Positive log-likelihoods are not a problem. The log-likelihood is
calculated by summing the log probability densities, which come from a
function that integrates to 1.0. Thus, if the variance of this
distribution is small, the value of the function will be large (i.e.,
Hi list,
Thanks all for the help and suggestions, think I've fixed the issue!
Traced the behavior can to the locale used by R. You can replicate the
error by using Sys.setlocale(locale=en_US.UTF-8) and fix the issue using
Sys.setlocale(locale=C)
It's not clear why having certain locales as
