Package {medrxivr}

Title:	Access and Search MedRxiv and BioRxiv Preprint Data
Version:	0.1.3
Depends:	R (≥ 4.1.0)
Description:	An increasingly important source of health-related bibliographic content are preprints - preliminary versions of research articles that have yet to undergo peer review. The two preprint repositories most relevant to health-related sciences are medRxiv https://www.medrxiv.org/ and bioRxiv, both of which are operated by the Cold Spring Harbor Laboratory. 'medrxivr' provides programmatic access to the 'Cold Spring Harbour Laboratory (CSHL)' API https://api.biorxiv.org/, allowing users to easily download medRxiv and bioRxiv preprint metadata (e.g. title, abstract, publication date, author list, etc) into R. 'medrxivr' also provides functions to search the downloaded preprint records using regular expressions and Boolean logic, as well as helper functions that allow users to export their search results to a .BIB file for easy import to a reference manager and to download the full-text PDFs of preprints matching their search criteria.
License:	GPL-2
Encoding:	UTF-8
Language:	en-US
URL:	https://github.com/ropensci/medrxivr
BugReports:	https://github.com/ropensci/medrxivr/issues
Imports:	methods, dplyr, curl, jsonlite, httr, stringr, rlang, bib2df, tibble, progress, lubridate, purrr, data.table
Suggests:	testthat (≥ 2.1.0), knitr, rmarkdown, covr, kableExtra, spelling
VignetteBuilder:	knitr
RoxygenNote:	7.3.2
NeedsCompilation:	no
Packaged:	2026-05-06 20:55:02 UTC; Bach
Author:	Yaoxiang Li [aut, cre], Luke McGuinness [aut], Lena Schmidt [aut], Tuija Sonkkila [rev], Najko Jahn [rev]
Maintainer:	Yaoxiang Li <liyaoxiang@outlook.com>
Repository:	CRAN
Date/Publication:	2026-05-07 12:01:16 UTC

medrxivr: Accessing medRxiv and bioRxiv preprint data from R

Description

The medrxivr package enables users to access data on preprints in the medRxiv and bioRxiv preprints repositories, both of which are run by the Cold Spring Harbour Laboratory.It also provides functions to search the preprint data, export it to a .bib file, and download the PDFs associated with specified records.

Author(s)

Maintainer: Yaoxiang Li liyaoxiang@outlook.com (ORCID)

Authors:

• Luke McGuinness

• Lena Schmidt

Other contributors:

• Tuija Sonkkila [reviewer]

• Najko Jahn [reviewer]

See Also

Useful links:

• https://github.com/ropensci/medrxivr

• Report bugs at https://github.com/ropensci/medrxivr/issues

Create link for API

Description

Create link for API

Usage

api_link(...)

Arguments

Value

Formatted link to API endpoint

Extract the page size from API metadata

Description

Extract the page size from API metadata

Usage

api_page_size(messages)

Arguments

Value

Numeric page size

Extract the total number of records from API metadata

Description

Extract the total number of records from API metadata

Usage

api_record_count(messages)

Arguments

Value

Numeric record count

Convert API data to data frame

Description

Convert API data to data frame

Usage

api_to_df(url)

Arguments

Value

Raw API data in a dataframe

Helper script to clean data from API to make it compatible with mx_search()

Description

Helper script to clean data from API to make it compatible with mx_search()

Usage

clean_api_df(df)

Arguments

Value

Cleaned dataframe

Allow for capitalisation of search terms

Description

Allow for capitalisation of search terms

Usage

fix_caps(x)

Arguments

Value

The same list or vector search terms, but with proper regular expression syntax to allow for capitalisation of the first letter of each term.

Replace user-friendly 'NEAR' operator with appropriate regex syntax

Description

Replace user-friendly 'NEAR' operator with appropriate regex syntax

Usage

fix_near(x)

Arguments

Replace user-friendly 'wildcard' operator with appropriate regex syntax

Description

Replace user-friendly 'wildcard' operator with appropriate regex syntax

Usage

fix_wildcard(x)

Arguments

Report the latest record date in a snapshot

Description

Report the latest record date in a snapshot

Usage

inform_snapshot_date(data)

Arguments

Value

Invisibly returns the latest snapshot date

Checks whether the user has internet, and returns a helpful message it not.

Description

Checks whether the user has internet, and returns a helpful message it not.

Usage

internet_check()

Value

Informative error if not connected to the internet

Access medRxiv/bioRxiv data via the Cold Spring Harbour Laboratory API

Description

Provides programmatic access to all preprints available through the Cold Spring Harbour Laboratory API, which serves both the medRxiv and bioRxiv preprint repositories.

