This repository gathers code I wrote for my Master 2 internship about the inference of co-occurrence networks.
functions/folder contains all custom functions written for data treatment.data/folder contains modified data (for confidentiality purposes, this is not the original data from Snapshot Safari).multiscale_inference/folder contains the code to infer networks and a sample PDF report and networks generated from the sample data.clustering/folder contains the code and a PDF report to define sites clusters and synthetic habitat covariates (modified data).low_abundances/folder contains the code to run simulations of PLN performances with low vs high abundances and a PDF report.null_model/contains the code used to evaluate the inferred networks against a null model with a sample code run on modified data.packrat/contains the packages tracked by packrat used for these analyses.