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: ```R library("devtools") devtools::install_github("ropenhealth/openfda")
Load it in like any other package:
library("openfda")
library("knitr") opts_knit$set(upload.fun = imgur_upload, base.url = NULL)
patient_ages = fda_query("/drug/event.json") %>% fda_count("patient.patientonsetage") %>% fda_exec() # 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
).
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.