⚠️ This package has been deprecated. following the end of the PREDICT project in September 2020. EIDITH Data is now accessible via the USAID Development Data Library at https://data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr ⚠️

With the shutdown of the EIDITH database and export to the DDL, this package can be used to process data from static backups.

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The EIDITH R Package

The eidith R package provides programmatic access and analytical tools for data from the PREDICT program.

The eidith package contains no data. To access data via this package, you must be a member of the PREDICT project.

Package Installation

You can install the package with remotes::install_github("ecohealthalliance/eidith").

Database download

Before downloading the database, run googledrive::drive_auth(email = "yourname@ecohealthalliance.org") and follow the prompts. If you are working on the server or running into any issues, try googledrive::drive_auth(email = "yourname@ecohealthalliance.org", use_oob=TRUE). If you are still running into issues, reach out to Emma.

Once your Google auth is set up, download the database with import_local_db(database = "eha"). If you have Malaysia or global PREDICT access, you can enter "eha_with_malaysia" or "global" for the database argument.

Reading in tables

As in earlier versions of this package, once your database is downloaded, you can use the ed2_x() functions to read in tables. Note these tables contain Predict 2 and Predict 1 data when available. Predict 1 data are no longer in separate tables.

The following functions are available:

ed2_animals(), ed2_behavior(), ed2_crop_production(), ed2_dwellings(), ed2_events(), ed2_extractive_industry(), ed2_human(), ed2_human_animal_production(), ed2_human_animal_production_ehp(), ed2_human_crop_production(), ed2_human_ehp(), ed2_human_extractive_industry(), ed2_human_hospital_worker(), ed2_human_hunter(), ed2_human_hunter_ehp(), ed2_human_market(), ed2_human_restaurant(), ed2_human_sick_person(), ed2_human_temporary_settlements(), ed2_human_zoo(), ed2_market_value_chain(), ed2_natural_areas(), ed2_specimens(), ed2_test_interpreted(), ed2_test_serology(), ed2_tests(), ed2_training(), ed2_wildlife_restaurant()

Basic database structure

The database is primarily represented by the above structure, with modules branching off these main nodes.

The following are fields for joining among these tables:

events project, country, gains4_event_id

animals project, country, gains4_event_id, gains4_sample_unit_id

humans project, country, gains4_event_id, gains4_sample_unit_id

specimens project, country, gains4_sample_unit_id, gains4_specimen_id

tests project, country, gains4_specimen_id, gains4_test_id

Data processing support functions

To unnest multi-response fields, see ?ed2_expand_long and ?ed2_expand_wide.

Metadata

Somewhat outdated, but ed2_metadata() contains tables, fields, and descriptions.

Use eha_countries() and predict_countries() to see list of country names

Note on deprecated functions

ed_db_download() and ed2_get(), which previously accessed the EIDITH API, are now disabled.