charisma

1.0.0

Reproducible Color Characterization of Digital Images for Biological Studies

0packages depend

1.7Kdownloads / year

29.1%test coverage

13/13checks pass

Overview

About

Maintained by Shawn SchwartzFirst published 2025-12-081 releasesCRAN page ↗GitHub ↗

Provides a standardized and reproducible framework for characterizing and classifying discrete color classes from digital images of biological organisms. The package automatically determines the presence or absence of 10 human-visible color categories (black, blue, brown, green, grey, orange, purple, red, white, yellow) using a biologically-inspired Color Look-Up Table (CLUT) that partitions HSV color space. Supports both fully automated and semi-automated (interactive) workflows with complete provenance tracking for reproducibility. Pre-processes images using the 'recolorize' package (Weller et al. 2024 doi:10.1111/ele.14378) for spatial-color binning, and integrates with 'pavo' (Maia et al. 2019 doi:10.1111/2041-210X.13174) for color pattern geometry statistics. Designed for high-throughput analysis and seamless integration with downstream evolutionary analyses.

Install

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

install.packages("charisma", 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("shawntz/charisma")

Development version from shawntz/charisma. 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-charisma

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-charisma

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 2.7 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.06

29.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 402 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 63%
Documented parameters: 100%
Return-value docs: 100%
References docs: 40%

Downloads

1.7K

CRAN downloads in the past year

Rank #15,658 · ~5/day · ~138/mo

Releases R versions

Daily download trend is not available in this view yet.

25930 days

69090 days

1.7K1 year

Compare downloads with other packages →

Also on107 r2u

Repository

GitHub ↗ shawntz/charisma

4Stars

0Forks

0Open issues

0Open PRs

2Releases

412Commits

4Contributors

412 commits · Last activity 2026-04-10 · 0% stars, 30d

Stars over time

2025-02-14 · 12026-07-07 · 4

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/shawntz/charisma on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Governance and community (2)

Issue templatesFunding

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (17)

magrittr plyr dplyr tibble purrr tidyrparallelrecolorize imager abind jpeg pnggrDevicesgraphicsstatstoolsutils

LinkingTo (0)

none

Suggests (5)

pavo testthat knitr rmarkdown pkgdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (8)

Maintainer (1)

Shawn Schwartz

Author, Maintainer, Copyright holder

Authors (8)

Shawn Schwartz

Author, Maintainer, Copyright holder

Author

Author

Author

Author

Author

Author

Author

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-08
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 0.5 KB / 1 file
Download size: 4.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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