| add_clip_off | Apply coordinate-system clip="off" (the only clip application... |
| add_geo_events | Add geological event bands (e.g., GOE, NOE) to a tree plot |
| add_geo_timescale | Add geological timescale to a tree plot |
| add_hpd_range | Add HPD (Highest Posterior Density) range to a tree plot |
| add_smart_legend | Add smart legend to a tree plot |
| add_support_labels | Add node support labels to a tree plot |
| annotate_clade | Add clade labels next to collapsed triangles |
| batch_plot | Batch plot timetrees from a directory of tree files |
| batch_with_interrupt | Execute batch operation with interrupt handling and progress |
| build_base_tree | Create base tree plot based on layout type |
| build_full_taxa_df | Build a full-rank taxonomy data.frame in a single pass (M-D4... |
| build_group_vec | Build a group vector from custom groups |
| build_path | Build file path safely (cross-platform) |
| build_plot_timetree_params | Build plot_timetree parameter list from CLI options |
| build_taxonomy_lookup | Build taxonomy lookup from file |
| check_dependency | Check a single dependency |
| check_example_tree | Check example tree loading and structure |
| check_input_validation | Check input validation functions |
| check_malicious_chars | Check for malicious characters in node names |
| check_monophyly | Check if a taxonomic group is monophyletic |
| check_monophyly_logic | Check monophyly logic with known cases |
| check_special_monophyly | Check if a special identifier corresponds to a monophyletic... |
| check_taxonomy_extraction | Check taxonomy extraction from example tree |
| cleanup_on_interrupt | Clean up resources on interruption |
| compute_legend_layout | Compute legend row/column layout |
| compute_mrca_map | Compute MRCA node mapping for each taxonomic group |
| compute_time_breaks | Compute adaptive time breaks for x-axis |
| compute_x_min | Compute x-axis minimum from tree depth |
| convert_unit | Convert time units (Ga -> Ma) |
| detect_alphabet | Detect sequence alphabet from characters |
| detect_encoding | Detect file encoding |
| detect_sequence_format | Detect sequence file format |
| detect_taxonomy_format | Detect taxonomy format from tip labels |
| detect_tree_format | Detect and validate tree file format |
| dot-acquire_log_lock | Acquire an advisory file lock for the active log file (L-C5) |
| dot-rclade_extract_config | Extract -config path from raw args (pre-parse) |
| dot-release_log_lock | Release the advisory log file lock acquired by... |
| ensure_dir | Ensure directory exists, create if needed |
| escape_regex | Escape a string for safe use inside a regular expression |
| example_tree | Example phylogenetic tree with GTDB-style labels |
| find_rank_cycles | Find circular dependencies between two rank columns |
| format_elapsed | Format elapsed time |
| format_step | Format step counter |
| format_timestamp | Format timestamp in ISO 8601 with milliseconds and timezone... |
| generate_colors | Generate color mapping for taxonomic groups |
| get_dependency_versions | Get dependency versions |
| get_git_hash | Get the current git short hash of the installed package... |
| get_level_prefix | Get level prefix |
| get_progress_summary | Get current progress summary |
| get_rank_name | Get display name for a taxonomic rank |
| get_supported_extensions | Get supported file extensions |
| get_taxonomy_levels | Get taxonomy level configuration |
| get_version_string | Get package version with git hash if available |
| highlight_clades | Highlight monophyletic clades on a tree plot |
| init_progress_tracking | Initialize progress tracking for a batch operation |
| init_steps | Initialize step counter for progress tracking |
| level_to_num | Get numeric value for log level |
| log_critical | Log a CRITICAL message |
| log_debug | Log a DEBUG message |
| log_error | Log an ERROR message |
| log_info | Log an INFO message |
| log_keyvalue | Log a key-value pair |
| log_memory | Log current memory usage at DEBUG level |
| log_message | Log a message with real-time flush |
| log_progress | Log a progress indicator |
| log_section | Print a formatted section header |
| log_stats | Print summary statistics |
| log_subsection | Print a formatted subsection header |
| log_table | Print a formatted table |
| log_warning | Log a WARNING message |
| managed_tempdir | Create and manage temporary directory with automatic cleanup |
| managed_tempfile | Create and manage temporary file with automatic cleanup |
| next_step | Increment step counter |
| normalize_file_newlines | Normalize line endings in a file |
