Movatterモバイル変換

Title:

'openFDA' API

Version:

0.1.0

Description:

The 'openFDA' API facilitates access to Federal Drug Agency (FDA) data on drugs, devices, foodstuffs, tobacco, and more with 'httr2'. This package makes the API easily accessible, returning objects which the user can convert to JSON data and parse. Kass-Hout TA, Xu Z, Mohebbi M et al. (2016) <doi:10.1093/jamia/ocv153>.

License:

GPL (≥ 3)

URL:

https://github.com/simpar1471/openFDA,https://simpar1471.github.io/openFDA/

BugReports:

https://github.com/simpar1471/openFDA/issues

Imports:

cli, httr2, checkmate, purrr, rlang, vctrs

Config/Needs/website:

rmarkdown

Suggests:

knitr, rmarkdown, testthat (≥ 3.0.0), stringr

Config/testthat/edition:

Encoding:

UTF-8

RoxygenNote:

7.3.2

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2024-10-17 10:10:15 UTC; tadeo

Author:

Simon Parker

[aut, cre, cph]

Maintainer:

Simon Parker <simon.parker.24@ucl.ac.uk>

Repository:

CRAN

Date/Publication:

2024-10-18 10:50:30 UTC

Format character vectors into`search` terms for openFDA API queries

Description

This function is a helper for constructing search queries. Whilst it handlessome of the available formatting for openFDA APIs, it does not recapture allof the search term syntax available to you. To get a full appreciation of theopenFDA search syntax, seehttps://open.fda.gov/apis/advanced-syntax/.

Usage

format_search_term(search, exact = TRUE, mode = "or")

Arguments

search

A character vector of length 1 or more. If scalar and unnamed,it will be assumed that you have already formatted your search string towork with the API. If named, the vector will be collapsed to include yourvarious search terms, separated by AND or OR terms based on the value ofoperator.

exact

A single-length logical vector. WhenTRUE (the default),individual search terms will be surrounded with double quotes (""). Setexact toFALSE if your search term contains multiple words to besearched on, e.g.c("openfda.generic_name" = "losartan+candesartan").

This parameter only applies ifsearch is a named character vector.

mode

A single-length character vector, which defines how searches inmultiple fields should be combined. By default ("or") they will becombined with an 'OR' operator, but you can make an 'AND' operator be usedinstead ("and"). This argument is case-sensitive and will throw an errorifmode is not one of either"and" or"or".

This parameter only applies ifsearch is a named character vector.

Value

A character vector of the S3 class⁠<AsIS>⁠, with a formatted searchterm which can be supplied toopenFDA().

Note

This function does not check that you're providing accurate field names orsearch terms. It is up to you to make sure you've provided correctly speltfields and search terms.

Examples

# Provide a formatted search string and the function will do no formattingformat_search_term("openfda.generic_name:verapamil")# Provide a named vector and the function will format it for youformat_search_term(c("openfda.generic_name" = "verapamil"))# If providing multiple elements in your search term, use `exact = FALSE`# to prevent the function from surrounding the term with double quotes.format_search_term(c("openfda.generic_name" = "verapamil+amlodipine"),                   exact = FALSE)# Provide a longer named vector and function will merge these with an OR# operatorformat_search_term(c("openfda.generic_name" = "verapamil",                     "openfda.manufacturer_name" = "glaxo*"))# Or you can set the `mode` argument to merge your search terms with an AND# operatorformat_search_term(c("openfda.generic_name" = "verapamil",                     "openfda.manufacturer_name" = "glaxo*"),                   mode = "and")

Format character vectors into`sort` terms for openFDA API queries

Description

This function acts as a helper for constructing a sort term in the openFDAAPI.

Usage

format_sort_term(sort)

Arguments

sort

A single-length character vector of length 1. If unnamed,it will be assumed that you have already formatted your search string towork with the API. If named, the vector will be collapsed to include yourfield and sorting choice.

Value

A character vector of the S3 class⁠<AsIS>⁠, with a formatted searchterm which can be supplied toopenFDA().

Note

This function does not check that you're providing accurate field names orsearch terms. It is up to you to make sure you've provided correctly speltfields and search terms.

Examples

# Provide a formatted search string and the function will do no formattingformat_sort_term("openfda.generic_name:asc")# Provide a named vector and the function will format it for youformat_sort_term(c("openfda.generic_name" = "asc"))# Errors will be thrown if you supply a bad inputtry(format_sort_term("receivedate:no_order"))try(format_sort_term(c("receivedate" = "ascending")))

Send requests to the openFDA API

Description

Send requests to the openFDA API

Usage

openFDA(  search = "",  sort = NULL,  count = NULL,  limit = 1000,  skip = NULL,  endpoint = "drug-drugsfda",  api_key = get_api_key(),  warn_on_http_error = TRUE)

Arguments

search

A character vector which will be passed toformat_search_term(). If search is"" (the default), openFDA willretrieve all records with no filtering. An error will be thrown if anyelements ofsearch are missing (NA).

sort

A single string or scalar named character vector describing howto sort the results. Thesort term should either be formatted as"[FIELD]:[asc/desc]", orc("[FIELD]" = "[asc/desc]"). For example, tosort results in the Drugs@FDA endpoint by ascending submission statusdates. If values other than"asc", or"desc" are supplied, the functionwill throw an error.

count

A single string denoting a field on which to count results. IfNULL (the default), results will be returned in full to the user. Specifythis parameter if you want to count occurrences of results within yoursearch term - go tohttps://open.fda.gov/apis/query-syntax/ for moreinformation.

limit

A single integerish value describing the limit on the number ofrecords to retrieve. An error will be thrown iflimit is more than1000(the default).

skip

A single integer describing how many records should be skipped.If more records are skipped than are found in your search, the openFDAAPI will return a 404 error.

endpoint

A single-length character vector describing which openFDAendpoint to target.

"animal-event": Adverse event reports for animal/veterinary drugs.
"drug-event": Adverse event reports fromFDA Adverse Event Reporting System
"drug-label": Drug documentation in theStructured Product Labeling(SPL) format.
"drug-ndc": Data from theNational Drug Code Directory (NDC).
"drug-enforcement": Data from theFDA Recall Enterprise System about drug products.
"drug-drugsfda": Data on products approved for human use by the FDAsince 1939, with mostly complete data after 1998.
"device-510k": Data from 510(k) submissions to the FDA regardingmedical devices.
"device-classification": Data from the FDAProduct Classification Database for medicaldevices.
"device-enforcement": Data from theFDA Recall Enterprise System (RES) for medical devices.
"device-event": Data on adverse events associated with FDA-approvedmedical devices.
"device-pma": Pre-market approval data for medical devices submitted tothe FDA.
"device-recall": Data on product recalls for medical devices whichviolate FDA law.
"device-reglist": Data on FDADevice Registrations and Listings.
"device-covid19serology": Data fromindependent evaluations of COVID-19 serological tests.
"device-udi": Data from the FDA's Global Unique Device IdentificationDatabase (GUDID).
"food-enforcement": Data from theFDA Recall Enterprise System for food products.
"food-event": Data from theCenter for Food Safety and Applied Nutrition Adverse Event Reporting System.
"other-historicaldocument": The majority of FDA Press Releases, from1913 to 2014.
"other-nsde": Data from theNational Drug Code Structured Product Labeling Data Elements.
"other-substance": Data regarding substances - individual molecules,proteins, nucleic acids, and more.
"other-unii": Data from theFDA's Global Substance Registration System.
"tobacco-problem": Data on problems (e.g. damage, defects,contamination, bad smell) with tobacco products.

This argument is case-sensitive. By default, the package will target theDrugs@FDA endpoint ("drugs-drugsfda").

api_key

A single-length character vector with your openFDA API key.By default this is the result ofget_api_key(). Ifapi_key is an emptystring, an error will be thrown.

warn_on_http_error

A scalar logical value. IfTRUE (the default),common openFDA HTTP errors will cause explanatory warnings to be printedIfFALSE, the underlying httr2 response object will be returned withno extra warnings.

Value

Anhttr2 response object fromhttr2::req_perform(). You can usehttr2::resp_body_json() to extract JSON data from the response.

References

Kass-Hout TA, Xu Z, Mohebbi M, Nelsen H, Baker A, LEvine J, Johansen E,Bright RA.OpenFDA: an innovative platform providing access to a wealth ofFDA's publicly available dataJ Am Med Inform Assoc 2016,23(3):596-600.doi:10.1093/jamia/ocv153

Examples

if (httr2::secret_has_key("OPENFDA_KEY")) {  set_api_key(httr2::secret_decrypt(    "TEaDtqdFMq9_Montij5p9IY6T57IyqkbF8IYFVOpk-ttxotFUNdJSxgccAnkq4nQhplaf-r3deQ",    "OPENFDA_KEY"  ))  resp <- openFDA(search = "openfda.manufacturer_name:gilead*",                  limit = 2,                  skip = 10)  # The function returns an `httr2` object  print(resp)}# Bad inputs will cause informative errors - here, a bad API key is suppliedtry(  openFDA(search = "openfda.manufacturer_name:gilead*",          api_key = "BAD_API_KEY",          limit = 1))

Get and set your openFDA API keys

Description

Get and set your openFDA API keys

Usage

set_api_key(api_key)get_api_key()

Arguments

api_key

A single-length character vector with your openFDA API key.You can generate an API key on theFDA website.

Value

A single length character vector with your API key. Forset_api_key(), this is returned invisibly.

Forget_api_key(), an error will be thrown if no key has been set.

Note

To permanently set the API key for a given project, setOPENFDA_TOKENin.Renviron.

Examples

# Set your openFDA API key with `set_api_key()`api_key <- "example_api_key"set_api_key(api_key)# Retrieve it with `get_api_key()`get_api_key()# An error will be thrown if your API key is an empty string.set_api_key("")try(get_api_key())

Movatterモバイル変換

Format character vectors into`search` terms for openFDA API queries

Description

Usage

Arguments

Value

Note

See Also

Examples

Format character vectors into`sort` terms for openFDA API queries

Description

Usage

Arguments

Value

Note

See Also

Examples

Send requests to the openFDA API

Description

Usage

Arguments

Value

References

See Also

Examples

Get and set your openFDA API keys

Description

Usage

Arguments

Value

Note

Examples

Movatterモバイル変換

Format character vectors intosearch terms for openFDA API queries

Description

Usage

Arguments

Value

Note

See Also

Examples

Format character vectors intosort terms for openFDA API queries

Description

Usage

Arguments

Value

Note

See Also

Examples

Send requests to the openFDA API

Description

Usage

Arguments

Value

References

See Also

Examples

Get and set your openFDA API keys

Description

Usage

Arguments

Value

Note

Examples

Format character vectors into`search` terms for openFDA API queries

Format character vectors into`sort` terms for openFDA API queries