Wednesday, June 15, 2011

New version of phytools package available, now with documentation files!!

I just posted a new "alpha" version of my phytools package to my R-phylogenetics page - now with documentation (i.e., "man") pages. In addition to still (hopefully) being able to install the package from source (either using my directions, here, or by following the helpful suggestions of my readers); Windows users can also now install the package binaries as follows. First, download; then type:

> install.packages("",repos=NULL)

Writing even the sparse documentation that I created for the present version of the package was a lot of work (Paradis' extensive documentation for {ape} now seems even more impressive), so I look forward to getting feedback.


  1. Works well for me from the package binaries!

    By the way, do you think you could add a 'phytools' man page? I find these summary pages helpful, if for nothing but when I can't remember anything about the function name, I can at least bring up the package's index from its summary page.

    Also, as a suggestion, you might want to specify in the man what the null hypotheses are in the significance tests for phylosig(). Took me a little while to figure whether they were trying to reject the hypothesis that there was no-signal or that there was signal.

    Anyway, looking great!

  2. Hi,

    This is great! Thanks very much!

    I noticed the documentation for phylosig() when called using help(phylosig) has the 'Description' for phyl.resid().

  3. Dave - Great suggestions.

    Raptor's Nest - Oops, so it does! Thanks for catching that.

    - Liam

  4. @Dave - also you can always get the package description and a list of functions using:

    > library(help=phytools)

  5. Thanks for giving the package a try, guys. Hope to see some of you at 'Evolution' in a couple of days.


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