basket

0.10.11

Basket Trial Analysis

0packages depend

4.1Kdownloads / year

78.2%test coverage

0/13checks pass

Overview

About

Maintained by Michael J. KaneFirst published 2019-05-145 releasesCRAN page ↗GitHub ↗

Implementation of multisource exchangeability models for Bayesian analyses of prespecified subgroups arising in the context of basket trial design and monitoring. The R 'basket' package facilitates implementation of the binary, symmetric multi-source exchangeability model (MEM) with posterior inference arising from both exact computation and Markov chain Monte Carlo sampling. Analysis output includes full posterior samples as well as posterior probabilities, highest posterior density (HPD) interval boundaries, effective sample sizes (ESS), mean and median estimations, posterior exchangeability probability matrices, and maximum a posteriori MEMs. In addition to providing "basketwise" analyses, the package includes similar calculations for "clusterwise" analyses for which subgroups are combined into meta-baskets, or clusters, using graphical clustering algorithms that treat the posterior exchangeability probabilities as edge weights. In addition plotting tools are provided to visualize basket and cluster densities as well as their exchangeability. References include Hyman, D.M., Puzanov, I., Subbiah, V., Faris, J.E., Chau, I., Blay, J.Y., Wolf, J., Raje, N.S., Diamond, E.L., Hollebecque, A. and Gervais, R (2015) doi:10.1056/NEJMoa1502309; Hobbs, B.P. and Landin, R. (2018) doi:10.1002/sim.7893; Hobbs, B.P., Kane, M.J., Hong, D.S. and Landin, R. (2018) doi:10.1093/annonc/mdy457; and Kaizer, A.M., Koopmeiners, J.S. and Hobbs, B.P. (2017) doi:10.1093/biostatistics/kxx031.

Install

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

install.packages("basket", 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("kaneplusplus/basket")

Development version from kaneplusplus/basket. 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-basket

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-basket

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-basket

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 6.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.34

78.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 610 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 96%
Return-value docs: 11%
References docs: 10%

Downloads

4.1K

CRAN downloads in the past year

Rank #11,197 · ~11/day · ~340/mo

Releases R versions

Daily download trend is not available in this view yet.

29530 days

95490 days

4.1K1 year

Compare downloads with other packages →

Also on215 r2u65 autocran

Repository

GitHub ↗ kaneplusplus/basket

4Stars

3Forks

3Open issues

0Open PRs

1Releases

260Commits

5Contributors

260 commits · Last activity 2023-07-17

Stars over time

2023-07-10 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/kaneplusplus/basket on 2026-07-19.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

CRAN release process (1)

cran-comments.md

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (15)

GenSA foreach ggplot2statstibble tidyr dplyr igraph gridExtra itertools crayon cli RColorBrewer tidygraph ggraph

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat doParallel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Michael J. Kane

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Contributors (1)

Ryan Hafen

Contributor · added in 0.10.11

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.10.11Latest
2021-10-17 · current release · diff ↗
unarchivedReturned to CRAN
2021-10-17
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2021-03-21
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
0.10.2
2020-04-07 · diff ↗
0.10.1
2020-03-11 · diff ↗
0.9.10
2019-10-23 · diff ↗
0.9.2
2019-05-14
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-14
Total releases: 5 / 7 yrs
License: LGPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.7 KB / 2 files
Download size: 764 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →