inst/docs/en/index.md

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

Rclade Documentation (English)

Welcome to the Rclade documentation. Rclade is an R package for automated deep-time phylogenetic tree collapsing and visualization with geological timescales.

This documentation is organized as a multi-level system:

1. Getting started — a guided first run.
2. Installation — how to install Rclade and its dependencies.
3. Core concepts — taxonomy formats, MRCA collapsing, timescales, colors, and special identifiers.
4. Tutorials — step-by-step workflows.
5. Reference — every exported function, grouped by module, each with a usage example.
6. Cookbook — copy-paste worked examples for common tasks.
7. FAQ — frequently asked questions and troubleshooting.

Where to go

| Page | Link | |------|------| | Getting started | getting-started.md | | Installation | installation.md | | Core concepts | core-concepts.md | | Tutorials | tutorials.md | | Reference index | reference/index.md | | Cookbook | cookbook.md | | FAQ | faq.md |

中文文档：../cn/index.md · Project README: ../../README.EN.md

Module reference

• Core Visualization — plot_timetree, batch_plot, save_timetree, summarize_timetree, theme_timetree
• Tree & Sequence I/O and Validation — read/validate trees and sequences, check monophyly
• Taxonomy Parsing — detect/parse labels, resolve groups to MRCAs, validate custom groups
• Colors & Legend — generate_colors, split_legend
• Command-line & Interactive — CLI, Shiny, self-test, interruption handling
• Logging & Timing — structured logging and timers
• Utilities — paths, encoding, temp files, misc helpers

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.