Introduction | What does charisma do? | Installation | System Dependencies | Development Version (GitHub) | Stable Version (CRAN) | Load the Package | Basic Workflow | Step 1: Load an Image | Step 2: Run charisma | Step 3: Visualize Results | Understanding the Pipeline | 1. Image Preprocessing | 2. Color Classification | 3. Optional Manual Curation | Working with Thresholds | Saving and Loading Results | Extracting Color Data | Custom Color Look-Up Tables | Integration with Evolutionary Analyses | Tips for Best Results | For Bird Museum Specimens | For Automated Workflows | For Custom Image Sets | Citation | Getting Help | Acknowledgments
Package: charisma 1.0.0
charisma: Reproducible Color Characterization of Digital Images for Biological Studies
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.
Authors:
charisma_1.0.0.tar.gz
charisma_1.0.0.zip(r-4.7-any)charisma_1.0.0.zip(r-4.6-any)charisma_1.0.0.zip(r-4.5-any)
charisma_1.0.0.tgz(r-4.6-any)charisma_1.0.0.tgz(r-4.5-any)
charisma_1.0.0.tar.gz(r-4.7-any)charisma_1.0.0.tar.gz(r-4.6-any)
charisma_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
charisma/json (API)
| # Install 'charisma' in R: |
| install.packages('charisma', repos = c('https://shawntz.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/shawntz/charisma/issues
Datasets:
- clut - Default Color
Last updated from:cbe681c21e. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 155 | ||
| source / vignettes | OK | 222 | ||
| linux-release | OK | 163 | ||
| macos-release | OK | 140 | ||
| macos-oldrel | OK | 117 | ||
| windows-devel | OK | 124 | ||
| windows-release | OK | 103 | ||
| windows-oldrel | OK | 118 | ||
| wasm-release | OK | 152 |
Exports:charismacharisma2color2labellaunch_clut_editormosaicsummarisesummarizevalidate
Dependencies:abindbmpclassclassIntcliclustercodetoolscolorRampscpp11curlDBIdigestdownloaderdplyre1071farverfuturefuture.applygenericsgeometryglobalsglueigraphimagerjpegKernSmoothlatticelifecyclelightrlinproglistenvlpSolvemagicmagickmagrittrMatrixmgcvmisc3dnlmeparallellypavopillarpkgconfigplot3DplotfunctionsplyrpngprogressrproxypurrrR6rasterRcppRcppProgressreadbitmaprecolorizerlangs2sfspstringistringrterratibbletidyrtidyselecttiffunitsutf8vctrswithrwkxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Characterize color classes in biological images | charisma |
| Re-analyze and edit saved charisma objects | charisma2 |
| Default Color (Labels) Look Up Table (CLUT) | clut |
| Convert RGB color triplets to discrete color labels | color2label |
| Launch the CLUT Editor | launch_clut_editor |
| Create a color mosaic visualization from color proportions | mosaic |
| Plot method for charisma objects | plot.charisma |
| Summarize color classification results | summarise summarize |
| Validate Color Look-Up Table completeness | validate |