README.md

In gideononline/gideon-api-r: GIDEON API Wrapper

GIDEON - R Interface (BETA)

A package for accessing the GIDEON API using R.

The gideon package provides functions to access the GIDEON API without the need of writing your own REST API queries.

R Prerequisites

R Programming Language

1. Choose a CRAN Mirror to download R
2. Select the appropriate operating system
3. Download installer
   • Windows - Choose the base subdirectory
   • macOS - Choose R-4.*.*.pkg for Intel Macs or R-4.*.*-arm64.pkg for Apple silicon Macs
   • Linux - Choose appropriate distribution and follow instructions

(Recommended) RStudio

Download and install RStudio Desktop for a complete R integrated development environment

GIDEON R Package Installation

Execute the following commands in the the R console:

1. Install the R devtools package with the command install.packages("devtools")
2. Install the GIDEON R package using devtools::install_github("gideononline/gideon-api-r")
3. Load GIDEON R package with library(gideon)

Package Help

Type ?gideon or help(gideon) into the R console to get the package documentation and overview of capabilities.

Authentication

All calls to the GIDEON API require an API key to work. Provide your GIDEON API key as an R environment variable by appending the following line to your .Renviron file: GIDEON_API_KEY=<YOUR API KEY>. The .Renviron file can be edited. by running the command usethis::edit_r_environ() in the R console.

GIDEON ID Codes

Many of the items in the GIDEON database use an id code, such as diseases, bacteria, drugs, etc. Use lookup_gideon_id to get specific item code to use when calling the GIDEON API.

Outbreak Functions

The functions to query outbreaks are:

• outbreaks_by_year
• outbreaks_by_country_year
• latest_outbreaks_by_country
• outbreaks_by_disease
• endemic_countries_by_disease
• endemic_diseases_by_country

GIDEON API access functions

Functions to access the GIDEON API directly

• query_gideon_api

Examples

library(gideon)

cholera_code <- lookup_gideon_id("diseases", "Cholera")
cholera_outbreaks <- outbreaks_by_disease(cholera_code)

us_country_code <- lookup_gideon_id("countries", "United States")
outbreaks_us_2007 <- outbreaks_by_country_year(us_country_code, 2007)

outbreaks_2009 <- outbreaks_by_year(2009)
to_geojson(outbreaks_2009, 'outbreaks2009.geojson')

mosquito_vector_code <- lookup_gideon_id("vectors", "Mosquito")
horse_reservoir_code <- lookup_gideon_id("reservoirs", "Horse")
diseases_from_horses_via_mosquitos <- filter_diseases(
    vector = mosquito_vector_code,
    reservoir = horse_reservoir_code
)

gideononline/gideon-api-r documentation built on March 19, 2022, 5:07 p.m.