psbcSpeedUp

2.1.0

Penalized Semiparametric Bayesian Cox Models

0packages depend

3Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Zhi ZhaoFirst published 2023-10-026 releasesCRAN page ↗GitHub ↗

Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 doi:10.2202/1557-4679.1301) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 doi:10.1002/bimj.201400160).

Install

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

install.packages("psbcSpeedUp", 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("ocbe-uio/psbcSpeedUp")

Development version from ocbe-uio/psbcSpeedUp. 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-psbcspeedup

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-psbcSpeedUp

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-psbcSpeedUp

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.8 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 343 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 14%

Downloads

CRAN downloads in the past year

Rank #13,171 · ~8/day · ~252/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

77690 days

3K1 year

Compare downloads with other packages →

Also on418 r2u

Repository

GitHub ↗ ocbe-uio/psbcspeedup

3Stars

1Forks

0Open issues

0Open PRs

6Releases

57Commits

2Contributors

bayesian-cox-modelsomics-datasurvival-analysisbayesian-lasso

License GPL-3.0 · 57 commits · Last activity 2025-09-30

Stars over time

2023-10-06 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ocbe-uio/psbcspeedup on 2026-07-31.

Continuous integration (1)

GitHub Actions

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (8)

Rcpp ggplot2 GGallyMASSsurvivalriskRegressionutilsstats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (1)

knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Zhi Zhao

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.1.0Latest
2025-09-30 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.7
2024-07-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.6
2024-03-21 · diff ↗
2.0.5
2023-12-08 · diff ↗
2.0.4
2023-10-12 · diff ↗
2.0.3
2023-10-02
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-02
Total releases: 6 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0
Bundled data: 52 KB / 2 files
Download size: 388 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Survival Analysis

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