Supplement 1. The R source code containing the algorithms used for modeling communities and a comma-delimited file containing the bird data set collected in the Atlantic Forest.

File List Site_by_species_matrix.csv (md5: 40436d5d0cf1f856df0a24d84bb2ebdc) Codes.r (md5: 65fc434d02b30cfccbc7b0a9b763710e) Codes_sensitivity_analysis.r (md5: 7eb16dfd396f2513d91b27893ca71367) Function_create.prob.r (md5: a30b99e9f10b1728a82bc9b000fc69dd) Function_CreateCommunity.r (md5: 59352753f4649ebd4cbbb5d15df06235) Description The Site_by_species_matrix.csv file is a comma delimited file. It contains the data on presence and absence of Atlantic Forest bird species captured in fragments and continuous sites. Rows contains sites and columns contain species. The Codes.r file is in R programming language. It contains the algorithm used for modeling communities and for analysing the data generated during simulations. The files Site_by_species_matrix.csv, Function_create.prob.r, and Function_CreateCommunity.r are needed to successfully run this code. The code is annotated throughout and written to improve clarity rather than to maximise processing times. Full time required for running all simulations is roughly four days, depending on processor and amount of RAM. The Codes_sensitivity_analysis.r file is in R programming language. It contains the algorithm used for running a sensitivity analysis on the values of Gaussian curve used to create SPEC communities. The files Site_by_species_matrix.csv, Function_create.prob.r, and Function_CreateCommunity.r are needed to successfully run this code. The code presented here was written to improve clarity rather than to maximise processing times. Full time required for running all simulations is roughly four or more days, depending on processor and amount of RAM. The Function_create.prob.r file is in R programming language. It contains the codes used to create the function create.prob, which creates a matrix of sampling probabilities necessary to create SPEC communities. This function is sourced directly from Codes.r and from Codes_sensitivity_analysis.r. The Function_CreateCommunity.r file is in R programming language. It contains the codes used to create the function create.community, which is necessary to create RAND, SFD, and SPEC communities. This function is sourced directly from Codes.r and from Codes_sensitivity_analysis.r, and it requires Function_create.prob.r to create SPEC communities. The function here presented was written to improve clarity and re-writing the function substantially speeds processing time.