mashr

0.2.79

Multivariate Adaptive Shrinkage

2packages depend

14.9Kdownloads / year

57.6%test coverage

11/13checks pass

Overview

About

Maintained by Peter CarbonettoFirst published 2020-06-096 releasesCRAN page ↗GitHub ↗

Implements the multivariate adaptive shrinkage (mash) method of Urbut et al (2019) DOI:10.1038/s41588-018-0268-8 for estimating and testing large numbers of effects in many conditions (or many outcomes). Mash takes an empirical Bayes approach to testing and effect estimation; it estimates patterns of similarity among conditions, then exploits these patterns to improve accuracy of the effect estimates. The core linear algebra is implemented in C++ for fast model fitting and posterior computation.

Install

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

install.packages("mashr", 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("stephenslab/mashr")

Development version from stephenslab/mashr. 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-mashr

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-mashr

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 7.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 3.78

57.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 438 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 98%
Return-value docs: 61%
References docs: 2%

Downloads

14.9K

CRAN downloads in the past year

Rank #3,811 · ~41/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

90430 days

2.7K90 days

14.9K1 year

Compare downloads with other packages →

Also on672 r2u6.9K conda_forge

Repository

GitHub ↗ stephenslab/mashr

99Stars

21Forks

59Open issues

0Open PRs

11Releases

906Commits

9Contributors

906 commits · Last activity 2024-11-07 · 0% stars, 30d

Stars over time

2025-04-30 · 912026-07-07 · 99

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/stephenslab/mashr on 2026-07-19.

Continuous integration (1)

Travis CI

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.3.0ashr

Imports (9)

assertthatutilsstatsplyr rmeta Rcpp mvtnorm abind softImpute

LinkingTo (3)

Rcpp RcppArmadillo RcppGSL

Suggests (10)

MASSREBayes corrplot testthat kableExtra knitr rmarkdown profmem flashier ebnm

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

limorhyde2 mr.mashr

Code & Tests

People & History

People (9)

Maintainer (1)

Peter Carbonetto

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Contributors (1)

Contributor

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
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.79Latest
2023-10-18 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.69
2022-12-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.57
2022-01-25 · diff ↗
0.2.50
2021-05-24 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.38
2020-06-19 · diff ↗
0.2.28
2020-06-09
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-09
Total releases: 6 / 6 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.3.0
Download size: 517 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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