Comparative 'Phylogenetic' Analyses of Diversification

Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.


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:

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.

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.

News

Reference manual

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install.packages("diversitree")

0.9-10 by Richard G. FitzJohn, 2 years ago


http://www.zoology.ubc.ca/prog/diversitree


Browse source code at https://github.com/cran/diversitree


Authors: Richard G. FitzJohn <[email protected]> , with 'GeoSSE' and 'ClaSSE' by Emma E. Goldberg <[email protected]> , and 'BiSSE-ness' by Karen Magnuson-Ford.


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


GPL (>= 2) license


Imports deSolve, graphics, grDevices, stats, subplex, Rcpp

Depends on methods, ape

Suggests numDeriv, minqa, lubridate, expm, caper, geiger

Linking to Rcpp

System requirements: fftw3 (>= 3.1.2), gsl (>= 1.15)


Imported by hisse.


See at CRAN