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diversitree: comparative phylogenetic analyses of diversification

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Octocat-spinner-32 R
Octocat-spinner-32 doc
Octocat-spinner-32 inst
Octocat-spinner-32 man
Octocat-spinner-32 pub
Octocat-spinner-32 src
Octocat-spinner-32 www
Octocat-spinner-32 .Rbuildignore
Octocat-spinner-32 .gitignore
Octocat-spinner-32 .travis.yml
Octocat-spinner-32 ChangeLog
Octocat-spinner-32 DESCRIPTION
Octocat-spinner-32 Makefile
Octocat-spinner-32 NAMESPACE
Octocat-spinner-32 TODO
Octocat-spinner-32 cleanup
Octocat-spinner-32 configure
Octocat-spinner-32 run_tests.R

diversitree: comparative phylogenetic analyses of diversification

Build Status

This repository contains "diversitree". It is my experimental sources though, and may not compile or work for you. You may prefer the released version from CRAN:

> install.packages("diversitree")

The interesting directories are:

  • inst/tests: testing functions that exercise most of the package's main features. Running ./run_tests.R will run the tests. These take too long to run on CRAN (over a minute), so are not set up in the usual way.
  • doc: Vignettes, and their required data files.

Installing diversitree

Clone the repository with

git clone git://

The package should then be installable the usual way. You'll need a C, C++ and Fortran compiler.

To install and specify the location of the fftw library in a non-standard place, a line like this is required: R CMD INSTALL diversitree --configure-args='--with-fftw=/path/to/fftw' where the path will be the path so that the files /path/to/fftw/include/fftw3.h /path/to/fftw/lib/lib/ exist.

On Windows, set the environment variable LIB_FFTW to point to the directory that contains include/fftw.h, and install the package.

If fftw is not found, installation will continue, but the (relatively) fast C based QuaSSE integration will not be available. The R based fft integrator and the method-of-lines integrator will be available.


The "master" branch contains the bleeding edge version of diversitree. It may or may not work for you. The "release" branch contains stable releases.

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