R Observatory: Metrics for OncoBayes2 version 0.10-0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OncoBayes2

0.10-0

Bayesian Logistic Regression for Oncology Dose-Escalation Trials

0packages depend

5.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Sebastian WeberFirst published 2019-08-2923 releasesCRAN page ↗GitHub ↗

Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive oncology Phase I dose-escalation trials which involve an arbitrary number of drugs. Please refer to Neuenschwander et al. (2008) doi:10.1002/sim.3230 and Neuenschwander et al. (2016) doi:10.1080/19466315.2016.1174149 for details on the methodology.

Install

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

install.packages("OncoBayes2", 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("Novartis/OncoBayes2")

Development version from Novartis/OncoBayes2. 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-oncobayes2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-OncoBayes2

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-OncoBayes2

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 12.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.97

not tracked

Coverage

100%

Documentation · exports

23

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 87%
Return-value docs: 82%
References docs: 26%

Downloads

5.3K

CRAN downloads in the past year

Rank #4,447 · ~15/day · ~443/mo

Releases R versions

Daily download trend is not available in this view yet.

46330 days

1.8K90 days

5.3K1 year

Compare downloads with other packages →

Also on428 r2u28 autocran

Repository

GitHub ↗ novartis/oncobayes2

4Stars

3Forks

0Open issues

1Open PRs

2Releases

47Commits

2Contributors

License GPL-3.0 · 47 commits · Last activity 2026-08-04 · 0% stars, 30d

Stars over time

2025-10-14 · 12026-08-06 · 4

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/novartis/oncobayes2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Makefile

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

35 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0RBesT

Imports (22)

methodsRcpp RcppParallel rstan (>= 2.32.0)rstantools posterior assertthat checkmate Formula bayesplot (>= 1.4.0)dplyr tibble tidyr abind rlang tidyselectutilsstatsmatrixStats lifecyclegrDevicesRdpack

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.32.0)

Suggests (10)

rmarkdown knitr testthat withr mvtnorm vdiffr cmdstanr ggplot2 scales ragg

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Sebastian Weber

Author, Maintainer

Authors (3)

Sebastian Weber

Author, Maintainer

Andrew Bean

Author

Lukas A. Widmer

Author · added in 0.5-3

Copyright holders (2)

Trustees of Columbia University

Copyright holder

Novartis Pharma AG

Copyright holder

Package Timeline

23 releases. Pick two to compare their code metrics. R releases are shown for context.

0.10-0Latest
2026-08-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.9-4
2025-12-18 · diff ↗
0.9-3
2025-04-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.9-2
2025-04-07 · diff ↗
0.9-1
2025-03-17 · diff ↗
0.9-0
2025-03-02 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.8-9
2023-07-20 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.8-8
2023-03-03 · diff ↗
0.8-7
2022-08-25 · diff ↗
0.8-6
2022-05-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.8-5
2022-03-01 · diff ↗

Show 15 earlier events

0.8-4
2022-02-18 · diff ↗
0.8-2
2021-09-14 · diff ↗
0.8-1
2021-09-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.7-0
2021-05-07 · diff ↗
0.6-5
2020-05-07 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.6-4
2020-04-07 · diff ↗
0.6-3
2020-03-19 · diff ↗
0.6-0
2020-02-11 · diff ↗
0.5-8
2019-12-12 · diff ↗
0.5-4
2019-11-19 · diff ↗
0.5-3
2019-11-15 · diff ↗
0.4-4
2019-08-29
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-29
Total releases: 23 / 7 yrs
License: GPL (>= 3) OSI
Additional repositories: stan-dev.r-universe.dev
Minimum R: ≥ 3.5.0
Bundled data: 2.1 KB / 6 files
Download size: 597 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Clinical Trial Design, Monitoring, Analysis and Reporting

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OncoBayes2")

Format

Weber, S., Bean, A., Columbia University, T. o., Pharma AG, N., & Widmer, L. A. (2026). OncoBayes2: Bayesian Logistic Regression for Oncology Dose-Escalation Trials (Version 0.10-0) [Computer software]. https://doi.org/10.32614/CRAN.package.OncoBayes2

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 OncoBayes2 version 0.10-0 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, 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 →