Files in Rclade

Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

LICENSE

R/sysdata.rda

R/options.R R/parse-taxonomy.R R/plot-timetree.R R/logo.R R/encoding.R R/monophyly.R R/plot-timetree-pipeline.R R/collapse-workflow.R R/batch.R R/taxonomy-file.R R/support-labels.R R/data.R R/interrupt.R R/compute-mrca.R R/save-timetree.R R/timescale.R R/selftest.R R/shiny-app.R R/logger.R R/special-identifiers.R R/theme-publication.R R/read-input.R R/aaa-utils.R R/annotate-clade.R R/custom-groups.R R/params-helpers.R R/validate-deep.R R/zzz.R R/cli.R R/legend-smart.R R/color-palette.R

inst/THIRDPARTY

inst/CITATION

inst/doc/publication_ready.Rmd

inst/doc/taxonomy_formats.html

inst/doc/quick_start.R inst/doc/taxonomy_formats.R

inst/doc/publication_ready.html

inst/doc/taxonomy_formats.Rmd inst/doc/publication_ready.R inst/doc/quick_start.Rmd

inst/doc/quick_start.html

inst/extdata/config.example.yaml

inst/extdata/manuscript_config.yaml

inst/extdata/moody2025_gbm_laca_timetree.nwk

inst/bin/rclade

inst/docs/cn/tutorials.md inst/docs/cn/faq.md inst/docs/cn/core-concepts.md inst/docs/cn/getting-started.md inst/docs/cn/installation.md inst/docs/cn/cookbook.md inst/docs/cn/index.md inst/docs/cn/reference/utilities.md inst/docs/cn/reference/logging-timing.md inst/docs/cn/reference/colors-legend.md inst/docs/cn/reference/cli-interactive.md inst/docs/cn/reference/taxonomy-parsing.md inst/docs/cn/reference/tree-sequence.md inst/docs/cn/reference/core-visualization.md inst/docs/cn/reference/index.md inst/docs/en/tutorials.md inst/docs/en/faq.md inst/docs/en/core-concepts.md inst/docs/en/getting-started.md inst/docs/en/installation.md inst/docs/en/cookbook.md inst/docs/en/index.md inst/docs/en/reference/utilities.md inst/docs/en/reference/logging-timing.md inst/docs/en/reference/colors-legend.md inst/docs/en/reference/cli-interactive.md inst/docs/en/reference/taxonomy-parsing.md inst/docs/en/reference/tree-sequence.md inst/docs/en/reference/core-visualization.md inst/docs/en/reference/index.md

build/vignette.rds

tests/testthat.R tests/testthat/test-timescale.R tests/testthat/test-adversarial.R tests/testthat/test-logo.R tests/testthat/test-example-tree.R tests/testthat/test-utils.R tests/testthat/test-validate-sequence-extra.R tests/testthat/test-detect-format.R tests/testthat/test-legend.R tests/testthat/test-rank-helpers.R tests/testthat/test-multitree.R tests/testthat/test-theme.R tests/testthat/test-custom-groups.R tests/testthat/test-logger-file.R tests/testthat/test-logger-validation.R tests/testthat/test-interrupt.R tests/testthat/test-legend-smart.R tests/testthat/test-special-identifiers.R tests/testthat/test-cli-h6-passthrough.R tests/testthat/test-encoding-fallback.R tests/testthat/test-straight-vdiffr.R tests/testthat/test-data-contract.R tests/testthat/test-annotate-clade.R tests/testthat/test-performance.R tests/testthat/test-group-accounting.R tests/testthat/test-batch.R tests/testthat/test-unit-contract.R tests/testthat/helper-internal.R tests/testthat/test-taxonomy-file.R tests/testthat/test-regression-high.R tests/testthat/test-encoding.R tests/testthat/test-support-labels.R tests/testthat/test-selftest.R tests/testthat/test-shiny.R tests/testthat/test-collapse.R tests/testthat/test-taxonomy.R tests/testthat/test-validate-deep.R

tests/testthat/_snaps/straight-vdiffr/rectangular-collapse.svg

tests/testthat/_snaps/straight-vdiffr/circular-straight-edge-collapse.svg

vignettes/publication_ready.Rmd vignettes/taxonomy_formats.Rmd vignettes/quick_start.Rmd

