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Supplement 1. R code for assessing covariance between environment and competition.

posted on 2016-08-05, 05:27 authored by Anna L. W. Sears, Peter Chesson

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This supplement contains an R program that does the calcuations listed in the text. This program is provided for convenience. The formulae are relatively straight forward to use and program. Bootstrap P value correction is a little more complex, but again would not be difficult for users to program in a language of their choice. The code (Assessing_CovEC.r), as written, analyzes the data from Appendix C, with no user inputs. These data are in the file Example_data.txt. To use this program for your own data, you need to substitute your own data file name. This file must be an ascii file with two columns, the first for the removal and the second for the control, with rows corresponding to blocks in the experiment. Users must also supply as input variables, nbl, the number of blocks in the experiment, theta, the error variance ratio, and reps, the number of bootstrap replicates to be used. The code provided has these values in the first section labeled "user inputs." To run the program with your own data, all you need to do is modify the values in this section of the code for yourself. The program is not provided as compiled code as it much simpler just to modify the first section of the source code for your own purposes.