{ "_id": "6ab850e899f7aa8c6aa350c6", "Package": "Rclade", "Title": "Automated Deep-Time Phylogenetic Tree Collapsing and\nVisualization", "Version": "1.1.5", "Authors@R": "person(\"Zeng\", \"Zichao\", email = \"zengzichao@sjtu.edu.cn\",\nrole = c(\"aut\", \"cre\"))", "Author": "Zeng Zichao [aut, cre]", "Maintainer": "Zeng Zichao ", "Description": "Provides a single-function pipeline for automated\ncollapsing and visualization of large phylogenetic trees with\ngeological timescales. Automatically parses taxonomic labels\nfrom multiple formats (GTDB, Silva, NCBI, embedded, custom),\nidentifies Most Recent Common Ancestors (MRCAs), assigns\ncolor-blind-safe palettes, executes batch collapsing with\nautomatic nesting-aware ordering, integrates 'deeptime'\ngeologic time scales with adaptive time breaks and unit\nswitching, and manages smart legend layout. Supports special\nancestral node identifiers (LUCA, LACA, LBCA) for highlighting\nkey nodes in the tree of life. Provides external taxonomy file\nsupport for trees with incomplete or missing taxonomic labels.\nFeatures real-time logging with timestamps, step tracking, and\nmultiple log levels. Includes comprehensive input validation\nfor tree and sequence file formats. Reduces a 60-line manual\nworkflow to a single function call while preserving full\ncompatibility with the 'ggtree'/'deeptime' ecosystem. The\nvisualization pipeline builds on 'ggtree' Yu et al. (2017)\n, 'deeptime' Gearty (2025)\n, and 'ape' Paradis and\nSchliep (2019) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/testthat/edition": "3", "URL": "https://github.com/zengzichao/Rclade,\nhttps://zengzichao.github.io/Rclade/", "BugReports": "https://github.com/zengzichao/Rclade/issues", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-26 23:06:22 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-09-26 16:40:32 UTC", "RemoteUrl": "https://github.com/cran/Rclade", "RemoteRef": "HEAD", "RemoteSha": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "_user": "cran", "_type": "src", "_file": "Rclade_1.1.5.tar.gz", "_fileid": "https://r2.ropensci.org/3653ccdc5361c3d35f8aad21f64c36963cee94f39a49d09e09e5720e8686c14c", "_filesize": 775115, "_sha256": "3653ccdc5361c3d35f8aad21f64c36963cee94f39a49d09e09e5720e8686c14c", "_expires": "2027-01-04T23:10:30.000Z", "_created": "2026-09-26T23:06:22.000Z", "_published": "2026-09-26T23:10:32.262Z", "_jobs": [ { "job": 108505496262, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10918212220" }, { "job": 108505496229, "time": 147, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10918695453" }, { "job": 108504900247, "time": 241, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10918400237" }, { "job": 108505496241, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10918365999" }, { "job": 108505496267, "time": 101, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10917960920" }, { "job": 108505496261, "time": 144, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10917881940" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/36278184931", "_status": "success", "_upstream": "https://github.com/cran/Rclade", "_commit": { "id": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "author": "Zeng Zichao ", "committer": "cran-robot ", "message": "version 1.1.5\n", "time": 1790440832 }, "_maintainer": { "name": "Zeng Zichao", "email": "zengzichao@sjtu.edu.cn", "login": "zengzichao", "description": "", "uuid": 301673815 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ape", "version": ">= 5.0", "role": "Imports" }, { "package": "ggtree", "version": ">= 4.0.0", "role": "Imports" }, { "package": "deeptime", "version": ">= 1.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "version": ">= 1.5", "role": "Imports" }, { "package": "tidytree", "version": ">= 0.4", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "treeio", "version": ">= 1.0", "role": "Suggests" }, { "package": "phangorn", "version": ">= 2.0", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "cowplot", "version": ">= 1.1", "role": "Suggests" }, { "package": "patchwork", "version": ">= 1.1", "role": "Suggests" }, { "package": "shiny", "version": ">= 1.7", "role": "Suggests" }, { "package": "optparse", "version": ">= 1.7", "role": "Suggests" }, { "package": "yaml", "role": "Suggests" }, { "package": "vdiffr", "version": ">= 1.0", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "filelock", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-39", "n": 1 } ], "_tags": [ { "name": "1.1.5", "date": "2026-09-26" } ], "_stars": 0, "_contributors": [ { "user": "zengzichao", "count": 1, "uuid": 301673815 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 630, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rclade" }, "_devurl": "https://github.com/zengzichao/rclade", "_pkgdown": "https://zengzichao.github.io/Rclade/", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/Rclade.