Code release for Schneider et al. “Animal diversity and ecosystem functioning in dynamic food webs”

This repository contains simulation code and code for statistical analysis of a research project. It applies allometric models of animal foraging and network structure to simulate the ecosystem-level stocks and rates of animal and plant biomass in relation to the number of animal species present in the ecosystem.

Code in this repository.

1. code/pdef_dynamics_2.4.c & code/pdef_dynamics_1.1.h: Original simulation code. This was compiled and run in multiple instances for simulations over the entire gradient of 10 to 100 animal species with a single file output file for each instance found in data/pdef_2.4/. Additional instances were run for sensitivity analyses and are found in the same location.
2. code/data.r : Data collect and compilation. The file reads in all output files, corrects some columns, calculates additional columns and saves everything into a single output file data/webstats.txt. Seperate files are created for the sensititvity analyses. Column names correspond do parameters as used in simulation code and slightly differ from nomenclature in the article.
3. code/analyse.r : contains function analyse() which fits the statistical models describing the relationships between animal diversity and ecosystem function. Call using analyse(webstats$S_c_fin, webstats$meanB_c, equation = TRUE, ylab = "")
4. code/sensitivity.r : contains function sensitivity() for calling the sensitivity analysis for any parameter x, as well as function sensitivity_plus() for visualising the simulations of the alternative model runs.
5. code/analysis.r : applies function analyse() to return the result figure 4 and 5 of the paper and an overview output table. applies functions in sensitivity.r to return sensitivity analysis of Supplementary Material.

Comments welcome

We encourage testing or reviewing this simulation code. Any comments, bug reports or mistakes should be reported in the Github issues.

License

Code for the article 'Animal diversity and ecosystem functioning in dynamic food webs'

Copyright (C) 2016 Christian Guill & Florian D. Schneider

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/>.