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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# openFDA
<!-- badges: start -->
[](https://CRAN.R-project.org/package=openFDA)
[](https://github.com/simpar1471/openFDA/actions/workflows/R-CMD-check.yaml)
[](https://github.com/simpar1471/openFDA/actions/workflows/check-no-suggests.yaml)
[](https://app.codecov.io/gh/simpar1471/openFDA)
<!-- badges: end -->
openFDA makes querying the [openFDA API](https://open.fda.gov/apis/) from R a breeze.
The API itself serves publicly available data from the FDA about foods, drugs, devices, and more.
This data includes data such as recall enforcement reports, adverse events, manufacturer details, and - again - even more!
Note that the data on openFDA has not been validated for clinical or production use.
## Installation
The easiest way to install openFDA is to get it from CRAN:
```r
install.packages("openFDA")
```
### Development version
```r
# install.packages("pak")
pak::pkg_install("simpar1471/openFDA")
```
## Using openFDA
```{r load_openFDA}
library(openFDA)
```
The full documentation for the API is online, so look at the [openFDA
website](https://open.fda.gov/apis/) to get a full feel for the API itself.
The R package lets you query the API directly from R, using [httr2](https://httr2.r-lib.org/).
```{r example1_query}
search <- openFDA(
search = "openfda.generic_name:furosemide",
limit = 5
)
search
```
The underlying response is JSON data - you can use `httr2::resp_body_json()` to get the JSON data as a nested list, then extract the fields you want.
```{r example2_json}
json <- httr2::resp_body_json(search)
json$results[[1]]$openfda$brand_name
json$results[[1]]$openfda$pharm_class_epc
```
I've found [purrr](https://purrr.tidyverse.org/) to be very useful for parsing this data quickly.
```{r example3_purrr}
purrr::map_chr(
.x = json$results,
.f = \(result) purrr::pluck(result, "openfda", "manufacturer_name", 1)
)
```
## Other R packages for openFDA
The [openfda](https://github.com/rOpenHealth/openfda) package from `rOpenHealth` also wraps the openFDA API from R, and is available on GitHub.
It's got a pretty neat structure whereby you build up a query using individual functions for each parameter - though it's my personal preference to keep these as parameters to a single function.
It also makes results available in data frames, which is nice, but I think working with the response object and parsing the underlying JSON yourself permits more powerful interactions with the API.
There is also [FDAopenR](https://github.com/ck2136/FDAopenR/), which I couldn't quite wrap my head around. The package appears to be in working order, though!