Code to perform species distribution modeling for Latinne et al. "Diversity and spillover risk of Swine Acute Diarrhea Syndrome and related coronaviruses in China and Southeast Asia"
Explanation of code organization:
The main_run.R script performs the species distribution modeling described in
the manuscript. It begins by loading packages (you will need to install them if
you do not already have them) and sourcing functions in the R folder. The script
next calls assemble_predictors.R, which assembles a set of predictor variables
(e.g. land cover, bioclimatic data). Some of the data files used in this
function are very large and/or have restrictions around their use, so you need
to download these on your own. Details on the original data sources can be found
in data_raw/data_sources.R. The main script next calls gbif_request.R, which
shows how a GBIF request was made to obtain occurrence records for the bat
species of interest. These data can be also be downloaded
here. For each of the bat species, the
same five functions are called to perform various steps of the species
distribution modeling process: 1) set_modeling_region.R creates the geographic
study region for model training, 2) grid_points.R performs spatial thinning on
occurrence points, 3) run_ENM.R performs model tuning and cross-validation, 4)
Ra_thresh.R selects the optimal model from the set of candidate models and
calculates a tenth percentile training presence threshold for later use, and 5)
project_model.R produces a continuous estimate of habitat suitability from
0-1, and produces a binary map of suitable vs unsuitable habitat based on the
threshold calculated earlier. Finally, Figures 3 and 4 of the manuscript are
generated with make_fig_3.R and make_fig_4.R respectively.