R Observatory: Metrics for escalation version 0.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

escalation

0.2.3

A Modular Approach to Dose-Finding Clinical Trials

0packages depend

5.2Kdownloads / year

77.1%test coverage

13/13checks pass

Overview

About

Maintained by Kristian BrockFirst published 2020-03-089 releasesCRAN page ↗GitHub ↗

Methods for working with dose-finding clinical trials. We provide implementations of many dose-finding clinical trial designs, including the continual reassessment method (CRM) by O'Quigley et al. (1990) doi:10.2307/2531628, the toxicity probability interval (TPI) design by Ji et al. (2007) doi:10.1177/1740774507079442, the modified TPI (mTPI) design by Ji et al. (2010) doi:10.1177/1740774510382799, the Bayesian optimal interval design (BOIN) by Liu & Yuan (2015) doi:10.1111/rssc.12089, EffTox by Thall & Cook (2004) doi:10.1111/j.0006-341X.2004.00218.x; the design of Wages & Tait (2015) doi:10.1080/10543406.2014.920873, and the 3+3 described by Korn et al. (1994) doi:10.1002/sim.4780131802. All designs are implemented with a common interface. We also offer optional additional classes to tailor the behaviour of all designs, including avoiding skipping doses, stopping after n patients have been treated at the recommended dose, stopping when a toxicity condition is met, or demanding that n patients are treated before stopping is allowed. By daisy-chaining together these classes using the pipe operator from 'magrittr', it is simple to tailor the behaviour of a dose-finding design so it behaves how the trialist wants. Having provided a flexible interface for specifying designs, we then provide functions to run simulations and calculate dose-paths for future cohorts of patients.

Install

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

install.packages("escalation", 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("brockk/escalation")

Development version from brockk/escalation. 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-escalation

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-escalation

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-escalation

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

Health

CRAN checks

13OK

Slowest check: 24.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.67

77.1%

Coverage · measured lines

100%

Documentation · exports

21

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 3 earlier snapshots

ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 5,262 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 99%
Return-value docs: 93%
References docs: 27%

Downloads

5.2K

CRAN downloads in the past year

Rank #6,571 · ~14/day · ~436/mo

Releases R versions

Daily download trend is not available in this view yet.

29730 days

1.2K90 days

5.2K1 year

Compare downloads with other packages →

Also on150 r2u26 autocran

Repository

GitHub ↗ brockk/escalation

17Stars

5Forks

4Open issues

0Open PRs

0Releases

220Commits

6Contributors

220 commits · Last activity 2025-10-08

Stars over time

2025-05-21 · 172026-07-07 · 17

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/brockk/escalation on 2026-08-23.

Continuous integration (2)

GitHub ActionsTravis CI

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

magrittr

Imports (20)

dplyr tidyr tidyselect stringr purrr tibble ggplot2 gtools dfcrm BOIN trialr DiagrammeR RColorBrewer viridis binom R6 mvtnormgraphicsIso testthat

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Kristian Brock

Author, Maintainer

Authors (3)

Kristian Brock

Author, Maintainer

Daniel Slade

Author · added in 0.1.5

Michael Sweeting

Author · added in 0.1.8

Contributors (2)

Bharat Bhushan

Contributor · added in 0.2.3

Conor Norris

Contributor · added in 0.2.3

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.3Latest
2025-10-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.10
2024-06-27 · diff ↗
0.1.9
2024-05-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.8
2024-02-23 · diff ↗
0.1.5
2023-05-29 · diff ↗
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
0.1.4
2020-10-18 · diff ↗
0.1.3
2020-05-13 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.2
2020-04-14 · diff ↗
0.1.1
2020-03-08

Show 1 earlier events

R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-08
Total releases: 9 / 6 yrs
License: GPL (>= 3) OSI
Download size: 4.8 MB
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("escalation")

Format

Brock, K., Bhushan, B., Norris, C., Slade, D., & Sweeting, M. (2025). escalation: A Modular Approach to Dose-Finding Clinical Trials (Version 0.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.escalation

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 escalation version 0.2.3 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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