squareone

Analyses supporting Diaz and Ernest, "Maintenance of community function through compensation breaks down over time in a desert rodent community", now published in Ecology: https://doi.org/10.1002/ecy.3709

Repository structure:

• analyses: Contains .Rmd scripts to replicate the figures and tables in the main text and supplements.
• data: Contains all data files necessary to replicate the analyses in the manuscript. (Alternatively, the analyses scripts contain code to re-download from the main Portal Data repo).
• manuscript: Contains past versions of the ms and iterations through review.

To replicate:

• Custom functions for downloading and processing data for these analyses are in the R package soar, at https://github.com/diazrenata/soar. This is to separate functions that are called repeatedly in these analyses from the scripts that are only run once.
• Install the R package soar using: remotes::install_github("diazrenata/soar"). Alternatively, you can download the archived version from Github (https://github.com/diazrenata/soar) or Zenodo (https://doi.org/10.5281/zenodo.5539880) and install from there.
• Rendering each .Rmd document (e.g. squareone/analyses/s1_model_results.Rmd) will reproduce the figures and/or tables as presented in the manuscript and supplemental materials, as journal-ready formatted Word documents. Running portions of the .Rmd documents interactively allows you to work through individual analyses and explore the data more fully.
• Note that the .Rmd documents contain additional notes (commented out) that are probably not of interest to most readers, but may be useful to anyone trying to replicate these analyses exactly or build off of them.