Hello list,
Has anyone else experienced the following error when trying to load
phytools on a Mac, even though it seems to have been successfully
installed? Note that this problem doesn't seem to be with phytools
itself, but with rgl:
library(phytools)
Loading required package: ape
Loading
Hi Gabe,
It looks like rgl is trying to load the x11 libraries. Apple no longer
supports x11 with the release of Mountain Lion. Try installing xquartz (the
x11 replacement) and see if it works.
Jonathan
On Mon, Dec 22, 2014 at 1:33 AM, Gabriel Yedid gyedi...@gmail.com wrote:
Hello list,
Has
Hi Peter,
We have taken a similar approach in this paper:
http://onlinelibrary.wiley.com/doi/10./evo.12582/abstract
We also use a Bayesian approach, with a prior that allows us to
integrate the ancestral state and the total variance analytically (no
need for MCMC for those parameters). Our
Hi Gabriel,
the dependency for the rgl package comes from my phangorn package. You can
download the development version which does not need rgl installed the
following way:
library(devtools)
install_github(KlausVigo/phangorn)
It seems that apple is trying hard not to be a linux system any more
Hi again Peter,
If matrix inversion and determinants are a bottleneck, there are
multiple ways to avoid them (without assigning random effects to
ancestral species), including Felsenstein (1973), FitzJohn (2012) and
Freckleton (2012). The speed-up is huge if you have thousands of tips.
This
Cecile, Peter, Joe and all-
As far as I understand, Peter's analysis involves paleontological data with
non-ultrametric trees, and based on my understanding of Slater (2014), the
Freckleton approach using PIC is invalid for that type of dataset, although
Fitzjohn's pruning algorithm might still
