Code and data to reproduce analyses in the manuscript, "Probabilistic co-occurrence analysis reveals community assembly processes"
Code for pairwise calculation of Fisher's exact test and its mid-P variant on an occurrence matrix is contained in Pair_Functions.R. This file also contains code to calculate weighted connectance and evenness. Note that PAIRS is an independent program written in Fortran, which can be downloaded with instructions from: http://www.keib.umk.pl/pairs/?lang=en Simulated data used in the main text of the manuscript is in Simulated_Datasets.RData. A brief description of the data object is in Data_Descriptions.txt.