Data & Code: "Predicting missing links in global host-parasite networks"

Data & Code from Farrell et al. "Predicting missing links in global host-parasite networks"ScriptsWithin the scripts folder are scripts to process the raw data and model results:1. Download, clean, and merge host-parasite interaction databases with mammal supertree (process_raw_data.R)2. Re-create raw data plots from the manuscript (raw_data_plots.R)3. Plot posterior interaction matrices, scaled trees, and pull out top predicted links (model_summaries.R)4. Re-create diagnostic plots from the manuscript (diagnostic_plots.R)5. Functions used for data manipulation and visualization that are sourced by other scripts (network_analysis.R)6. Investiage bias propagation via node degree product (bias_investigation.R)7. Generate risk maps (risk_maps.R)Data- raw_data: folder includes the data necessary to amalgamate the host-parasite interaction databases (via script 'process_raw_data.R').- clean_data: folder includes the full host-parasite interaction list 'hp_list' in both .csv and .rds formats, as well as the binary interaction matrices for the full dataset and ones subset by parasite type (virus, bacteria, fungi, etc...), and model diagnostics ('model_diagnostics.csv') used in 'diagnostic_plots.R' .- model_results: folder contains .rds files per model, which has the output interaction matrix from each simulation ('P'), the table of model diagnostics ('TB'), and the phylogeny scaling parameter ('Eta'), if applicable. Note that to save space the full cross-fold fit posteriors are omitted (these total ~ 4.5GB). Please contact MF if these are required. - literature_results: folder contains a .csv version of the results of the literature search outlined in the Supplementary Information.- plots_tables: folder contains .csv files for the top 100 'missing' links for each model, and a .csv for the top 1000 links from the full model run on the full dataset.