Supplement 1. Code for conducting the analyses and generating the figures in this paper.

File List PortalPlants_ms12-0370R2.R <br> R script that cleans the data of errors, constructs the macroecological patterns, pulls out descriptive parameters of these patterns, runs the statistical analyses, and outputs figures. PortalPlants_fxns.R<br> R script that holds the relevant functions for executing the PortalPlants_ms12-0370R2.R script. PortalSummerAnnuals_1995_2009.csv <br> Data file containing raw summer annual plant community abundance data for years 1995–2009. PortalWinterAnnuals_1995_2009.csv <br> Data file containing raw winter annual plant community abundance data for years 1995–2009. Description The code and data in this supplement allow for the analyses and figures in the paper to be fully replicated using a subset of the published Portal data set which includes annual plant data from 1995–2009. Requirements: R 2.x and the following packages: Biodiversity R, car, CCA, equivalence, gplots, graphics, languageR, lme4, nlme, plotrix, poilog, vegan, VGAM and the file containing functions specific to this code, PortalPlants_fxns.R. The analyses can then be replicated by changing the working directory at the top of the file PortalPlants_ms12-0370R2.R to the location on your computer where you have stored the .R and .csv files and running the code. Please note that the <i>p</i> values generated for Appendix D in the published paper were generated using R 2.12.2. Because of approximations, the values for SAD sigma and mu may differ slightly (around the 10th decimal place) from Appendix D, Tables D2 and D3. Because the equivalence testing also uses approximations, there may be very small differences in the exact values generated compared to Appendix D, Tables D4 and D5. It should take approximately 30 minutes to run all the code from start to finish. Figures should output as pdfs in your working directory. Version Control Repository: The full version control repository for this project (including post-publication improvements) is publicly available at https://github.com/weecology/portal-experimental-macroeco. 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. Data use: 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 the published source (Ecological Archives E090-118-D1; S. K. Morgan Ernest, Thomas J. Valone, and James H. Brown. 2009. Long-term monitoring and experimental manipulation of a Chihuahuan Desert ecosystem near Portal, Arizona, USA. Ecology 90:1708. doi:10.1890/08-1222.1)