Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

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Documentation for package ‘Rclade’ version 1.1.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

batch_plot	Batch plot timetrees from a directory of tree files
check_monophyly	Check if a taxonomic group is monophyletic
check_special_monophyly	Check if a special identifier corresponds to a monophyletic group
detect_taxonomy_format	Detect taxonomy format from tip labels
example_tree	Example phylogenetic tree with GTDB-style labels
get_supported_extensions	Get supported file extensions
parse_taxonomy	Unified taxonomy parsing entry point
plot_timetree	Plot a phylogenetic tree with geological timescale and taxonomic collapsing
polytomy_tree	Example phylogenetic tree with polytomies
rclade_logo	Display Rclade ASCII art logo
rclade_options	Construct a validated options list for 'plot_timetree()'
read_taxonomy_file	Read taxonomy information from a table file
read_tree_auto	Read tree from file with automatic format detection
run_rclade_cli	Run Rclade from the command line
run_rclade_selftest	Run Rclade self-test
run_rclade_shiny	Launch Rclade Shiny app
save_session_info	Save sessionInfo() for reproducibility
save_timetree	Save a timetree plot to file
set_log_enabled	Enable or disable logging
set_log_file	Set log file for dual output
set_log_level	Set log level
summarize_taxonomy_quality	Report taxonomy label parsing quality
summarize_taxonomy_quality_with_file	Summarize taxonomy quality with external file support
summarize_timetree	Print a summary of a Rclade timetree plot
theme_timetree	Publication-ready theme for timetree plots
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