R Observatory: Metrics for opticut version 0.1-4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

opticut

0.1-4

Likelihood Based Optimal Partitioning and Indicator Species Analysis

0packages depend

3.2Kdownloads / year

90.8%test coverage

13/13checks pass

Overview

About

Maintained by Peter SolymosFirst published 2016-12-175 releasesCRAN page ↗GitHub ↗

Likelihood based optimal partitioning and indicator species analysis. Finding the best binary partition for each species based on model selection, with the possibility to take into account modifying/confounding variables as described in Kemencei et al. (2014) doi:10.1556/ComEc.15.2014.2.6. The package implements binary and multi-level response models, various measures of uncertainty, Lorenz-curve based thresholding, with native support for parallel computations.

Install

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

install.packages("opticut", 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("psolymos/opticut")

Development version from psolymos/opticut. 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-opticut

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-opticut

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-opticut

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

Health

CRAN checks

13OK

Slowest check: 8.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.24

90.8%

Coverage · measured lines

100%

Documentation · exports

7

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
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-07
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 100%
References docs: 40%

Downloads

3.2K

CRAN downloads in the past year

Rank #17,322 · ~9/day · ~264/mo

Releases R versions

Daily download trend is not available in this view yet.

16030 days

61990 days

3.2K1 year

Compare downloads with other packages →

Also on98 r2u14 autocran

Repository

GitHub ↗ psolymos/opticut

2Stars

1Forks

4Open issues

0Open PRs

2Releases

851Commits

1Contributors

cranspeciesindicator-species-analysislikelihoodoptimal-partitioningrecology

851 commits · Last activity 2026-04-25

Stars over time

2020-12-25 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/psolymos/opticut on 2026-08-16.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.1.0pbapply

Imports (6)

MASSpscl betareg ResourceSelectionparallelmefa4

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Peter Solymos

Author, Maintainer

Authors (1)

Peter Solymos

Author, Maintainer

Contributors (1)

Ermias T. Azeria

Contributor

Listed in earlier versions (2)

Peter Solymos ()

no longer listed · 0.1-3

Azeria

no longer listed · 0.1-4

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
0.1-4Latest
2025-07-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1-3
2024-05-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1-2
2018-02-01 · diff ↗
0.1-1
2018-01-31 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1-0
2016-12-17
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-12-17
Total releases: 5 / 10 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1.0
Bundled data: 132 KB / 3 files
Download size: 186 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("opticut")

Format

Solymos, P., & Azeria, E. T. (2025). opticut: Likelihood Based Optimal Partitioning and Indicator Species Analysis (Version 0.1-4) [Computer software]. https://doi.org/10.32614/CRAN.package.opticut

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 opticut version 0.1-4 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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