GeoSSE and ClaSSE

The Geographic State Speciation and Extinction model (Goldberg, Lancaster & Ree 2011) allows inference from a phylogeny of geographic range shifts and the effect of range on speciation and extinction rates. Its original description only allows coarse spatial structure, with space being divided into two regions. The Cladogenetic State change Speciation and Extinction model (Goldberg & Igic, in review) allows all combinations of character state changes within lineages (anagenetic change) and during speciation events (cladogenetic change). It thus generalizes GeoSSE to allow for more geographic range states, and it can also be applied to other, non-geographic characters.

Model Fitting

The GeoSSE and ClaSSE models are implemented in the R package diversitree, also available from CRAN (though not always the latest version). Source code, manual, and examples are all included.

Model Simulation

SimTreeSDD is a program for batch simulation of phylogenetic trees under two kinds of state-dependent diversification: binary character or three-state geographic character. It is fast and fairly well-documented.

For more states, simulation with cladogenetic change is available in the development version of diversitree.

PieTree

PieTree is a program for producing pictures of phylogenetic trees, particularly for the purpose of displaying ancestral state reconstructions of discrete characters.

Example output

Here are some examples of the images PieTree can produce. Output as EPS or PNG is also available.

You can tweak PieTree's output in many ways (see the manual below). For customized fine-tuning, you can edit SVG files in, for example, Inkscape or Illustrator, or you can use ImageMagick or pstoedit to produce other formats. Vector graphics look sharp and scale well, of course.

Manual/Instructions

Download

The manual includes installation instructions. PieTree is written in Python 2.5 using the Cairo graphics library, so those and pycairo are the dependencies.

Web Demo

I've also made an experimental web interface for trying PieTree without installing it. It is for an older version, though.

Acknowledgements

The first incarnation of PieTree was written by Walter Brisken. Here is his C code.

Boris Igic and Lesley Lancaster provided some beta-testing. I would be grateful for feedback from anyone else who gives it a try.


edgefx

edgefx is an R package for computing the ecological effects of habitat edges in landscapes. It extends a mathematical description of the "edge response" (how a species' population density or other property is affected by the distance to a change in habitat type) to an arbitrarily-complex landscape of edges. This enables parameter estimation from survey data and predictions to other landscapes. I wrote it for Leslie Ries and her award-winning project.

Download