R Observatory: Metrics for EbayesThresh version 1.4-12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EbayesThresh

1.4-12

Empirical Bayes Thresholding and Related Methods

8packages depend

538.5Kdownloads / year

43.9%test coverage

13/13checks pass

Overview

About

Maintained by Peter CarbonettoFirst published 2005-03-265 releasesCRAN page ↗GitHub ↗

Empirical Bayes thresholding using the methods developed by I. M. Johnstone and B. W. Silverman. The basic problem is to estimate a mean vector given a vector of observations of the mean vector plus white noise, taking advantage of possible sparsity in the mean vector. Within a Bayesian formulation, the elements of the mean vector are modelled as having, independently, a distribution that is a mixture of an atom of probability at zero and a suitable heavy-tailed distribution. The mixing parameter can be estimated by a marginal maximum likelihood approach. This leads to an adaptive thresholding approach on the original data. Extensions of the basic method, in particular to wavelet thresholding, are also implemented within the package.

Install

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

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

Development version from stephenslab/EbayesThresh. 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-ebayesthresh

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-EbayesThresh

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-EbayesThresh

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

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.18

43.9%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 94%
References docs: 100%

Downloads

538.5K

CRAN downloads in the past year

Rank #1,852 · ~1.5K/day · ~44.9K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.2K30 days

11.8K90 days

538.5K1 year

Compare downloads with other packages →

Also on155 r2u22 autocran1.8K conda_forge66 c2d4u

Repository

GitHub ↗ stephenslab/ebayesthresh

5Stars

1Forks

2Open issues

0Open PRs

3Releases

126Commits

9Contributors

License GPL-3.0 · 126 commits · Last activity 2017-12-18

Stars over time

2025-02-04 · 52026-07-07 · 5

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/stephenslab/ebayesthresh on 2026-08-16.

Continuous integration (2)

Travis CIAppVeyor

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

statswavethresh

LinkingTo (0)

none

Suggests (5)

testthat knitr rmarkdown dplyr ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

8direct

7indirect

CVThresh GSD adlift binhf nlt POCRE icmm smashr

Code & Tests

People & History

People (5)

Maintainer (1)

Peter Carbonetto

Author, Maintainer · added in 1.4-12

Authors (5)

Peter Carbonetto

Author, Maintainer · added in 1.4-12

Ludger Evers

Author · added in 1.4-12

Bernard W. Silverman

Author · added in 1.3.0

Matthew Stephens

Author · added in 1.4-12

Kan Xu

Author · added in 1.4-12

Listed in earlier versions (1)

Bernard Silverman (with major intellectual input from Iain Johnstone)

no longer listed · 1.02

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
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R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
1.4-12Latest
2017-08-08 · current release · diff ↗
R
R 3.4.0 released · 2017-04-21
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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.1.0 released · 2014-04-10
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R 3.0.0 released · 2013-04-03
1.3.2
2012-10-29 · diff ↗

Show 20 earlier events

R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
1.3.1
2010-05-08 · diff ↗
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R 2.11.0 released · 2010-04-22
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R 2.10.0 released · 2009-10-26
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R 2.9.0 released · 2009-04-17
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R 2.8.0 released · 2008-10-20
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R 2.7.0 released · 2008-04-22
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R 2.6.0 released · 2007-10-03
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R 2.5.0 released · 2007-04-24
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R 2.4.0 released · 2006-10-03
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R 2.3.0 released · 2006-04-24
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R 2.2.0 released · 2005-10-06
R
R 2.1.0 released · 2005-04-18
1.3.0
2005-03-26 · diff ↗
R
R 2.0.0 released · 2004-10-04
1.02
2004-09-04
R
R 1.9.0 released · 2004-04-12

Package metadata

First published: 2005-03-26
Total releases: 5 / 21 yrs
License: GPL (>= 2) OSI
Download size: 692 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Bayesian Inference

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("EbayesThresh")

Format

Carbonetto, P., Evers, L., Silverman, B. W., Stephens, M., & Xu, K. (2017). EbayesThresh: Empirical Bayes Thresholding and Related Methods (Version 1.4-12) [Computer software]. https://doi.org/10.32614/CRAN.package.EbayesThresh

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 EbayesThresh version 1.4-12 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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