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.
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outbreak reports
inst/processing_scripts/process_outbreak_reports.R
provides an example workflow for retrieving wahis outbreak reportsscrape_outbreak_report_list()
returns a master list of available outbreak reportsingest_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 andurl_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 withoutbreak_reports_events
byreport_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.
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six month reports
inst/processing_scripts/process_six_month_reports.R
provides an example workflow for retrieving wahis 6 mognth reportsscrape_six_month_report_list()
returns a master list of available 6 month reportsingest_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.
The following data sets can be accessed through this package:
- Birdlife data for migratory bird species (
download_bird_migration()
andtransform_bird_migration()
) - FAO livestock population (
download_livestock()
andtransform_livestock()
) - Country borders from CIA factbook (
get_country_borders()
) - UN human migration data (
download_human_migration()
andtransform_human_migration()
) - Wildlife migration data combined from IUCN and GROMS (
download_wildlife()
andtransform_wildlife_migration()
) - OTS trade data (
download_trade()
andtransform_trade()
) - WTO tourism data (
download_tourism()
andtransform_tourism()
) - FAO taxa population data (
download_taxa_population()
andtransform_taxa_population()
) - Raster data of livestock and human populations, climatic variables, economic activity and transit accessibility (
download_rasters()
andtransform_rasters()
)