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C++ code for stochastic spacial neutral/hierarchical models
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R
nbproject
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CITATION
IpsNeutral.cpp
IpsNeutral.h
IpsNeutralAux.cpp
IpsNeutralCont.cpp
IpsNeutralStats.cpp
IpsNeutralZero.cpp
MainIPS.cpp
ModelDescription.md
README.md
bgi.cpp
bgi.hpp
cabase.cpp
cabase.hpp
makefile
makefileCont.mak
makefileWin.mak
pomac.lin
q.sed
ran.h
smattpl.hpp
t64Exp.inp
t64Exp.par
t64ExpDensity.txt
t64ExpmfOrd.txt
test.inp
test.par
test.set

README.md

Multiespecific neutral/hierachical stochastic spatial model

This is C++ code for neutral/hierarchical competition models. In these all species have the same parameters except the probability of colonization from metacommunity. More details are given in the file ModelDescription.md

There are actually 5 similar models built in

  1. Non-saturated neutral (Etienne 2007)
  2. Saturated Neutral
  3. Non-saturated Hierarchical (Tilman 1994)
  4. Saturated Hierarchical
  5. Continuum model between 2 and 4 (or 1 and 3)

And three dispersal kernels

  1. Uniform
  2. Exponential
  3. Inverse power

It was compiled using Gnu C++ (g++ v4.8.5). For a crude and slow graphical output you will need the X11 SDL development libraries and the GRX graphics library http://grx.gnu.de/grx246um.htm

You also need the code from:

  1. https://github.com/lsaravia/mfsba if you want the multifractal spectra output otherwise you have to comment the calls to the function MultifractalSBA and the includes to mf.h header.
  2. https://github.com/lsaravia/Clusters to calculate cluster statistics.

To compile under Windows there is a separate makefileWin.mak, you might have to modify the folders of the mfsba and Clusters sources.

The folder R has functions to interface R with the model

Citation

If you use the model please cite:

  1. Saravia, L.A. (2015). A new method to analyse species abundances in space using generalized dimensions. Methods Ecol. Evol., 6, 1298–1310

  2. Saravia L.A. (2014) Neutral: A sofwtware to simulate spatially explicit neutral/hierarchical models. http://dx.doi.org/10.6084/m9.figshare.969692.

Bibliography

Tilman, D., 1994. Competition and biodiversity in spatially structured habitats. Ecology, 75(1), pp.2-16.

Etienne, R.S., Alonso, D. & McKane, A.J., 2007. The zero-sum assumption in neutral biodiversity theory. Journal of Theoretical Biology, 248(3), pp.522-536.

License

Copyright 2011 Leonardo A. Saravia

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
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