R Observatory: Metrics for Cyclops version 3.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Cyclops

3.7.1Package record

Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

6packages dependsuggested by 1

17.5Kdownloads / year

75.0%test coverage

12/13flavors OK

Overview

About

Maintained by Marc A. SuchardCRAN page ↗GitHub ↗Issues ↗

This model fitting tool incorporates cyclic coordinate descent and majorization-minimization approaches to fit a variety of regression models found in large-scale observational healthcare data. Implementations focus on computational optimization and fine-scale parallelization to yield efficient inference in massive datasets. Please see: Suchard, Simpson, Zorych, Ryan and Madigan (2013) doi:10.1145/2414416.2414791.

Changes in 3.7.1

Changes:

1. more robust unit-test for bootstrapping

From NEWS.md in the release

Install

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

install.packages("Cyclops", 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("ohdsi/cyclops")

Development version from ohdsi/cyclops. 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-cyclops

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-Cyclops

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-Cyclops

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

1ERROR12OK

Check messages

ERRORtestsr-devel-linux-x86_64-debian-gcc

Running ‘testthat.R’ [168s/237s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("Cyclops")
  Loading required package: Cyclops
  Sparseness = 52.175 %
  Sorting outcomes by rowId
  Sorting covariates by covariateId and rowId
  Sorting outcomes by rowId
  Sorting covariates by covariateId and rowId
  Sparseness = 52.175 %
  Sorting outcomes by rowId
  Sorting covariates by covariateId and rowId
  Sorting outcomes by rowId
  Sorting covariates by covariateId and rowId
  Sparseness = 52.175 %
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sorting outcomes by stratumId and rowId
  Sorting covariates by covariateId, stratumId, and rowId
  Sparseness = 98.99 %
  Sorting covariates by covariateId and
...[truncated]...
ine ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `a$specials[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─survival::survfit(goldFit) at test-survfit.R:77:5
   2. └─survival:::survfit.coxph(goldFit)
   3.   └─survival:::model.matrix.coxph(object, data = mf)
   4.     └─stats::delete.response(object$terms)
   5.       └─stats (local) off(a$specials[[i]])
  ── Error ('test-survfit.R:104:5'): Check very small Cox example with failure ties, with risk-set contribution after tie, breslow baseline ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `a$specials[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─survival::survfit(goldFit) at test-survfit.R:104:5
   2. └─survival:::survfit.coxph(goldFit)
   3.   └─survival:::model.matrix.coxph(object, data = mf)
   4.     └─stats::delete.response(object$terms)
   5.       └─stats (local) off(a$specials[[i]])
  
  [ FAIL 10 | WARN 0 | SKIP 26 | PASS 328 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 14.7 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERROR2026-10-24
OK13 OK2026-09-29
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01

Show 10 earlier changesHide 10 earlier changes

OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK13 OK2026-05-02
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.7.1

READMEYes · 299 wordsVignettesNoNEWSYes · 0% structured · mentions 3.7.1Citation fileYes · cites a publication

Help pages: 62 (12 internal)includes a package overview page
Examples that run: 92%12 run in a plain check · 1 never run
Exported functions with examples: 28%
Documented parameters: 100%
Return-value docs: 56%
Help pages citing references: 2%

How these are measured

Downloads

17.5K

CRAN downloads in the past year

Rank #3,140 · ~48/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.7K30 days

4K90 days

17.5K1 year

Compare downloads with other packages →

Also on538 r2u10 autocran142 c2d4u

How downloads are counted

Repository

ohdsi/cyclops ↗Organization: OHDSI

45Stars

36Forks

20Open issues

4Open PRs

9Releases

1,679Commits

17Commit identities

hades

1,679 commits · Last activity 2026-05-26 · +2.3% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 68%
Median days to close, 50 most recently updated closed issues: 28
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-12 · 412026-10-23 · 45

How these are measured

PracticesBeta

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

Checks run against github.com/ohdsi/cyclops on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-05-28

Coverage (2)

Coverage reporting.covrignore

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-10-20
Pull request it wrote: opened by a project member

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing Cyclops adds 31 packages (19 with compiled code, 32 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 7.9 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (10)

rlangMatrixRcpp Andromeda dplyrmethodssurvivaltidyr bit bit64

LinkingTo (2)

