R Observatory: Metrics for medrxivr version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

medrxivr

0.1.4Package record

Access and Search MedRxiv and BioRxiv Preprint Data

0packages depend

2.2Kdownloads / year

100.0%test coverage

13/13flavors OK

Overview

About

Maintained by Yaoxiang LiCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.1.4

Isolated snapshot-cache tests so package checks do not leave files in the user cache directory.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("medrxivr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/medrxivr")

Development version from ropensci/medrxivr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-medrxivr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-medrxivr

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-medrxivr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK6 OK2026-05-08

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.4

READMEYes · 846 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.4Citation fileNoWebsiteYes · pkgdown

Help pages: 24 (13 internal)includes a package overview page
Examples that run: 100%6 run in a plain check (6 of them under a condition)
Exported functions with examples: 75%
Documented parameters: 98%
Return-value docs: 63%
Help pages citing references: 0%

Vignettes (1)

medrxivr

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #8,350 · ~6/day · ~186/mo

Releases R versions

Daily download trend is not available in this view yet.

46430 days

1.1K90 days

2.2K1 year

Compare downloads with other packages →

Also on80 r2u6 autocran1.2K conda_forge

How downloads are counted

Repository

ropensci/medrxivr ↗Organization: ropensci

65Stars

9Forks

0Open issues

1Open PRs

1Releases

62Commits

2Commit identities

evidence-synthesissystematic-reviewsbibliographic-databaserstatsr-packagerpreprint-recordsmedrxiv-data

62 commits · Last activity 2026-08-09 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 79%
Median days to close, 50 most recently updated closed issues: 86
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-24 · 592026-09-06 · 65

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/ropensci/medrxivr on 2026-10-11.

Continuous integration (3)

GitHub ActionsR CMD check workflowAppVeyor

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (4)

Code of conduct (inherited from ropensci)Contributing guideIssue templatesPR template

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2020-09-17

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing medrxivr adds 36 packages (22 with compiled code, 28 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, Rcpp 1.8 MB.

Depends (1)

R >= 4.1.0

Imports (13)

methodsdplyr curl jsonlite httr stringr rlang bib2df tibble progress lubridate purrr data.table

LinkingTo (0)

none

Suggests (6)

testthat knitr rmarkdown covr kableExtra spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Yaoxiang Li

Author, Maintainer since 0.1.1 (2024) · added in 0.1.1

Author

Author

Reviewer

Reviewer

Previously maintained by Luke McGuinness (0.0.3 to 0.0.5).

Releases (6)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-05-07
0.1.4Latest
record
2026-05-07 · current release · diff ↗
0.1.3
record
2026-05-07 · diff ↗
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-05-27
policy violation On Internet access
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2024-10-04
0.1.1
record
2024-10-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-03
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.0.5
record
2021-02-24 · diff ↗ ·
added 1 export
mx_caps
0.0.4
record
2020-12-11 · diff ↗
0.0.3
record
2020-09-28

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-28
Total releases: 6 / 6 yrs
License: GPL-2 OSI · relicensed from MIT + file LICENSE in 0.1.1
Minimum R: ≥ 4.1.0
Download size: 964 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("medrxivr")

Format

Li, Y., Jahn, N., McGuinness, L., Schmidt, L., & Sonkkila, T. (2026). medrxivr: Access and Search MedRxiv and BioRxiv Preprint Data (Version 0.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.medrxivr

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for medrxivr version 0.1.4 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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