R scripts for Ushio et al. "Fluctuating interaction network and time-varying stability of a natural fish community"
This R code is released under the MIT License, see LICENSE.txt.
Following packages are required: rEDM version 0.2.4 (included as a zip file in the inst/ folder), tseriesChaos, deSolve, GGally, intergraph, network, igraph, ggplot2, gridExtra, devtools, pforeach, sna
The original results were generated using rEDM v0.2.4 and R3.2.1 on Mac OSX.
All packages except for pforeach can be installed from CRAN.
To install pforeach from github:
devtools::install_github("hoxo-m/pforeach")
To install rEDM from the inst/ folder:
install.packages("inst/rEDM.zip", type = "source", repos = "NULL")
or decompress rEDM.zip and copy it to your R library folder.
The main script file is RunAllScripts.R. Sourcing this file will run the analyses and produce the figures for the paper.
The results are published in Ushio M, Hsieh CH, Masuda R, Deyle RE, Ye H, Chang CW, Sugihara G, Kondoh M (2018) "Fluctuating interaction entwork and time-varying stability of a natural fish community" Nature 554 (7692): 360–363 doi:101038/nature25504