R Observatory: Metrics for crmPack version 2.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

crmPack

2.3.0Package record

Object-Oriented Implementation of Dose Escalation Designs

0packages depend

6.2Kdownloads / year

78.5%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel Sabanés BovéCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Bayer AG, F. Hoffmann-La Roche AG and 2 more

Implements a wide range of dose escalation designs. The focus is on model-based designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy to setup a new design with custom JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules. Further details are presented in Sabanés Bové et al. (2019) doi:10.18637/jss.v089.i10.

Changes in 2.3.0

New Features

Added StoppingDoseStabilized, a stopping rule that stops when the current next best dose has been administered to a prespecified number of consecutive cohorts.
Additional plotting options for one-dimensional nextBest methods are available, including log and equally spaced factor dose scales, lollipop layers instead of bars, and dose-grid or regularly spaced axis ticks.

Enhancements

HierarchicalModel now compiles exchangeable normal priors in non-centered form for JAGS, including analytic Cholesky transformations for correlated parameter pairs. Non-centered hypermean nodes use a reserved z_mu_ prefix so pool names such as "x" and "x_z" cannot generate conflicting JAGS nodes. In the comparison_decider example, this increased the minimum effective sample size across monitored parameters from approximately 450 to 47,000 for 100,000 retained draws, without increasing runtime.

Show all changes in 2.3.0Hide the rest of the changes in 2.3.0

HierarchicalModel and HierarchicalDesign now support exchangeable "eta" pools for TwoDrugsCombo arms. Each combination arm retains its own interaction parameter while sharing hyperparameters, and singleton interaction pools are supported so that the same hierarchical marginal prior can be used with one combination arm.

Miscellaneous

Next-dose probability plots now identify the increment, safety, and overdose rules and the recommended dose in legends. It is also possible to use a triangle to mark the highest safe dose. Multi-panel plots put overdose information first and align their plotting areas.
Extended GeneralSimulationsSummary with a true_mtd slot and enhanced summary plotting accordingly.
Extended Simulations and SimulationsSummary classes with overdose probability at the final selected dose.
Simulation trajectory plots now use stepped blue ribbons to show the minimum and maximum and interquartile ranges alongside the median, with a legend and patient-axis ticks inferred from cohort boundaries. Patient tick positions can also be supplied with the new patient_scale argument.
Minor grid lines are suppressed when dose-grid or factor axes are used, making next-dose and simulation plots easier to read.
The dependency ggplot2 package now needs to have minimum version 3.2.0 instead of previously 3.0.0. This should not be a practical restriction because version 3.2.0 was already released in 2019.

Bug Fixes

examine() for DADesign now identifies the current cohort in cohort and lists one cohort index per additional hypothetical DLT in DLT_cohorts. The numeric DLTsearly_1 column has been replaced by DLT_scenario, with values "no additional DLTs", "late DLTs", and "early DLTs". DLT_time includes the onset time of each hypothetical DLT relative to its cohort start and is aligned with DLT_cohorts. Documentation now explains the scenario allocations and that DLTs can include patients from earlier cohorts. The method also correctly counts eligible patients, evaluates both timing scenarios without duplicate allocations, and advances using only the current cohort's zero-DLT recommendation. These fixes remove replacement-length warnings and correct the no-increment stopping logic.

From NEWS.md in the release

Install

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

install.packages("crmPack", 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("openpharma/crmPack")

Development version from openpharma/crmPack. 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-crmpack

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-crmPack

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-crmPack

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: 11.1 min · r-release-windows-x86_64

Status changes

OK13 OK2026-10-14
ERROR10 OK, 3 ERROR2026-10-05
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
ERROR8 OK, 1 NOTE, 4 ERROR2026-07-27

Show 5 earlier changesHide 5 earlier changes

NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.0

README· In the repository, left out of the releaseVignettesYes · 16 · staticNEWSYes · 100% structured · mentions 2.3.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JSS article

Help pages: 433 (78 internal)includes a package overview page
Examples that run: 100%226 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 72%
Documented parameters: 98%
Return-value docs: 29%
Help pages citing references: 3% with a bibliography file

Vignettes (16)

Show 6 moreHide 6 vignettes

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #4,685 · ~17/day · ~520/mo

Releases R versions

Daily download trend is not available in this view yet.

84330 days

1.8K90 days

6.2K1 year

Compare downloads with other packages →

Also on232 r2u8 autocran157 c2d4u

How downloads are counted

Repository

openpharma/crmpack ↗Organization: openpharma

22Stars

14Forks

80Open issues

4Open PRs

6Releases

995Commits

31Commit identities

995 commits · Last activity 2026-10-19 · 0% stars, 30d · The default branch showed an older version (2.2.1.9000) than CRAN on 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 115
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-21 · 222026-07-07 · 22

How these are measured

PracticesBeta

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

Checks run against github.com/openpharma/crmpack on 2026-10-18.

