by Florian D. Schneider & Christian Guill
Published: 01 December 2015
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.
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.
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.
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 = "")
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.
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.
We encourage testing or reviewing this simulation code. Any comments, bug reports or mistakes should be reported in the Github issues.
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/>.
- Brose, U., Blanchard, J. L., Eklöf, A., Galiana, N., Hartvig, M., R. Hirt, M., Kalinkat, G., Nordström, M. C., O'Gorman, E. J., Rall, B. C., Schneider, F. D., Thébault, E. and Jacob, U. (2016), Predicting the consequences of species loss using size-structured biodiversity approaches, Biological Reviews, 92 2:684-697 doi: 10.1111/brv.12250
- Kalinkat, G., Schneider, F.D., Digel, C., Guill, C., Rall, B. C., Brose, U. (2013), Body masses, functional responses and predator–prey stability, Ecology Letters, 16 :1126–-1134 doi: 10.1111/ele.12147
- Schneider, F.D., Scheu, S. & Brose, U. (2012), Body mass constraints on feeding rates determine the consequences of predator loss, Ecology Letters, 15 :436–443 doi: 10.1111/j.1461-0248.2012.01750.x
- Schneider, F.D., Brose, U. (2013), Beyond diversity: how nested predator effects control ecosystem functions, Journal of Animal Ecology, 82 :64–71 doi: 10.1111/1365-2656.12010 (pdf)
- Schneider, F.D., Scheu, S. & Brose, U. (2014), Corrigendum to Schneider, Scheu & Brose (2012) DOI: 10.1111/j.1461-0248.2012.01750.x, Ecology Letters, 17 10:1339–1340 doi: 10.1111/ele.12333 (pdf)
- Schneider, F. D., Brose, U., Rall, B. C., Guill, C. (2016), Animal diversity and ecosystem functioning in dynamic food webs, Nature Communications, 7 :12718 doi: 10.1038/ncomms12718 (pdf)