data/example_tree.rda

data/polytomy_tree.rda

man/pt_step3_compute_mrca.Rd man/validate_tree_deep.Rd man/log_message.Rd man/compute_x_min.Rd man/log_memory.Rd man/set_log_enabled.Rd man/sort_by_depth.Rd man/validate_tree_structure.Rd man/escape_regex.Rd man/highlight_clades.Rd man/timer_start.Rd man/detect_taxonomy_format.Rd man/pt_step1_prepare_inputs.Rd man/validate_file_not_empty.Rd man/strip_tree_annotations.Rd man/log_error.Rd man/build_group_vec.Rd man/validate_custom_groups.Rd man/polytomy_tree.Rd man/prepare_geo_timescales.Rd man/build_path.Rd man/theme_timetree.Rd man/parse_custom_regex.Rd man/resolve_taxonomy_source_priority.Rd man/set_log_file.Rd man/parse_taxonomy_with_file.Rd man/resolve_target_domains.Rd man/generate_colors.Rd man/compute_legend_layout.Rd man/log_critical.Rd man/cleanup_on_interrupt.Rd man/get_git_hash.Rd man/detect_alphabet.Rd man/summarize_multi_trees.Rd man/dot-release_log_lock.Rd man/save_timetree.Rd man/get_level_prefix.Rd man/convert_unit.Rd man/log_keyvalue.Rd man/managed_tempdir.Rd man/check_example_tree.Rd man/log_progress.Rd man/pt_step5_render_and_collapse.Rd man/run_rclade_shiny.Rd man/parse_plot_params.Rd man/normalize_rank.Rd man/add_clip_off.Rd man/add_geo_timescale.Rd man/normalize_file_newlines.Rd man/log_warning.Rd man/parse_taxonomy.Rd man/log_section.Rd man/validate_file_exists.Rd man/validate_collapse_plan.Rd man/parse_gtdb.Rd man/log_subsection.Rd man/rclade_logo.Rd man/build_plot_timetree_params.Rd man/validate_inputs.Rd man/pt_step6_add_annotations.Rd man/with_graceful_interrupt.Rd man/RCLADE_HADEAN_END.Rd man/check_monophyly.Rd man/rclade_logger.Rd man/validate_taxonomy_no_cycles.Rd man/pt_step7_finalize_plot.Rd man/log_stats.Rd man/add_support_labels.Rd man/summarize_taxonomy_quality.Rd man/detect_tree_format.Rd man/log_debug.Rd man/batch_with_interrupt.Rd man/summarize_timetree.Rd man/find_rank_cycles.Rd man/validate_fastq_content.Rd man/add_smart_legend.Rd man/read_file_utf8.Rd man/RCLADE_X_MARGIN_FACTOR.Rd man/build_full_taxa_df.Rd man/init_progress_tracking.Rd man/normalize_newlines.Rd man/timer_stop.Rd man/ensure_dir.Rd man/log_table.Rd man/managed_tempfile.Rd man/pt_single_tree.Rd man/get_version_string.Rd man/format_elapsed.Rd man/check_special_monophyly.Rd man/validate_cli_params.Rd man/log_info.Rd man/next_step.Rd man/check_input_validation.Rd man/parse_custom_rank.Rd man/build_taxonomy_lookup.Rd man/save_session_info.Rd man/validate_fasta_content.Rd man/plot_timetree.Rd man/compute_mrca_map.Rd man/add_geo_events.Rd man/dot-acquire_log_lock.Rd man/selftest_report.Rd man/parse_silva.Rd man/update_progress.Rd man/check_taxonomy_extraction.Rd man/print_version.Rd man/dot-rclade_extract_config.Rd man/build_base_tree.Rd man/add_hpd_range.Rd man/get_rank_name.Rd man/pt_step2_resolve_taxonomy.Rd man/get_dependency_versions.Rd man/batch_plot.Rd man/format_timestamp.Rd man/validate_sequence_file.Rd man/check_dependency.Rd man/detect_encoding.Rd man/validate_sequence_deep.Rd man/print.rclade_options.Rd man/set_log_level.Rd man/validate_tree_sequence_match.Rd man/get_taxonomy_levels.Rd man/resolve_group.Rd man/summarize_taxonomy_quality_with_file.Rd man/run_rclade_selftest.Rd man/write_file_utf8.Rd man/split_legend.Rd man/annotate_clade.Rd man/resolve_special_identifier.Rd man/RCLADE_X_MIN_FLOOR.Rd man/example_tree.Rd man/run_rclade_cli.Rd man/validate_newick_syntax.Rd man/parse_semicolon_delimited.Rd man/level_to_num.Rd man/get_supported_extensions.Rd man/read_tree_auto.Rd man/parse_embedded.Rd man/init_steps.Rd man/check_monophyly_logic.Rd man/get_progress_summary.Rd man/rclade_options.Rd man/SUPPORTED_TREE_EXTENSIONS.Rd man/pt_step4_generate_colors.Rd man/parse_ncbi.Rd man/detect_sequence_format.Rd man/read_taxonomy_file.Rd man/format_step.Rd man/compute_time_breaks.Rd man/check_malicious_chars.Rd

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