diversitree: comparative phylogenetic analyses of diversification
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:
The interesting directories are:
- inst/tests: testing functions that exercise most of the
package's main features. Running
./run_tests.Rwill 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.
Clone the repository with
git clone git://github.com/richfitz/diversitree.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/fftw3.so 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.