Supplement 1. Details on the computational analyses needed to replicate the results.

2016-08-10T06:11:44Z (GMT) by Sarah R. Supp S. K. Morgan Ernest
<h2>File List</h2><div> <p><a href="community_response.R">community_response.R</a> (MD5: fb68bd4556d88efa258ef31df99bd9ba)<br> R script that imports the data, summarizes the species-level and community-level diversity measures, runs the statistical analyses, and outputs figures.</p> <p><a href="ExpRADsFunctions.R">ExpRADsFunctions.R</a> (MD5: 33f248b2586218cdfd39d1bdab7d5078)<br> R script that holds the relevant functions for executing the community_response.R script.</p> <p><a href="ref_analysis_data.csv">ref_analysis_data.csv</a> (MD5: 9711e20465ed8f66a3093cf49b1ca477)<br> Data file containing the citations and details for the references where the studies were found.</p> <p><a href="community_analysis_data.csv">community_analysis_data.csv</a> (MD5: 7bded51aa20016eefc079a079500eb96)<br> Data file containing the community-level data.</p> <p><a href="orderedcomparisons.csv">orderedcomparisons.csv</a> (MD5: 11cdc68441e8dd2011da2594f6a70dfe)<br> Data file containing the details on which sites should be compared.</p> <p><a href="experiments_analysis_data.csv">experiments_analysis_data.csv</a> (MD5: 9052fc375916c1fa36be1316988a5c13)<br> Data file containing the details about the controls and experimental treatments.</p> <p><a href="sites_analysis_data.csv">sites_analysis_data.csv</a> (MD5: 93ee3e4c9c4f9cfa99bddbe473b9c5ef)<br> Data file containing site-specific information for the studies.</p> </div><h2>Description</h2><div> <p>The code and data in this supplement allow for the analyses and figures in the paper to be fully replicated using a data set of manipulated communities collected from the literature.</p> <p><i>Requirements: </i>R 3.x, and the following packages: vegan, BiodiversityR, plotrix, graphics, CCA, VGAM, nlme, lme4, poilog, scatterplot3d, hydroGOF, and VennDiagram, knitr, ggplot2, ggmap, gridExtra, GGally, and the file containing functions specific to this code, expRADsFunctions.R.</p> <p>The analyses can then be replicated by changing the working directory at the top of the file community_response.R to the location on your computer where you have stored the .R and .csv files and running the code.</p> <p>It should take approximately 10 minutes to run all the code from start to finish. Figures should output as pdfs in your working directory.</p> <p><i>Version Control Repository: </i>The full version control repository for this project (including post- publication improvements) is publicly available at <a href="https://github.com/weecology/experimental-rads">https://github.com/weecology/experimental- </a><a href="https://github.com/weecology/experimental-rads">rads</a>. If you would like to use the code in this Supplement for your own analyses it is strongly suggested that you use the equivalent code in the repositories as this is the code that is being actively maintained.</p> <p><i>Data use: </i>Data is provided in this supplement for the purposes of replication. If you wish to use the data for additional research, they should be obtained from S. R. Supp or from the original authors who are cited in ref_analysis_data.csv and Appendix Table A1. The data is also published in a public figshare repository (MACD: Manipulated Animal Community Database. S. R. Supp. figshare. <a href="http://dx.doi.org/10.6084/m9.figshare.96831">http://dx.doi.org/10.6084/m9.figshare.96831</a>).</p> </div>