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ecohealthalliance / predict-ma-reports

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PREDICT modeling and analytics reports

This repository contains R code to generate M&A summary reports using EIDITH data.

To use, clone this repository and set it as your working directory. (You may open the predict-ma-reports.Rproj file if you use RStudio.)

  1. First run devtools::install_deps(upgrade = "always") in R to get all packages required to run this code and ensure that they are up to date. These packages are listed in the DESCRIPTION file. You should in general keep up to date with the latest version of the eidith package, which tracks changes made upstream in the EIDITH database.

  2. Run 00-get-data.R

    • This will download EIDITH data from EHA's static backup.
    • This will also download supporting data (IUCN species, population and mammal density map layers) from a public AWS repository.

  3. Run scripts/generate_viral_species_lookups.R.

  4. Run scripts/generate_mammal_country_lookup.R.

    • Note that line 96 in this script will print any species names that need to be added to data/iucn_to_hp3_taxonomic_harmonization.csv to reconcile IUCN and HP3 species names.

  5. Modify report-template.Rmd however you like.

  6. Run make.R to generate the reports (from report-template.Rmd). Specify your countries.

Output reports are saved to the outputs/ folder.

*.encrypted, dropbox_upload.R, and .gitlab-ci.yml files are specific to EcoHealth Alliance's automated pipeline infrastructure and require EHA encryption keys to use.