README.md

In ecohealthalliance/sars_cov_risk: What the Package Does (One Line, Title Case)

sars_cov_risk

Data and code to support: A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

Repo Structure

• scripts/ contains all the scripts used to download large data files, conduct pre-processing, run the analyses, and generate outputs
• R/ contains files with functions used in other scripts
• data-raw/ contains data used in these analyses, including
  • a SARSrCoVhosts/ directory with lists and citations of SARSr-CoV bat hosts
  • a dataset of the prevalence of human-bat contact in Southeast Asia (bat_contact_data.csv)
  • a dataset of viral seroprevalence among humans reporting bat contact in Southeast Asia (detection_data.csv)
  • a dataset of SARS IgG positivity over time after infection (IgGtimeseries.csv)
  • spatial datasets (karst_wgs.zip and ne_50m_land.zip)
  • IUCN shapefiles (once downloaded from the release) (MAMMALS_TERRESTRIAL_ONLY.zip)
  • habitat classification files (once downloaded from the release) (iucn_habitatclassification_composite_1km_ver001.zip)
  • WorldPop 2020 population count raster (once downloaded from the release) (ppp_2020_1km_Aggregated.tif)
• data/ is a holding directory for intermediate data files
• figures/ contains generated figures

ecohealthalliance/sars_cov_risk documentation built on May 12, 2022, 6:35 p.m.