R Observatory: Metrics for ashr version 2.2-63

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ashr

2.2-63Package record

Methods for Adaptive Shrinkage, using Empirical Bayes

7packages dependsuggested by 4

107.9Kdownloads / year

60.9%test coverage

13/13flavors OK

Overview

About

Maintained by Peter CarbonettoCRAN page ↗GitHub ↗Issues ↗

The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", DOI:10.1093/biostatistics/kxw041. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).

Install

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

install.packages("ashr", 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("stephens999/ashr")

Development version from stephens999/ashr. 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-ashr

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-ashr

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-ashr

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: 5.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2-63

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 2.2-63Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 99includes a package overview page
Examples that run: 100%20 run in a plain check
Exported functions with examples: 28%
Documented parameters: 92%
Return-value docs: 49%
Help pages citing references: 0%

Vignettes (1)

Illustration of Adaptive Shrinkage

How these are measured

Downloads

107.9K

CRAN downloads in the past year

Rank #1,132 · ~296/day · ~9K/mo

Releases R versions

Daily download trend is not available in this view yet.

10.2K30 days

31.6K90 days

107.9K1 year

Compare downloads with other packages →

Also on1.5K r2u38 autocran90.4K conda_forge111 c2d4u

How downloads are counted

Repository

stephens999/ashr ↗Account: stephens999

88Stars

37Forks

44Open issues

4Open PRs

10Releases

706Commits

23Commit identities

License file reads as GPL-3.0 · 706 commits · Last activity 2026-05-04 · 0% stars, 30d · Default branch at 2.2-69, ahead of CRAN 2.2-63 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 12
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-17 · 852026-07-07 · 88

How these are measured

PracticesBeta

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

Checks run against github.com/stephens999/ashr on 2026-10-21.

Continuous integration (2)

Travis CI (config file)AppVeyor

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing ashr adds 8 packages (5 with compiled code, 6.1 MB of source tarballs). Heaviest: invgamma 2.5 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (1)

R >= 3.1.0

Imports (9)

MatrixstatsgraphicsRcpp truncnorm mixsqp SQUAREM etrunct invgamma

LinkingTo (1)

Rcpp

Suggests (5)

testthat knitr rmarkdown ggplot2 REBayes

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

7direct

3indirect

Depends 1 · Imports 6

Suggested by 4

Depends, Imports or LinkingTo, most downloaded first

mashr fastTopics ebnm ldsep limorhyde2 MixTwice smashr

Suggests, most downloaded first

ncvreg colocboost palasso flashier

How these are counted

Code & Tests

People & History

People (9)

Peter Carbonetto

Author, Maintainer since 2.0.5 (2016)

Author

Author

Author

Author · added in 2.2-7

Jason Willwerscheid

Author · added in 2.2-7

Nan Xiao

Author

Chaoxing Dai

Contributor

Mazon Zeng

Contributor · added in 2.2-7

Releases (8)

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
2.2-63Latest
record
2023-08-22 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.2-54
record
2022-02-22 · diff ↗ ·
added 1 export
tnormalmix
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.2-47
record
2020-02-20 · diff ↗
unarchivedReturned to CRAN
2020-02-03
2.2-40
record
2020-02-03 · diff ↗
archivedRemoved from CRAN
2020-01-16
requires archived package 'mixsqp'
2.2-39
record
2019-10-17 · diff ↗ ·
added 1 export
ash_pois
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-02-22

Show 7 earlier eventsHide 7 earlier events

2.2-32
record
2019-02-22 · diff ↗ ·
added 1 export
mixSQP
archivedRemoved from CRAN
2019-02-05
check errors were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
2.2-7
record
2018-03-01 · diff ↗ ·
removed 3 exports
logF_lik, normal_lik, t_lik

added 17 exports
compute_lfsr, cxxMixSquarem, get_post_sample, lik_binom, lik_logF, lik_normal, lik_normalmix, lik_pois, lik_t, my_e2truncbeta, my_e2truncgamma, my_etruncbeta, my_etruncgamma, plot_diagnostic, post_sample, prune, w_mixEM
R
R 3.4.0 released · 2017-04-21
2.0.5
record
2016-12-27
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-12-27
Total releases: 8 / 10 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.1.0
Download size: 913 KB

Appears in task views

Bayesian Inference

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ashr")

Format

Carbonetto, P., Dai, C., Gerard, D., Lu, M., Stephens, M., Sun, L., Willwerscheid, J., Xiao, N., & Zeng, M. (2023). ashr: Methods for Adaptive Shrinkage, using Empirical Bayes (Version 2.2-63) [Computer software]. https://doi.org/10.32614/CRAN.package.ashr

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 ashr version 2.2-63 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →