Licenses:

Data:

See licenses_data_sources.csv for data licenses and terms of use.

One Health Database Africa

The “One Health and Veterinary Systems in Africa: Taking stock of current coverage, needs, and opportunities to meet present and changing threats and optimize collaboration” is reviewing current capacity and programmatic status, gaps, and operations in each country and by sub-regions of Africa.

This repository combines datasets from multiple sources to produce a single One Health database containing all the selected indicators. The database encompasses 54 countries across the continent (according the UN).

Data

Downloaded data files are stored in the data folder. The sources of each data file and their associated indicators are listed in the 'OHDAfrica_indicators_metadata.csv' file. This file also contains links to the relevant webpages.

The column entitled 'manual update needed' idenitifes those datasets for which an api call/direct download wasn't available and that will need manually updating as required.

Definitions for columns in metadata file

• Indicator - measure used to assess one health capacity.
• filename - name of file storing the data.
• source_url - website/api endpoint where data can be.
• Notes - Additional context about a source.
• function_names - name of the file that holds the ingest function.
• api_call_or_direct_download - suffix of the function contained in function_names. Used to call functions. ingetst_indicators.{api_call_or_direct_download}.
• Manual update needed - Is the data updated by hand, not via an automated data ingest.
• base_url - domain name for source_url.
• terms_of_use - Data terms of use as stated by source.
• potential_violation - is our data use out of line with the terms of use.

Functions

Individual functions for extracting the data for individual indicators are available in the 'R_api' folders

'R_api' contains functions to retrieve data using direct downloads or api calls where available. For those where a direct download/api call is not possible, the functions use the data stored in the 'data' folder.

Compiling full dataset

'top_script_api' uses direct downloads or api calls where they are available. When not available it draws on the downloaded data in the 'data' folder.

There are three outputs from each of these scripts:

• full data factor api - contains the data where outcome values are factors
• full data number api - contains the data where outcome values are numeric
• full data combined api - combined the numeric and factor datasets. Values are stored as characters and there is an additional column identifying whether the value is numeric or factor

'top_script_api_clean' merges duplicate vet data and cleans SPAR indicator names.

Country reports

'country.report.Rmd' produces a report for a specified year and country which the user specifies in lines 21 and 23 of the script. Only variables for which data are available for the specified country and years will appear in the report.