R Observatory: Metrics for EbayesThresh version 1.4-12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EbayesThresh

1.4-12Package record

Empirical Bayes Thresholding and Related Methods

6packages dependsuggested by 1

332.4Kdownloads / year

43.9%test coverage

13/13flavors OK

Overview

About

Maintained by Peter CarbonettoCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 2.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4-12

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSNoCitation fileNo

Help pages: 16 (2 internal)
Examples that run: 100%11 run in a plain check
Exported functions with examples: 69%
Documented parameters: 98%
Return-value docs: 94%
Help pages citing references: 100%

Vignettes (1)

EbayesThresh HTML

How these are measured

Downloads

332.4K

CRAN downloads in the past year

Rank #1,896 · ~911/day · ~27.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.7K30 days

10.4K90 days

332.4K1 year

Compare downloads with other packages →

Also on136 r2u5 autocran1.7K conda_forge148 c2d4u

How downloads are counted

Repository

stephenslab/ebayesthresh ↗Organization: stephenslab

5Stars

1Forks

2Open issues

0Open PRs

3Releases

126Commits

9Commit identities

License file reads as GPL-3.0 · 126 commits · Last activity 2017-12-18 · Default branch at 1.4-13, ahead of CRAN 1.4-12 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-02-04 · 52026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/stephenslab/ebayesthresh on 2026-10-21.

Continuous integration (2)

Travis CI (config file)AppVeyor

Docs source (1)

GitHub Pages site last deployed 2017-12-18

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing EbayesThresh adds 1 package (1 with compiled code, 567 KB of source tarballs). Heaviest: wavethresh 567 KB.

Depends (0)

none

Imports (2)

statswavethresh

LinkingTo (0)

none

Suggests (5)

testthat knitr rmarkdown dplyr ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

7indirect

Depends 5 · Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

adlift binhf nlt CVThresh icmm GSD

Suggests, most downloaded first

smashr

How these are counted

Code & Tests

People & History

People (5)

Peter Carbonetto

Author, Maintainer since 1.4-12 (2017) · 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

Previously maintained by Ludger Evers (1.02 to 1.3.2).

Listed in earlier versions (1)

Bernard Silverman

no longer listed · 1.02

Releases (5)

Pick two releases to compare their code metrics.

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
record
2017-08-08 · current release · diff ↗ ·
removed 1 export
pattern:.

added 24 exports
beta.cauchy, beta.laplace, ebayesthresh, ebayesthresh.wavelet, isotone, laplace.threshzero, cauchy.threshzero, negloglik.laplace, postmean, postmean.cauchy, postmean.laplace, postmed, postmed.cauchy, postmed.laplace, cauchy.medzero, tfromw, tfromx, threshld, vecbinsolv, wandafromx, wfromt, wfromx, wmonfromx, zetafromx
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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
record
2012-10-29 · diff ↗ ·
added 1 export
pattern:.

Show 20 earlier eventsHide 20 earlier events

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R 2.15.0 released · 2012-03-30
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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
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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
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R 2.1.0 released · 2005-04-18
1.3.0
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2005-03-26 · diff ↗
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R 2.0.0 released · 2004-10-04
1.02
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2004-09-04
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R 1.9.0 released · 2004-04-12

Package metadata

First published: 2004-09-04
Total releases: 5 / 22 yrs
License: GPL (>= 2) OSI
Download size: 692 KB

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 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 EbayesThresh version 1.4-12 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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