Package index • Rclade

Core visualization

Main plotting and pipeline functions

plot_timetree(): Plot a phylogenetic tree with geological timescale and taxonomic collapsing
rclade_options(): Construct a validated options list for plot_timetree()
batch_plot(): Batch plot timetrees from a directory of tree files
save_timetree(): Save a timetree plot to file
summarize_timetree(): Print a summary of a Rclade timetree plot
theme_timetree(): Publication-ready theme for timetree plots

Taxonomy parsing

Format detection, label parsing and quality summary

parse_taxonomy(): Unified taxonomy parsing entry point
detect_taxonomy_format(): Detect taxonomy format from tip labels
read_taxonomy_file(): Read taxonomy information from a table file
summarize_taxonomy_quality(): Report taxonomy label parsing quality
summarize_taxonomy_quality_with_file(): Summarize taxonomy quality with external file support

Tree input, MRCA and collapsing

Tree reading, monophyly checks and group resolution

read_tree_auto(): Read tree from file with automatic format detection
get_supported_extensions(): Get supported file extensions
check_monophyly(): Check if a taxonomic group is monophyletic
check_special_monophyly(): Check if a special identifier corresponds to a monophyletic group

Input validation

Deep validation and robustness

validate_sequence_deep(): Deep validation of sequence files
validate_sequence_file(): Validate sequence file format
validate_tree_sequence_match(): Cross-validate tree tip labels against sequence IDs

CLI and Shiny

Command-line, web interface and self-test

run_rclade_cli(): Run Rclade from the command line
run_rclade_shiny(): Launch Rclade Shiny app
run_rclade_selftest(): Run Rclade self-test

Logging

Real-time logging control

set_log_enabled(): Enable or disable logging
set_log_file(): Set log file for dual output
set_log_level(): Set log level

Utilities

Helper functions

rclade_logo(): Display Rclade ASCII art logo
save_session_info(): Save sessionInfo() for reproducibility

Data

Bundled example datasets

example_tree: Example phylogenetic tree with GTDB-style labels
polytomy_tree: Example phylogenetic tree with polytomies