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.
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:
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).
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