[R-sig-phylo] 99 Ways to ruin an open source project

Here is a cheeky post by Brandon Keepers on how to do things wrong when developing open source software. Lots of good stuff in there! JWB Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of

[R-sig-phylo] simulate tree by specifying taxa distance

Dear all, I want to simulate tree with restricted taxa distances (e.g. all taxa distance should be less than 0.1). Is there any R package can do this? Best wishes, Guangchuang -- --~--~-~--~~~---~--~~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging

[R-sig-phylo] phylogenetic signal test for discrete trait

Dear all, I would like to test for phylogenetic signal in a discrete trait with 3 states (trait “str”) and another discrete trait with 7 states (trait “hab") using Pagel’s lambda. I have tried to apply the function “fitDiscrete” in geiger to my data, but not sure whether this is correct or

Re: [R-sig-phylo] simulate tree by specifying taxa distance

Dear Guangchuang, Wouldn't that require that the distance between root and current time is, at most, 0.05 (= 0.1 /2) ? In that case, I believe you just need to rescale the tree you simulated. That can be done in a number of way according to which package you use, e.g., in phytool:

Re: [R-sig-phylo] simulate tree by specifying taxa distance

Dear Guilio, Thank you! I will try phytools. Best wishes, Guangchuang On Thu, Nov 3, 2016 at 11:57 PM, Giulio V. Dalla Riva wrote: > Dear Guangchuang, > > > Wouldn't that require that the distance between root and current time is, > at most, 0.05 (= 0.1 /2) ? > > In that