to https://github.com/ecohealthalliance/wahisdb

This package provides access to veterinary disease data from OIE WAHIS as well as several other data sets that may support analysis of veterinary diseases.

wahis data

• outbreak reports

  • inst/processing_scripts/process_outbreak_reports.R provides an example workflow for retrieving wahis outbreak reports
  • scrape_outbreak_report_list() returns a master list of available outbreak reports
  • ingest_report() accepts a curl response from the wahis API and returns outbreak report content as a list. safe_ingest() is a wrapper to handle errors when ingesting reports.
  • transform_outbreak_reports() converts outbreak report content into formatted data. It yields three tibbles (saved in a single list object):
    • outbreak_reports_events contains high-level outbreak event data. Each row corresponds to a report. report_id is the unique report ID and url_report_id is the value appended to the API url for the given report.
    • outbreak_reports_outbreaks provides detailed location and impact data for outbreak events. This table can be joined with outbreak_reports_events by report_id. outbreak_location_id is a unique ID for each location (e.g, farm or village) within a outbreak.
    • outbreak_reports_diseases_unmatched lists diseases from the outbreak reports that did not match the ANDO ontology. These diseases are not removed from the database.

• six month reports

  • inst/processing_scripts/process_six_month_reports.R provides an example workflow for retrieving wahis 6 mognth reports
  • scrape_six_month_report_list() returns a master list of available 6 month reports
  • ingest_report() accepts a curl response from the wahis API and returns 6 month report content as a list. safe_ingest() is a wrapper to handle errors when ingesting reports.
  • transform_six_month_reports() converts six month report content into formatted data. It yields three tibbles (saved in a single list object):
    • six_month_reports_summary contains high-level six-month data. It provides disease status (present/absent/unreported) and case counts by country, disease, taxa. It also includes control measures.
    • six_month_reports_detail provides case data at finer temportal and/or spatial resolutions, as available.
    • six_month_reports_diseases_unmatched lists diseases from the six month reports that did not match the ANDO ontology. These diseases are not removed from the database.

other data sets

The following data sets can be accessed through this package:

• Birdlife data for migratory bird species (download_bird_migration() and transform_bird_migration())
• FAO livestock population (download_livestock() and transform_livestock())
• Country borders from CIA factbook (get_country_borders())
• UN human migration data (download_human_migration() and transform_human_migration())
• Wildlife migration data combined from IUCN and GROMS (download_wildlife() and transform_wildlife_migration())
• OTS trade data (download_trade() and transform_trade())
• WTO tourism data (download_tourism() and transform_tourism())
• FAO taxa population data (download_taxa_population() and transform_taxa_population())
• Raster data of livestock and human populations, climatic variables, economic activity and transit accessibility (download_rasters() and transform_rasters())