Usage

mx_api_content(
  from_date = "2013-01-01",
  to_date = as.character(Sys.Date()),
  clean = TRUE,
  server = "medrxiv",
  include_info = FALSE
)

Arguments

Value

Dataframe with 1 record per row

See Also

Other data-source: mx_api_doi(), mx_snapshot()

Examples

if (interactive()) {
  mx_data <- mx_api_content(
    from_date = "2020-01-01",
    to_date = "2020-01-07"
  )
}

Access data on a single medRxiv/bioRxiv record via the Cold Spring Harbour Laboratory API

Description

Provides programmatic access to data on a single preprint identified by a unique Digital Object Identifier (DOI).

Usage

mx_api_doi(doi, server = "medrxiv", clean = TRUE)

Arguments

Value

Dataframe containing details on the preprint identified by the DOI.

See Also

Other data-source: mx_api_content(), mx_snapshot()

Examples

if (interactive()) {
  mx_data <- mx_api_doi("10.1101/2020.02.25.20021568")
}

Search term wrapper that allows for different capitalization of term

Description

Inspired by the varying capitalization of "NCOV" during the corona virus pandemic (e.g. ncov, nCoV, NCOV, nCOV), this function allows for all possible configurations of lower- and upper-case letters in your search term.

Usage

mx_caps(x)

Arguments

Value

The input string is return, but with each non-space character repeated in lower- and upper-case, and enclosed in square brackets. For example, mx_caps("ncov") returns "[Nn][Cc][Oo][Vv]"

See Also

Other helper: mx_crosscheck(), mx_download(), mx_export()

Check how up-to-date the maintained medRxiv snapshot is

Description

Provides information on how up-to-date the maintained medRxiv snapshot provided by 'mx_snapshot()' is by checking whether there have been any records added to, or updated in, the medRxiv repository since the last snapshot was taken.

Usage

mx_crosscheck()

See Also

Other helper: mx_caps(), mx_download(), mx_export()

Examples

if (interactive()) {
  mx_crosscheck()
}

Download PDF's of preprints returned by a search

Description

Download PDF's of all the papers in your search results

Usage

mx_download(
  mx_results,
  directory,
  create = TRUE,
  name = c("ID", "DOI"),
  print_update = 10
)

Arguments

See Also

Other helper: mx_caps(), mx_crosscheck(), mx_export()

Examples

if (interactive()) {
  mx_results <- mx_search(mx_snapshot(), query = "10.1101/2020.02.25.20021568")
  mx_download(mx_results, directory = tempdir())
}

Export references for preprints returning by a search to a .bib file

Description

Export references for preprints returning by a search to a .bib file

Usage

mx_export(data, file = "medrxiv_export.bib")

Arguments

Value

Exports a formatted .BIB file, for import into a reference manager

See Also

Other helper: mx_caps(), mx_crosscheck(), mx_download()

Examples

if (interactive()) {
  mx_results <- mx_search(mx_snapshot(), query = "brain")
  mx_export(mx_results, tempfile(fileext = ".bib"))
}

Provide information on the medRxiv snapshot used to perform the search

Description

Provide information on the medRxiv snapshot used to perform the search

Usage

mx_info(commit = "main", manifest_url = default_snapshot_manifest_url())

Arguments

Value

Message with snapshot details

Search and print output for individual search items

Description

Search and print output for individual search items

Usage

mx_reporter(mx_data, num_results, query, fields, deduplicate, NOT)

Arguments

See Also

Other main: mx_search(), print_full_results(), run_search()

Search preprint data

Description

Search preprint data

Usage

mx_search(
  data = NULL,
  query = NULL,
  fields = c("title", "abstract", "authors", "category", "doi"),
  from_date = NULL,
  to_date = NULL,
  auto_caps = FALSE,
  NOT = "",
  deduplicate = TRUE,
  report = FALSE
)

Arguments

See Also

Other main: mx_reporter(), print_full_results(), run_search()

Examples

if (interactive()) {
  # Using the static snapshot
  mx_results <- mx_search(data = mx_snapshot(), query = "dementia")
}

Access a static snapshot of the medRxiv repository

Description

[Available for medRxiv only] This function allows users to import a maintained static snapshot of the medRxiv repository, instead of downloading a copy from the API, which can become unavailable during peak usage times. The function reads a manifest-driven snapshot artifact from the package's GitHub release assets by default.

Usage

mx_snapshot(
  commit = "main",
  from_date = NULL,
  to_date = NULL,
  manifest_url = default_snapshot_manifest_url(),
  cache = TRUE
)

Arguments

Value

A formatted dataframe containing the data from the snapshot artifact, with reconstructed 'link_page' and 'link_pdf' columns.

See Also

Other data-source: mx_api_content(), mx_api_doi()

Search for terms in the dataset

Description

Search for terms in the dataset

Usage

print_full_results(num_results, deduplicate)

Arguments

See Also

Other main: mx_reporter(), mx_search(), run_search()

Search for terms in the dataset

Description

Search for terms in the dataset

Usage

run_search(mx_data, query, fields, deduplicate, NOT = "")

Arguments

See Also

Other main: mx_reporter(), mx_search(), print_full_results()

Skips API tests if API isn't working correctly

Description

Skips API tests if API isn't working correctly

Usage

skip_if_api_message()