fpom / mee-18-07-465

Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem: implementation and models

Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem: implementation and models

Authors: Cédric Gaucherel, Franck Pommereau

Journal: Methods in Ecology and Evolution

Content

• file termites-ca.rr holds the termites model discussed throughout the paper
• file termites-ac.pnml is the corresponding Petri net in PNML format (see http://www.pnml.org/)
• the Python implementation of the analysis method is in files *.py and ktz.pyx
• directory ktzlib contains C files to read Tina KTZ format (courtesy of Bernard Berthomieu)
• Makefile allows to build the software and produce the figures for the paper

Dependencies

• Python 2.7: https://www.python.org/
• Cython: https://cython.org/
• matplotlib: https://matplotlib.org/
• pydot: https://github.com/pydot/pydot
• NetworkX: https://networkx.github.io/
• SNAKES: http://snakes.ibisc.univ-evry.fr/
• pandas: https://pandas.pydata.org/
• Tina: http://projects.laas.fr/tina/

Installation

No installation is required (and no setup.py is provided), just run make ktz.so to build the Cython module ktz that is needed.

Usage

Run python econet.py to get help about the available commands. Then run python econet.py MODEL.rr COMMAND... to execute commands as instructed in the help.

Run make figs to build the figures used in the paper. Looking into file Makefile may help to see how commands are used.

Licence

File termites.rr is released under the terms of Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)

The source code is released under the GNU General Public Licence version 3

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 <https://www.gnu.org/licenses/>.