R Observatory: Metrics for hsstan version 0.8.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hsstan

0.8.2Package record

Hierarchical Shrinkage Stan Models for Biomarker Selection

0packages dependsuggested by 1

3.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Marco ColomboCRAN page ↗GitHub ↗Issues ↗

Linear and logistic regression models penalized with hierarchical shrinkage priors for selection of biomarkers (or more general variable selection), which can be fitted using Stan (Carpenter et al. (2017) doi:10.18637/jss.v076.i01). It implements the horseshoe and regularized horseshoe priors (Piironen and Vehtari (2017) doi:10.1214/17-EJS1337SI), as well as the projection predictive selection approach to recover a sparse set of predictive biomarkers (Piironen, Paasiniemi and Vehtari (2020) doi:10.1214/20-EJS1711).

Changes in 0.8.2

Smaller Changes and Bug Fixes

Update deprecated syntax for future rstan compatibility (thanks to Andrew Johnson for the patch).

From NEWS.md in the release

Install

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

install.packages("hsstan", 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("mcol/hsstan")

Development version from mcol/hsstan. 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-hsstan

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-hsstan

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-hsstan

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: 19.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.2

READMEYes · 194 wordsVignettesNoNEWSYes · 100% structured · mentions 0.8.2Citation fileNoWebsitenot declared in DESCRIPTION

Description cites a JSS article

Help pages: 21 (3 internal)includes a package overview page
Examples that run: 80%12 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 10%

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #11,914 · ~10/day · ~306/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

93190 days

3.7K1 year

Compare downloads with other packages →

Also on372 r2u3 autocran42 c2d4u

How downloads are counted

Repository

mcol/hsstan ↗Account: mcol

7Stars

3Forks

0Open issues

1Open PRs

0Releases

307Commits

2Commit identities

bayesianfeature-selectionmcmcr-package

License file reads as GPL-3.0 · 307 commits · Last activity 2025-08-27 · Default branch at 0.8.2.9000, ahead of CRAN 0.8.2 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 126

How these are measured

PracticesBeta

Checks run against github.com/mcol/hsstan on 2026-10-25.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing hsstan adds 49 packages (23 with compiled code, 44 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, loo 2.7 MB.

Depends (1)

R >= 3.6

Imports (10)

ggplot2 looparallelpROC Rcppmethodsrstan rstantoolsstatsutils

LinkingTo (6)

BH Rcpp RcppEigen (>= 0.3.3.4.0)RcppParallel StanHeaders rstan

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

nestedcv

How these are counted

Code & Tests

Datasets

People & History

People (3)

Marco Colombo

Author, Maintainer since 0.6 (2019)

Paul McKeigue

Author

Athina Spiliopoulou

Contributor

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
0.8.2Latest
record
2024-01-13 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.8.1
record
2021-09-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.8
record
2020-06-29 · diff ↗
0.7
record
2020-05-01 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.6
record
2019-09-22
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-09-22
Total releases: 5 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6
Bundled data: 157 KB / 1 file
Download size: 196 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hsstan")

Format

Colombo, M., McKeigue, P., & Spiliopoulou, A. (2024). hsstan: Hierarchical Shrinkage Stan Models for Biomarker Selection (Version 0.8.2) [Computer software]. https://doi.org/10.32614/CRAN.package.hsstan

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 hsstan version 0.8.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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