R Observatory: Metrics for CohortSurvival version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CohortSurvival

1.2.1Package record

Estimate Survival from Common Data Model Cohorts

0packages dependsuggested by 3

9.2Kdownloads / year

99.5%test coverage

13/13flavors OK

Overview

About

Maintained by Kim López-GüellCRAN page ↗GitHub ↗Website ↗Issues ↗

Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.

Changes in 1.2.1

Fix SQL Server translation of configurable outcome-censoring tie handling.

From NEWS.md in the release

Install

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

install.packages("CohortSurvival", 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("darwin-eu/CohortSurvival")

Development version from darwin-eu/CohortSurvival. 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-cohortsurvival

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-CohortSurvival

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-CohortSurvival

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: 12.3 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-09-30
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-03

Show 12 earlier changesHide 12 earlier changes

ERROR12 OK, 1 ERROR2026-06-27
OK13 OK2026-06-12
ERROR12 OK, 1 ERROR2026-06-05
OK13 OK2026-06-01
ERROR12 OK, 1 ERROR2026-05-30
OK13 OK2026-05-27
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 1,653 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 1.2.1Citation fileNoWebsiteYes · pkgdown

Help pages: 17 (4 internal)includes a package overview page
Examples that run: 8%1 run in a plain check · 12 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 86%
Help pages citing references: 0%

Vignettes (4)

Competing risk survival HTML
Creating cohorts for survival analyses HTML
Further survival analyses HTML
Single outcome event of interest HTML

How these are measured

Downloads

9.2K

CRAN downloads in the past year

Rank #3,936 · ~25/day · ~766/mo

Releases R versions

Daily download trend is not available in this view yet.

84130 days

2.4K90 days

9.2K1 year

Compare downloads with other packages →

Also on140 r2u11 autocran

How downloads are counted

Repository

darwin-eu/cohortsurvival ↗Organization: darwin-eu

5Stars

1Forks

0Open issues

0Open PRs

15Releases

37Commits

3Commit identities

License file reads as Apache-2.0 · 37 commits · Last activity 2026-10-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: 206
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-17 · 42026-07-07 · 5

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/darwin-eu/cohortsurvival on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (1)

Contributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

pkgdown site last built 2026-10-21

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing CohortSurvival adds 30 packages (15 with compiled code, 22 MB of source tarballs). Heaviest: stringi 11 MB, vctrs 1.0 MB, PatientProfiles 951 KB.

Depends (1)

R >= 4.1.0

Imports (14)

broom cli clock dplyr glue omopgenerics PatientProfiles purrr rlangsurvivalstatsstringr tibble tidyr

LinkingTo (0)

none

Suggests (19)

testthat CodelistGenerator DBI dbplyr roxygen2 omock knitr tictoc rmarkdown ggplot2 patchwork cmprsk duckdb gt flextable scales visOmopResults extrafont CDMConnector

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 3

Suggests, most downloaded first

DrugUtilisation PhenotypeR OmopViewer

How these are counted

Code & Tests

People & History

People (6)

Kim López-Güell

Author, Maintainer since 1.0.0 (2025) · added in 0.6.0

Edward Burn

Author

Martí Català

Author · added in 1.1.0

Xintong Li

Author

Nuria Mercade-Besora

Author · added in 0.6.0

Danielle Newby

Author

Previously maintained by Edward Burn (0.2.5 to 0.6.2).

Listed in earlier versions (2)

Marti Catala

no longer listed · 0.2.5 to 1.0.3

Kim Lopez

no longer listed · 0.2.5 to 0.5.2

Releases (18)

Pick two releases to compare their code metrics.

1.2.1Latest
record
2026-10-21 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-21 10:55 UTC, so it stayed less than the time between readings.
1.2.0
record
2026-10-01 · diff ↗ ·
added 1 export
filterSurvivalChanges
1.1.2
record
2026-07-03 · diff ↗
1.1.1
record
2026-05-13 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.0
record
2025-12-04 · diff ↗ ·
removed 7 exports
%>%, :=, .data, as_label, as_name, enquo, enquos

added 2 exports
tableSurvivalAttrition, tableSurvivalEvents
1.0.3
record
2025-08-18 · diff ↗ ·
added 1 export
availableSurvivalGrouping
1.0.2
record
2025-06-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.1
record
2025-04-02 · diff ↗
unarchivedReturned to CRAN
2025-03-19
1.0.0
record
2025-03-19 · diff ↗ ·
removed 2 exports
addCompetingRiskCohortSurvival, generateDeathCohortSet

added 1 export
riskTable
archivedRemoved from CRAN
2025-03-07
issues were not corrected in time
0.6.2
record
2025-01-22 · diff ↗
0.6.1
record
2024-11-28 · diff ↗
0.6.0
record
2024-11-10 · diff ↗ ·
removed 2 exports
benchmarkCohortSurvival, survivalParticipants

added 8 exports
attrition, bind, cohortCodelist, cohortCount, exportSummarisedResult, importSummarisedResult, settings, suppress

Show 8 earlier eventsHide 8 earlier events

0.5.2
record
2024-06-29 · diff ↗
0.5.1
record
2024-05-18 · diff ↗ ·
removed 1 export
summariseCharacteristics
0.5.0
record
2024-05-06 · diff ↗ ·
removed 1 export
splitNameLevel

added 2 exports
addCompetingRiskCohortSurvival, optionsTableSurvival
R
R 4.4.0 released · 2024-04-24
0.4.0
record
2024-04-02 · diff ↗ ·
removed 2 exports
plotCumulativeIncidence, survivalSummary

added 2 exports
asSurvivalResult, tableSurvival
0.3.0
record
2024-02-08 · diff ↗ ·
added 1 export
splitNameLevel
0.2.5
record
2023-12-07
R
R 4.3.0 released · 2023-04-21

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2023-12-07
Total releases: 18 / 3 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.1.0
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CohortSurvival")

Format

López-Güell, K., Burn, E., Català, M., Li, X., Mercade-Besora, N., & Newby, D. (2026). CohortSurvival: Estimate Survival from Common Data Model Cohorts (Version 1.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.CohortSurvival

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 CohortSurvival version 1.2.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →