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:

> 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://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.

Unresolved clades

As of version 0.10.0, diversitree can no longer work with unresolved clades (FitzJohn, Maddison and Otto 2009's method), due to the package being long in retirement from development and difficulties adapting the Fortran code to meet CRAN's requirements. Users can install an older package from github (e.g., with remotes::install_github("mrc-ide/diversitree@e587755") to install the last released version that contained this code). This will require a working Fortran compiler. Alternatively, a suitably motivated person could restore the code (reverting changes contained in aaaa) and patch the code to work with the current version of flang as used by CRAN.

Branches

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