| normalize_newlines | Normalize line endings in text |
| normalize_rank | Normalize rank abbreviation to full name |
| parse_custom_rank | Parse custom rank format labels (Format A wrapper) |
| parse_custom_regex | Parse custom regex format labels |
| parse_embedded | Parse Format A: Embedded taxonomy labels |
| parse_gtdb | Parse GTDB format labels (wrapper for... |
| parse_ncbi | Parse NCBI format labels |
| parse_plot_params | Parse raw UI / CLI strings into structured plot parameters |
| parse_semicolon_delimited | Parse Format B: Semicolon-delimited taxonomy (GTDB-style) |
| parse_silva | Parse Silva format labels |
| parse_taxonomy | Unified taxonomy parsing entry point |
| parse_taxonomy_with_file | Parse taxonomy with external file support |
| plot_timetree | Plot a phylogenetic tree with geological timescale and... |
| polytomy_tree | Example phylogenetic tree with polytomies |
| prepare_geo_timescales | Load internal geological timescale data |
| print.rclade_options | Print method for rclade_options |
| print_version | Print version information |
| pt_single_tree | Single-tree plotting pipeline |
| pt_step1_prepare_inputs | Step 1: Prepare and validate inputs |
| pt_step2_resolve_taxonomy | Step 2: Resolve taxonomy / collapsing mode |
| pt_step3_compute_mrca | Step 3: Compute MRCA and check monophyly |
| pt_step4_generate_colors | Step 4: Generate colors |
| pt_step5_render_and_collapse | Step 5: Render base tree and collapse clades |
| pt_step6_add_annotations | Step 6: Add annotations (tip labels, timescale, support, HPD,... |
| pt_step7_finalize_plot | Step 7: Finalize plot (legend, theme, title, save, metadata) |
| RCLADE_HADEAN_END | End of the Hadean eon / start of the Archean eon (Ma, ICS... |
| rclade_logger | Rclade Logger |
| rclade_logo | Display Rclade ASCII art logo |
| rclade_options | Construct a validated options list for 'plot_timetree()' |
| RCLADE_X_MARGIN_FACTOR | Default margin factor for x-axis range extension |
| RCLADE_X_MIN_FLOOR | Minimum x-axis value used when the tree root reaches into the... |
| read_file_utf8 | Read file with explicit UTF-8 encoding |
| read_taxonomy_file | Read taxonomy information from a table file |
| read_tree_auto | Read tree from file with automatic format detection |
| resolve_group | Resolve group name or special identifier to MRCA node |
| resolve_special_identifier | Resolve special ancestral node identifiers |
| resolve_target_domains | Resolve the target/expected taxonomy domains for a special... |
| resolve_taxonomy_source_priority | Resolve taxonomy source priority (embedded vs table) |
| 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 |
| selftest_report | Report a self-test progress line |
| set_log_enabled | Enable or disable logging |
| set_log_file | Set log file for dual output |
| set_log_level | Set log level |
| sort_by_depth | Sort groups by MRCA node depth (deepest first) |
| split_legend | Extract legend as separate grob and combine with patchwork |
| strip_tree_annotations | Strip node annotations from a tree (ยง9.1.1... |
| summarize_multi_trees | Summarize multiple trees in a file |
| 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 |
| SUPPORTED_TREE_EXTENSIONS | Supported tree file extensions |
| theme_timetree | Publication-ready theme for timetree plots |
| timer_start | Start a timer for performance measurement |
| timer_stop | Stop a timer and log elapsed time |
| update_progress | Update progress counter |
| validate_cli_params | Validate input parameters |
| validate_collapse_plan | Detect nesting conflicts in a collapse plan |
| validate_custom_groups | Validate user-defined custom groups for tree collapsing |
| validate_fasta_content | Validate FASTA content |
| validate_fastq_content | Validate FASTQ content |
| validate_file_exists | Validate file existence and readability |
| validate_file_not_empty | Validate file is not empty |
| validate_inputs | Validate and preprocess tree input |
| validate_newick_syntax | Validate Newick string syntax |
| validate_sequence_deep | Deep validation of sequence files |
| validate_sequence_file | Validate sequence file format |
| validate_taxonomy_no_cycles | Detect circular dependencies in taxonomy table |
| validate_tree_deep | Deep tree validation after parsing |
| validate_tree_sequence_match | Cross-validate tree tip labels against sequence IDs |
| validate_tree_structure | Validate tree object structure |
| with_graceful_interrupt | Execute expression with graceful interrupt handling |
| write_file_utf8 | Write file with explicit UTF-8 encoding and Unix line endings |
