R Observatory: Metrics for basket version 0.10.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

basket

0.10.11Package record

Basket Trial Analysis

0packages depend

4Kdownloads / year

78.2%test coverage

0/13flavors OK

Overview

About

Maintained by Michael J. KaneCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) basket-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basket-package.Rd:40
...[truncated]...
bility
       |                     ^
checkRd: (-1) plot_pep.Rd:33: Lost braces
    33 |  \item{[tile_color]}{A text string setting the color of the edges of the
       |       ^
checkRd: (-1) plot_pep.Rd:33-34: Lost braces
    33 |  \item{[tile_color]}{A text string setting the color of the edges of the
       |                     ^
checkRd: (-1) plot_pep.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_pep.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_pep.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_pep.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_pep.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_pep.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vemu.Rd:20: Lost braces; missing escapes or markup?
    20 | concluded that nonmelanoma tumor types harboring $BRAF^{V600}$ mutations
       |                                                        ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Michael J. Kane <michael.kane@yale.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 4.6 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.10.11

READMEYes · 610 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 0.10.11Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites an R Journal article

Help pages: 20includes a package overview page
Examples that run: 0%14 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 83%
Documented parameters: 96%
Return-value docs: 11%
Help pages citing references: 10%

Vignettes (1)

Using the basket Package

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #8,306 · ~11/day · ~334/mo

Releases R versions

Daily download trend is not available in this view yet.

44430 days

1.1K90 days

4K1 year

Compare downloads with other packages →

Also on105 r2u24 autocran

How downloads are counted

Repository

kaneplusplus/basket ↗Account: kaneplusplus

4Stars

3Forks

3Open issues

0Open PRs

1Releases

260Commits

5Commit identities

260 commits · Last activity 2023-07-17 · 0% stars, 30d · Default branch at 0.12.2, ahead of CRAN 0.10.11 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-07-10 · 42026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/kaneplusplus/basket on 2026-10-11.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

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

Governance and community (1)

Code of conduct

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing basket adds 52 packages (31 with compiled code, 49 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Michael J. Kane

Author, Maintainer since 0.9.2 (2019)

Author

Author

Author

Contributor · added in 0.10.11

Releases (5)

Pick two releases to compare their code metrics.

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
unarchivedReturned to CRAN
2021-10-17
0.10.11Latest
record
2021-10-17 · current release · diff ↗
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
record
2020-04-07 · diff ↗
0.10.1
record
2020-03-11 · diff ↗ ·
added 2 exports
get_seed, plot_pep_graph
0.9.10
record
2019-10-23 · diff ↗ ·
added 2 exports
basket, cluster_membership
0.9.2
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("basket")

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

It points to 10.32614/rj-2021-020.

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 basket version 0.10.11 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, 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 →