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
