R Observatory: Metrics for autothresholdr version 1.4.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

autothresholdr

1.4.3Package record

An R Port of the 'ImageJ' Plugin 'Auto Threshold'

4packages depend

13.5Kdownloads / year

95.3%test coverage

13/13flavors OK

Overview

About

Maintained by Rory NolanCRAN page ↗GitHub ↗Website ↗Issues ↗

Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See https://imagej.net/plugins/auto-threshold and Landini et al. (2017) DOI:10.1111/jmi.12474.

Changes in 1.4.3

BUG FIXES

purrr::map_chr() should have been a purrr::map_dbl().

From NEWS.md in the release

Install

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

install.packages("autothresholdr", 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("rorynolan/autothresholdr")

Development version from rorynolan/autothresholdr. 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-autothresholdr

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-autothresholdr

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-autothresholdr

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: 3.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.3

README· In the repository, left out of the releaseVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.4.3Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 7
Examples that run: 0%3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 43%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 14%

Vignettes (3)

How these are measured

Downloads

13.5K

CRAN downloads in the past year

Rank #3,702 · ~37/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

2.6K90 days

13.5K1 year

Compare downloads with other packages →

Also on405 r2u38 autocran425 conda_forge

How downloads are counted

Repository

rorynolan/autothresholdr ↗Account: rorynolan

6Stars

3Forks

0Open issues

0Open PRs

7Releases

179Commits

3Commit identities

License file reads as GPL-3.0 · 179 commits · Last activity 2025-09-25

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 13
Median days to close, 50 most recently updated closed PRs: 204

How these are measured

PracticesBeta

15 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/rorynolan/autothresholdr on 2026-10-18.

Continuous integration (3)

GitHub ActionsR CMD check workflowAppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-09-25 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 5 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

codemeta.json

Automation and maintenance (1)

pre-commit

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2025-09-24
Commits: at least 1 crediting it in the message

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing autothresholdr adds 38 packages (25 with compiled code, 26 MB of source tarballs). Heaviest: stringi 11 MB, ijtiff 2.2 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5

Imports (9)

checkmate ijtiff magrittr purrr Rcpp rlangstatsstrex (>= 1.4.1)stringr

LinkingTo (1)

Rcpp

Suggests (8)

covr dplyr ggplot2 knitr rmarkdown spelling testthatutils

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Imports 4

Depends, Imports or LinkingTo, most downloaded first

detrendr nandb hemispheR coveR2

How these are counted

Code & Tests

People & History

People (4)

Rory Nolan

Author, Maintainer since 0.2.0 (2017), Translator

Luis Alvarez

Contributor · added in 0.4.0

Gabriel Landini

Contributor, Copyright holder

Sergi Padilla-Parra

Contributor, Thesis advisor · added in 0.4.0

Releases (25)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4.3Latest
record
2025-09-27 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.4.2
record
2023-12-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.1
record
2023-01-28 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.4.0
record
2022-01-04 · diff ↗
1.3.12
record
2021-11-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.3.11
record
2021-05-12 · diff ↗ ·
removed 1 export
arr_mask

added 1 export
masked_arr
1.3.10
record
2021-04-19 · diff ↗
1.3.9
record
2020-10-18 · diff ↗
1.3.7
record
2020-10-10 · diff ↗
1.3.6
record
2020-05-08 · diff ↗

Show 20 earlier eventsHide 20 earlier events

R
R 4.0.0 released · 2020-04-24
1.3.5
record
2019-07-08 · diff ↗
1.3.4
record
2019-06-28 · diff ↗
1.3.3
record
2019-06-12 · diff ↗
1.3.2
record
2019-05-30 · diff ↗
1.3.1
record
2019-05-21 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.3.0
record
2018-11-05 · diff ↗
1.2.1
record
2018-07-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.2.0
record
2018-03-25 · diff ↗
1.1.2
record
2018-02-13 · diff ↗
1.1.1
record
2018-01-28 · diff ↗
1.1.0
record
2018-01-23 · diff ↗ ·
removed 4 exports
mean_pillars, median_pillars, sum_pillars, var_pillars

added 6 exports
apply_mask, arr_mask, mask, stack_threshed_img, th, threshed_arr
0.6.0
record
2017-07-06 · diff ↗ ·
removed 1 export
CanBeInteger

added 1 export
sum_pillars
0.5.0
record
2017-05-17 · diff ↗ ·
removed 5 exports
MeanPillars, MeanStackThresh, MedStackThresh, MedianPillars, VarPillars

added 5 exports
mean_pillars, mean_stack_thresh, med_stack_thresh, median_pillars, var_pillars
0.4.0
record
2017-04-23 · diff ↗ ·
added 5 exports
MeanPillars, MeanStackThresh, MedStackThresh, MedianPillars, VarPillars
R
R 3.4.0 released · 2017-04-21
0.2.0
record
2017-02-24
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-02-24
Total releases: 25 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Download size: 795 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("autothresholdr")

The package provides a citation file, so citation() returns the authors' own entry.

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 autothresholdr version 1.4.3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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