index.md
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Reference Manual

All functions and commands organized by module. Each function includes a description and a simple usage example.

Note: Functions marked as "internal" are not exported in the NAMESPACE; access them with the Rclade:::function_name() triple-colon syntax.

| Module | Description | |------|------| | Core Visualization | Main functions for plotting, saving and summarizing phylogenetic timetrees. | | Tree & Sequence I/O and Validation | Read tree files, validate sequence files, and check monophyly. | | Taxonomy Parsing | Detect formats, parse taxonomic labels, resolve groups to MRCAs, and validate custom groups. | | Colors & Legend | Generate color-blind-safe palettes and split legends for publication-ready plots. | | Command-line & Interactive Interfaces | Run Rclade from the command line, launch the Shiny app, run the self-test, and batch with interruption handling. | | Logging & Timing | Structured, leveled logging and timers for pipeline observability. | | Utilities | Cross-platform path building, encoding detection, temporary file management, and miscellaneous helpers. |

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