A model to study speciation patterns in complex landscapes.
C++
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README.md

Wagner

A theoretical model to study macroevolution and phylogeographies.

Named after Moritz Wagner (1813-1887), who made important contributions to our understanding of speciation.

The program is written in ANSI C++11. Tested on Linux 64-bit with clang++ 3.0 and g++ 4.7.0.

reference

Working paper: http://arxiv.org/abs/1203.1790

usage and options

Compile with make (requires a modern ANSI C++11 compiler) and execute with

$ ./wagner

You can change the model with:

-model

The current version supports four models:

0   Neutral model
1   Model with aleph (see arXiv paper) [default]
2   Model with logistic speciation (decreases with the total number of species).
3   Model with both aleph and logistic speciation.    

You can also use the following options [default values]:

-seed       Seed for the random number generator [6].
-c          Number of communities (or vertices, or nodes, or patches) [64].
-t          Number of time steps. Needs to be a power of two [512].
-e          Per population extinction rate [0.05].
-m          Max migration rate [0.04].
-a          Aleph for models 1 and 3 [10.0].
-s          Speciation rate (or max speciation rate for logistic models) [0.04].
-se         With logistic speciation and n species, the speciation rate is 2s/(1 + se^n) [1.02].
-r          Radius of the random geometric network [0.2].

Options not followed by an argument

-shuffle    After t/2 time steps, shuffle all populations [false].

For example:

$ ./ẃagner -model 1 -a 50 -seed 88

Will run the model 1 with aleph = 50, and seed = 88. The order of the options doesn't matter and all parameters should be printed in the xml output file. If the number of time steps supplied is not a power of two, the problem will find the largest power of two that fits in this number.

language

ANSI C++11.

I use many features from the C++11 standard so it requires a modern compiler.

license

MIT http://opensource.org/licenses/MIT

author

Philippe Desjardins-Proulx philippe.d.proulx@gmail.com