BayesSurvive

0.1.0

Bayesian Survival Models for High-Dimensional Data

0packages depend

2.8Kdownloads / year

74.8%test coverage

13/13checks pass

Overview

About

Maintained by Zhi ZhaoFirst published 2024-04-233 releasesCRAN page ↗GitHub ↗

An implementation of Bayesian survival models with graph-structured selection priors for sparse identification of omics features predictive of survival (Madjar et al., 2021 doi:10.1186/s12859-021-04483-z) and its extension to use a fixed graph via a Markov Random Field (MRF) prior for capturing known structure of omics features, e.g. disease-specific pathways from the Kyoto Encyclopedia of Genes and Genomes database (Hermansen et al., 2025 doi:10.48550/arXiv.2503.13078).

Install

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

install.packages("BayesSurvive", 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/BayesSurvive")

Development version from ocbe-uio/BayesSurvive. 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-bayessurvive

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-BayesSurvive

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-BayesSurvive

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

Health

CRAN checks

13OK

Slowest check: 13.5 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.13

74.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 327 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 8%

Downloads

2.8K

CRAN downloads in the past year

Rank #13,352 · ~8/day · ~234/mo

Releases R versions

Daily download trend is not available in this view yet.

24930 days

77790 days

2.8K1 year

Compare downloads with other packages →

Also on422 r2u

Repository

GitHub ↗ ocbe-uio/bayessurvive

4Stars

0Forks

5Open issues

0Open PRs

3Releases

162Commits

2Contributors

bayesian-cox-modelsbayesian-variable-selectiongraph-learningomics-data-integrationsurvival-analysishigh-dimensional-statistics

License GPL-3.0 · 162 commits · Last activity 2025-09-18 · 0% stars, 30d

Stars over time

2025-06-12 · 32026-07-07 · 4

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/ocbe-uio/bayessurvive on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (9)

Rcpp ggplot2 GGally mvtnormsurvivalriskRegressionutilsstatsmethods

LinkingTo (3)

Rcpp RcppArmadillo testthat

Suggests (3)

knitr testthatMatrix

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Zhi Zhao

Author, Maintainer

Authors (4)

Zhi Zhao

Author, Maintainer

Waldir Leoncio

Author · added in 0.1.0

Katrin Madjar

Author

Tobias Østmo Hermansen

Author

Contributors (2)

Jörg Rahnenführer

Contributor

Manuela Zucknick

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.0Latest
2025-03-25 · current release · diff ↗
0.0.2
2024-06-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.0.1
2024-04-23
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-23
Total releases: 3 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 609 KB / 1 file
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Survival Analysis

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