Rcpp RcppEigen

Suggests (9)

testthat readrMASSgnm ggplot2 microbenchmark cmprskbootrsample

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

1indirect

Depends 4 · Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

PatientLevelPrediction EvidenceSynthesis CohortMethod SelfControlledCaseSeries BrokenAdaptiveRidge IterativeHardThresholding

Suggests, most downloaded first

EmpiricalCalibration

How these are counted

Code & Tests

Datasets

People & History

People (11)

Marc A. Suchard

Author, Maintainer since 1.2.0 (2016)

Eric Kawaguchi

Author · added in 3.1.0

Martijn J. Schuemie

Author

Trevor R. Shaddox

Author

Yuxi Tian

Author · added in 1.3.4

Jianxiao Yang

Author · added in 2.0.0

R Development Core Team

Copyright holder, Contributor · added in 1.3.4

provided the ZeroIn routine

Rutgers University

Copyright holder, Contributor · added in 1.3.4

provided the HParSearch routine

Marcus Geelnard

Copyright holder, Contributor · added in 1.3.4

provided the TinyThread library

Sushil Mittal

Contributor · added in 1.3.4

Observational Health Data Sciences and Informatics

Copyright holder · added in 1.3.4

Releases (25)

Pick two releases to compare their code metrics.

3.7.1Latest
record
2026-05-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.7.0
record
2026-02-28 · diff ↗
3.6.0
record
2025-07-18 · diff ↗ ·
added 3 exports
cacheCyclopsModelForJava, clearCyclopsModelCache, gradient
3.5.2
record
2025-06-24 · diff ↗
3.5.1
record
2025-04-11 · diff ↗ ·
added 1 export
testProportionality
R
R 4.5.0 released · 2025-04-11
3.5.0
record
2024-12-02 · diff ↗
3.4.1
record
2024-06-06 · diff ↗ ·
added 4 exports
aconfint, listGPUDevices, runBootstrap, setOpenCLDevice
R
R 4.4.0 released · 2024-04-24
3.4.0
record
2023-10-31 · diff ↗ ·
added 3 exports
convertToTimeVaryingCoef, createWeightBasedSearchControl, splitTime
R
R 4.3.0 released · 2023-04-21
3.3.1
record
2023-04-11 · diff ↗
3.3.0
record
2023-04-05 · diff ↗
unarchivedReturned to CRAN
2022-08-10
3.2.1
record
2022-08-10 · diff ↗

Show 26 earlier eventsHide 26 earlier events

archivedRemoved from CRAN
2022-08-08
issues were not corrected in time
3.2.0
record
2022-07-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
3.1.2
record
2021-06-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
3.1.1
record
2021-03-23 · diff ↗
3.1.0
record
2020-11-05 · diff ↗ ·
added 1 export
getFineGrayWeights
unarchivedReturned to CRAN
2020-06-06
3.0.0
record
2020-06-06 · diff ↗ ·
removed 1 export
isSorted
archivedRemoved from CRAN
2020-06-05
policy violation Call to std::terminate in C++ code
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2020-04-11
2.0.3
record
2020-04-11 · diff ↗ ·
added 1 export
getCyclopsProfileLogLikelihood
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
2.0.2
record
2019-03-17 · diff ↗
2.0.1
record
2018-09-23 · diff ↗
2.0.0
record
2018-09-19 · diff ↗ ·
removed 1 export
printMatrixMarket

added 1 export
getFloatingPointSize
1.3.4
record
2018-06-15 · diff ↗ ·
added 2 exports
createNonSeparablePrior, getUnivariableSeparability
1.3.2
record
2018-05-04 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.3.0
record
2017-08-24 · diff ↗ ·
removed 1 export
createAbridgePrior

added 4 exports
createAutoGridCrossValidationControl, createParameterizedPrior, meanLinearPredictor, printMatrixMarket
R
R 3.4.0 released · 2017-04-21
1.2.2
record
2016-10-06 · diff ↗ ·
added 1 export
createAbridgePrior
1.2.0
record
2016-08-01
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-08-01
Total releases: 25 / 10 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.6 KB / 1 file
Download size: 520 KB

Appears in task views

Survival Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("Cyclops")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1145/2414416.2414791.

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 Cyclops version 3.7.1 [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.

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