R Observatory: Metrics for BSET version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BSET

1.0

A Bayesian Surrogate Evaluation Test

0packages depend

1.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Pietro CarlottiFirst published 2026-05-221 releasesCRAN page ↗GitHub ↗

An implementation of the Bayesian Surrogate Evaluation Test (BSET) for assessing the validity of surrogate markers in clinical trials. Provides hypothesis testing tools to evaluate whether a surrogate can reliably estimate the causal effect of a treatment on a primary outcome. Implements the imputation-based Bayesian methodology of Carlotti and Parast (2026) doi:10.48550/arXiv.2603.14381, extending the frequentist rank-based approach of Parast et al. (2024) doi:10.1093/biomtc/ujad035. Addresses key limitations of the frequentist method, including the lack of causal interpretability and the inability to adjust for covariates in the estimation process.

Install

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

install.packages("BSET", 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("PietroCarlotti/BSET")

Development version from PietroCarlotti/BSET. 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-bset

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-BSET

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-BSET

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

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-23
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 207 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 75%

Downloads

1.1K

CRAN downloads in the past year

Rank #8,790 · ~3/day · ~88/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

1.1K90 days

1.1K1 year

Compare downloads with other packages →

Also on23 r2u28 autocran

Repository

GitHub ↗ pietrocarlotti/bset

1Stars

0Forks

0Open issues

0Open PRs

0Releases

211Commits

1Contributors

211 commits · Last activity 2026-06-19 · 0% stars, 30d

Stars over time

2026-04-18 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/pietrocarlotti/bset on 2026-08-16.

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-04-21

claude

Most recent: claude on 2026-04-21

Evidence

claude: on or before 2026-04-21 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (9)

rstan ggplot2 futureparallelmvtnorm dplyr SurrogateRank Rdpack rlang

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown bookdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Pietro Carlotti

Author, Maintainer

Authors (2)

Pietro Carlotti

Author, Maintainer

Layla Parast

Author

Package Timeline

1 release. R releases are shown for context.

1.0Latest
2026-05-22 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-22
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 33 KB / 4 files
Download size: 827 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BSET")

Format

Carlotti, P., & Parast, L. (2026). BSET: A Bayesian Surrogate Evaluation Test (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.BSET

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 BSET version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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