R Observatory: Metrics for beastt version 0.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

beastt

0.0.3Package record

Bayesian Evaluation, Analysis, and Simulation Software Tools for Trials

0packages dependsuggested by 1

6.8Kdownloads / year

90.2%test coverage

13/13flavors OK

Overview

About

Maintained by Christina FillmoreCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: GlaxoSmithKline Research & Development Limited

Bayesian dynamic borrowing with covariate adjustment via inverse probability weighting for simulations and data analyses in clinical trials. This makes it easy to use propensity score methods to balance covariate distributions between external and internal data. This methodology based on Psioda et al (2025) doi:10.1080/10543406.2025.2489285.

Changes in 0.0.3

Add sweet_spot_plot() to make it easier to graphically summarise simulation results
Add a number of functions to make it easier to simulate binary and time to event data
Add trim_ps() and rescale_ps() function to trim and re-scale the propensity score object
Add prop_scr_cloud() function

From NEWS.md in the release

Install

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

install.packages("beastt", 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("GSK-Biostatistics/beastt")

Development version from GSK-Biostatistics/beastt. 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-beastt

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-beastt

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-beastt

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: 15.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29

Show 7 earlier changesHide 7 earlier changes

ERROR12 OK, 1 ERROR2026-07-27
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.3

READMEYes · 492 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.0.3Citation fileNoWebsiteYes · pkgdown

Help pages: 41 (1 internal)includes a package overview page
Examples that run: 100%31 run in a plain check
Exported functions with examples: 97%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 5%

Vignettes (3)

How these are measured

Downloads

6.8K

CRAN downloads in the past year

Rank #6,155 · ~19/day · ~563/mo

Releases R versions

Daily download trend is not available in this view yet.

48230 days

1.3K90 days

6.8K1 year

Compare downloads with other packages →

Also on483 r2u50 autocran

How downloads are counted

Repository

gsk-biostatistics/beastt ↗Organization: GSK-Biostatistics

6Stars

2Forks

7Open issues

0Open PRs

3Releases

521Commits

6Commit identities

License file reads as GPL-3.0 · 521 commits · Last activity 2026-04-20 · 0% stars, 30d · Default branch at 0.0.3.9000, ahead of CRAN 0.0.3 (checked 2026-10-11) · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 24
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-10-16 · 62026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/gsk-biostatistics/beastt on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-20 · The repository has a site deploy workflow

pkgdown site last built 2026-04-20

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

Installing beastt adds 94 packages (50 with compiled code, 96 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (17)

cli cobalt distributional dplyr generics ggdist ggplot2methodsmixtools purrr Rcpp RcppParallel (>= 5.0.1)rlang rstan rstantools stringr tidyr

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (8)

knitr mvtnorm rmarkdown spelling testthat tibble vdiffrsurvival

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

shrinkr

How these are counted

Code & Tests

Datasets

People & History

People (6)

Christina Fillmore

Author, Maintainer since 0.0.1 (2024)

Ben Arancibia

Author

Nate Bean

Author

Abi Terry

Author · added in 0.0.2

GlaxoSmithKline Research & Development Limited

Copyright holder, Funder

Trustees of Columbia University

Copyright holder · added in 0.0.2

R/stanmodels.R, configure, configure.win

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.0.3Latest
record
2025-05-15 · current release · diff ↗ ·
added 14 exports
approx_mvn_at_time, avg_dist, bootstrap_cov, calc_cond_binary, calc_cond_weibull, calc_study_duration, inv_logit, prop_scr_cloud, rescale_ps, sim_accrual, sim_pw_const_haz, sim_weib_ph, sweet_spot_plot, trim_ps
R
R 4.5.0 released · 2025-04-11
0.0.2
record
2025-02-24 · diff ↗ ·
added 5 exports
calc_post_weibull, calc_power_prior_weibull, mix_means, mix_sigmas, robustify_mvnorm
0.0.1
record
2024-06-20
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-20
Total releases: 3 / 2 yrs
License: GPL (>= 3) OSI · relicensed from Apache License (>= 2) in 0.0.2
Minimum R: ≥ 4.1.0
Bundled data: 39 KB / 8 files
Download size: 766 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("beastt")

Format

Fillmore, C., GlaxoSmithKline Research & Development Limited, Arancibia, B., Bean, N., Columbia University, T. o., & Terry, A. (2025). beastt: Bayesian Evaluation, Analysis, and Simulation Software Tools for Trials (Version 0.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.beastt

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 beastt version 0.0.3 [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.

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