Continuous integration (1)

GitHub Actions

Governance and community (3)

Issue templatesPR templateCODEOWNERS

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-24

pkgdown site last built 2026-09-24, before release 2.3.0 (2026-10-11)

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

Reproducibility and dev environment (1)

Dev Container

Lint, format, editor (5)

lintrjarlAirVS CodeRStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-07-06
Pull request: opened by its own account
Codexfirst seen 2026-09-18
Seen in the repository: .codex

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing crmPack adds 68 packages (36 with compiled code, 50 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (3)

R >= 4.1.0ggplot2graphics

Imports (21)

checkmate dplyr futile.logger GenSA gridExtra kableExtra knitr lifecycle magrittrmethodsmvtnormparallelparallelly Rdpack rjags rlangsurvivaltibble tidyselecttoolsutils

LinkingTo (0)

none

Suggests (13)

bookdown broom covr data.tree DiagrammeR ggmcmc quarto rmarkdown stringr testthat tidyr vdiffr withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (21)

Daniel Sabanés Bové

Author, Maintainer · added in 2.1.0

Robert Adams

Author · added in 2.0.0

Clara Beck

Author · added in 2.0.0

Oliver Boix

Author · added in 2.0.0

Prerana Chandratre

Author · added in 2.0.0

Burak Kuersad Guenhan

Author · added in 2.0.0

Thomas Jaki

Author

Doug Kelkhoff

Author · added in 2.0.0

John Kirkpatrick

Author · added in 2.0.0

Dimitris Kontos

Author · added in 2.0.0

Ziwei Liao

Author · added in 2.0.0

Giuseppe Palermo

Author

Guanya Peng

Author · added in 2.0.0

Marlene Schulte-Goebel

Author · added in 2.0.0

Wojciech Wójciak

Author · added in 2.0.0

Wai Yin Yeung

Author

Jiawen Zhu

Author · added in 2.0.0

Bayer AG

Copyright holder, Funder · added in 2.0.0

F. Hoffmann-La Roche AG

Copyright holder, Funder · added in 2.0.0

Merck Healthcare KGaA

Copyright holder, Funder · added in 2.0.0

RPACT GmbH

Copyright holder, Funder · added in 2.0.0

Maintainer since 1.0.2 (2022), previously Giuseppe Palermo (0.2.9 to 1.0.0) and Daniel Sabanes Bove (0.1.5 to 0.2.7)

Listed in earlier versions (1)

Daniel Sabanes Bove

no longer listed · 0.1.5 to 2.0.2

Releases (23)

Pick two releases to compare their code metrics.

2.3.0Latest
record
2026-10-11 · current release · diff ↗ ·
added 3 exports
.DefaultStoppingDoseStabilized, .StoppingDoseStabilized, StoppingDoseStabilized
2.2.1
record
2026-07-27 · diff ↗
2.2.0
record
2026-07-05 · diff ↗ ·
added 69 exports
.ArmCondition, .ArmConditionAll, .ArmConditionAny, .ArmConditionList, .ArmFinishedCondition, .ArmMinDoseCondition, .ComboSimulations, .ComboSimulationsSummary, .DataCombo, .DefaultArmCondition, .DefaultArmConditionAll, .DefaultArmConditionAny, .DefaultArmConditionList, .DefaultArmFinishedCondition, .DefaultArmMinDoseCondition, .DefaultComboSimulations, .DefaultComboSimulationsSummary, .DefaultDataCombo, .DefaultDesignArm, .DefaultDesignCombo, .DefaultHierarchicalData, .DefaultHierarchicalDesign, .DefaultHierarchicalModel, .DefaultHierarchicalSamples, .DefaultHierarchicalSimulations, .DefaultHierarchicalSimulationsSummary, .DefaultIncrementsComboCartesian, .DefaultIncrementsComboOneDrugOnly, .DefaultNoArmCondition, .DefaultTITELogisticLogNormalSub and 39 more
R
R 4.6.0 released · 2026-04-24
2.1.0
record
2026-01-30 · diff ↗ ·
added 37 exports
.Backfill, .CohortSizeRandom, .DefaultBackfill, .DefaultCohortSizeRandom, .DefaultOpening, .DefaultOpeningAll, .DefaultOpeningAny, .DefaultOpeningList, .DefaultOpeningMinCohorts, .DefaultOpeningMinDose, .DefaultOpeningMinResponses, .DefaultOpeningNone, .DefaultRecruitment, .DefaultRecruitmentRatio, .DefaultRecruitmentUnlimited, .Opening, .OpeningAll, .OpeningAny, .OpeningList, .OpeningMinCohorts, .OpeningMinDose, .OpeningMinResponses, .OpeningNone, .Recruitment, .RecruitmentRatio, .RecruitmentUnlimited, Backfill, CohortSizeRandom, OpeningAll, OpeningAny and 7 more
2.0.2
record
2026-01-08 · diff ↗
2.0.1
record
2025-12-04 · diff ↗
2.0.0
record
2025-11-29 · diff ↗ ·
removed 17 exports
%~%, .AllModels, .IncrementMin, .IncrementsNumDoseLevels, .Model, .StoppingGstarCIRatio, ExpEff, IncrementMin, IncrementsNumDoseLevels, StoppingGstarCIRatio, biomLevel, getMinInfBeta, matchTolerance, multiplot, sampleSize, setSeed, writeModel

added 283 exports
%>%, .CohortSizeOrdinal, .CrmPackClass, .DADesign, .DALogisticLogNormal, .DASimulations, .DataDA, .DataGrouped, .DataOrdinal, .DefaultCohortSize, .DefaultCohortSizeConst, .DefaultCohortSizeDLT, .DefaultCohortSizeMax, .DefaultCohortSizeMin, .DefaultCohortSizeOrdinal, .DefaultCohortSizeParts, .DefaultCohortSizeRange, .DefaultDADesign, .DefaultDALogisticLogNormal, .DefaultDASimulations, .DefaultData, .DefaultDataDA, .DefaultDataDual, .DefaultDataGeneral, .DefaultDataGrouped, .DefaultDataMixture, .DefaultDataOrdinal, .DefaultDataParts, .DefaultDesign, .DefaultDesignGrouped and 253 more
R
R 4.5.0 released · 2025-04-11
1.0.6
record
2024-06-26 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.5
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2024-02-04 · diff ↗
1.0.4
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2024-01-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.3
record
2022-09-03 · diff ↗ ·
added 78 exports
.AllModels, .CohortSizeConst, .CohortSizeDLT, .CohortSizeMax, .CohortSizeMin, .CohortSizeParts, .CohortSizeRange, .Data, .DataDual, .DataMixture, .DataParts, .Design, .DualDesign, .DualEndpoint, .DualEndpointBeta, .DualEndpointEmax, .DualEndpointRW, .DualResponsesDesign, .DualResponsesSamplesDesign, .DualSimulations, .DualSimulationsSummary, .EffFlexi, .Effloglog, .GeneralData, .GeneralModel, .GeneralSimulations, .GeneralSimulationsSummary, .IncrementMin, .IncrementsNumDoseLevels, .IncrementsRelative and 48 more
1.0.2
record
2022-04-25 · diff ↗

Show 21 earlier eventsHide 21 earlier events

R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2019-06-13 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.2.9
record
2018-12-21 · diff ↗ ·
added 1 export
IncrementsNumDoseLevels
R
R 3.5.0 released · 2018-04-23
0.2.7
record
2018-03-13 · diff ↗
unarchivedReturned to CRAN
2018-02-16
0.2.6
record
2018-02-16 · diff ↗ ·
added 3 exports
%~%, IncrementMin, matchTolerance
archivedRemoved from CRAN
2018-01-27
it depends on the archived 'BayesLogit'
0.2.1
record
2017-05-03 · diff ↗ ·
added 2 exports
ProbitLogNormal, probit
R
R 3.4.0 released · 2017-04-21
0.2.0
record
2016-07-16 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.1.9
record
2016-02-29 · diff ↗ ·
added 1 export
multiplot
0.1.8
record
2016-02-17 · diff ↗
0.1.7
record
2016-01-26 · diff ↗
0.1.6
record
2015-12-22 · diff ↗ ·
removed 2 exports
StoppingGstarsamplesCIRatio, StoppingTDsamplesCIRatio

added 3 exports
DataMixture, LogisticLogNormalMixture, StoppingHighestDose
0.1.5
record
2015-11-12
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-11-12
Total releases: 23 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Download size: 7.8 MB

Appears in task views

Clinical Trial Design, Monitoring, Analysis and Reporting Design of Experiments (DoE) & Analysis of Experimental Data

Cite

Cite this package

Run in R for the authors' entry:

citation("crmPack")

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

It points to 10.18637/jss.v089.i10.

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 crmPack version 2.3.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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