This package was removed from CRAN on 2025-12-25. Its history is shown below.

Reason: issues were not addressed in time

Details below reflect version 1.1.9, its last release before removal.

BVSNLP

1.1.9

Bayesian Variable Selection in High Dimensional Settings using Nonlocal Priors

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Amir Nikooienejad9 releasesCRAN page ↗

Variable/Feature selection in high or ultra-high dimensional settings has gained a lot of attention recently specially in cancer genomic studies. This package provides a Bayesian approach to tackle this problem, where it exploits mixture of point masses at zero and nonlocal priors to improve the performance of variable selection and coefficient estimation. product moment (pMOM) and product inverse moment (piMOM) nonlocal priors are implemented and can be used for the analyses. This package performs variable selection for binary response and survival time response datasets which are widely used in biostatistic and bioinformatics community. Benefiting from parallel computing ability, it reports necessary outcomes of Bayesian variable selection such as Highest Posterior Probability Model (HPPM), Median Probability Model (MPM) and posterior inclusion probability for each of the covariates in the model. The option to use Bayesian Model Averaging (BMA) is also part of this package that can be exploited for predictive power measurements in real datasets.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/BVSNLP/BVSNLP_1.1.9.tar.gz"
pkgFile <- "BVSNLP_1.1.9.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1.9) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-bvsnlp

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

# 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-BVSNLP

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Downloads

Releases R versions

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Also on424 r2u45 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (4)

Rcpp doParallel foreachparallel

LinkingTo (4)

Rcpp RcppArmadillo RcppEigen RcppNumerical

Suggests (1)

doMPI

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

C++ 1,940 (42%)R 1,534 (33%)Rd 1,105 (24%)C 10 (0%)

Code characteristics

Cyclomatic complexity: 1.0 median / 39 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

77 8 exported

Complexity

5.4 avg / 39 max

Call network

77 nodes / 37 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Amir Nikooienejad

Author, Maintainer

Authors (1)

Amir Nikooienejad

Author, Maintainer

Other (1)

Valen E. Johnson

Thesis advisor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-12-25
issues were not addressed in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.9
2020-08-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.8
2019-06-12 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.5
2018-05-17 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.1.0
2018-03-26 · diff ↗
0.9.10
2018-02-07 · diff ↗
0.9.8
2018-01-13 · diff ↗

Show 4 earlier events

0.9.7
2018-01-08 · diff ↗
0.9.6
2017-12-19 · diff ↗
0.9.5
2017-12-18
R
R 3.4.0 released · 2017-04-21

Package metadata

Total releases: 9
License: GPL (>= 2) OSI
Minimum R: ≥ 3.1.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet