rOpenHealth / openfda

Convenient access to the OpenFDA API

openfda

Convenient access to the OpenFDA API

This package provides some simple helpers for accessing the OpenFDA API from R. It uses the jsonlite and magrittr packages to provide a simple way to convert from OpenFDA queries to R dataframes suitable for quick analysis and plotting.

Installation

This library has not yet been added to CRAN, so you'll need the devtools package to install it:

install.packages("devtools")

Once devtools is installed, you can grab this package:

library("devtools")
devtools::install_github("ropenhealth/openfda")

Load it in like any other package:

library("openfda")

Examples

patient_ages = fda_query("/drug/event.json") %>%
               fda_count("patient.patientonsetage") %>%
               fda_exec()

## Fetching: https://api.fda.gov/drug/event.json?search=&count=patient.patientonsetage

# patient ages is now a data frame with "term" and "count" columns
# let's plot it with ggplot2
library("ggplot2")
qplot(x=term, y=count, data=patient_ages)

You can filter the results to count on using the fda_filter() method:

paxil_ages = fda_query("/drug/event.json") %>%
               fda_filter("patient.drug.openfda.generic_name", "paroxetine") %>%
               fda_count("patient.patientonsetage") %>%
               fda_exec()

Using this API with your API key is easy: just add fda_api_key("MY_KEY") to your pipeline.

patient_ages = fda_query("/drug/event.json") %>%
               fda_api_key("MYKEY") %>%
               fda_count("patient.patientonsetage") %>%
               fda_exec()

You can also specify options up front and re-use the query:

age_query = fda_query("/drug/event.json") %>%
            fda_api_key("MYKEY") %>%
            fda_count("patient.patientonsetage");

paxil_ages = age_query %>% fda_filter("patient.drug.openfda.generic_name", "paroxetine") %>% fda_exec()
zoloft_ages = age_query %>% fda_filter("patient.drug.openfda.generic_name", "sertraline") %>% fda_exec()

R documentation for each method is also provided in the package (? fda_exec).