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:
./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.Clone the repository with
git clone git://github.com/richfitz/diversitree.gitThe 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.