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_releases": [ { "version": "1.1.5", "date": "2026-09-26" } ], "_exports": [ "batch_plot", "check_monophyly", "check_special_monophyly", "detect_taxonomy_format", "get_supported_extensions", "parse_taxonomy", "plot_timetree", "rclade_logo", "rclade_options", "read_taxonomy_file", "read_tree_auto", "run_rclade_cli", "run_rclade_selftest", "run_rclade_shiny", "save_session_info", "save_timetree", "set_log_enabled", "set_log_file", "set_log_level", "summarize_taxonomy_quality", "summarize_taxonomy_quality_with_file", "summarize_timetree", "theme_timetree", "validate_sequence_deep", "validate_sequence_file", "validate_tree_sequence_match" ], "_datasets": [ { "name": "example_tree", "title": "Example phylogenetic tree with GTDB-style labels", "object": "example_tree", "file": "example_tree.rda", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "polytomy_tree", "title": "Example phylogenetic tree with polytomies", "object": "polytomy_tree", "file": "polytomy_tree.rda", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "batch_plot", "title": "Batch plot timetrees from a directory of tree files", "topics": [ "batch_plot" ] }, { "page": "check_monophyly", "title": "Check if a taxonomic group is monophyletic", "topics": [ "check_monophyly" ] }, { "page": "check_special_monophyly", "title": "Check if a special identifier corresponds to a monophyletic group", "topics": [ "check_special_monophyly" ] }, { "page": "detect_taxonomy_format", "title": "Detect taxonomy format from tip labels", "topics": [ "detect_taxonomy_format" ] }, { "page": "example_tree", "title": "Example phylogenetic tree with GTDB-style labels", "topics": [ "example_tree" ] }, { "page": "get_supported_extensions", "title": "Get supported file extensions", "topics": [ "get_supported_extensions" ] }, { "page": "parse_taxonomy", "title": "Unified taxonomy parsing entry point", "topics": [ "parse_taxonomy" ] }, { "page": "plot_timetree", "title": "Plot a phylogenetic tree with geological timescale and taxonomic collapsing", "topics": [ "plot_timetree" ] }, { "page": "polytomy_tree", "title": "Example phylogenetic tree with polytomies", "topics": [ "polytomy_tree" ] }, { "page": "rclade_logo", "title": "Display Rclade ASCII art logo", "topics": [ "rclade_logo" ] }, { "page": "rclade_options", "title": "Construct a validated options list for 'plot_timetree()'", "topics": [ "rclade_options" ] }, { "page": "read_taxonomy_file", "title": "Read taxonomy information from a table file", "topics": [ "read_taxonomy_file" ] }, { "page": "read_tree_auto", "title": "Read tree from file with automatic format detection", "topics": [ "read_tree_auto" ] }, { "page": "run_rclade_cli", "title": "Run Rclade from the command line", "topics": [ "run_rclade_cli" ] }, { "page": "run_rclade_selftest", "title": "Run Rclade self-test", "topics": [ "run_rclade_selftest" ] }, { "page": "run_rclade_shiny", "title": "Launch Rclade Shiny app", "topics": [ "run_rclade_shiny" ] }, { "page": "save_session_info", "title": "Save sessionInfo() for reproducibility", "topics": [ "save_session_info" ] }, { "page": "save_timetree", "title": "Save a timetree plot to file", "topics": [ "save_timetree" ] }, { "page": "set_log_enabled", "title": "Enable or disable logging", "topics": [ "set_log_enabled" ] }, { "page": "set_log_file", "title": "Set log file for dual output", "topics": [ "set_log_file" ] }, { "page": "set_log_level", "title": "Set log level", "topics": [ "set_log_level" ] }, { "page": "summarize_taxonomy_quality", "title": "Report taxonomy label parsing quality", "topics": [ "summarize_taxonomy_quality" ] }, { "page": "summarize_taxonomy_quality_with_file", "title": "Summarize taxonomy quality with external file support", "topics": [ "summarize_taxonomy_quality_with_file" ] }, { "page": "summarize_timetree", "title": "Print a summary of a Rclade timetree plot", "topics": [ "summarize_timetree" ] }, { "page": "theme_timetree", "title": "Publication-ready theme for timetree plots", "topics": [ "theme_timetree" ] }, { "page": "validate_sequence_deep", "title": "Deep validation of sequence files", "topics": [ "validate_sequence_deep" ] }, { "page": "validate_sequence_file", "title": "Validate sequence file format", "topics": [ "validate_sequence_file" ] }, { "page": "validate_tree_sequence_match", "title": "Cross-validate tree tip labels against sequence IDs", "topics": [ "validate_tree_sequence_match" ] } ], "_readme": "https://github.com/cran/Rclade/raw/HEAD/README.md", "_rundeps": [ "ape", "aplot", "base64enc", "bslib", "cachem", "cli", "commonmark", "cpp11", "curl", "deeptime", "deeptimedata", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "ggfittext", "ggforce", "ggfun", "ggh4x", "ggiraph", "ggplot2", "ggplotify", "ggtree", "glue", "gridExtra", "gridGraphics", "gridtext", "grImport2", "gtable", "highr", "htmltools", "htmlwidgets", "isoband", "jpeg", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "litedown", "magrittr", "markdown", "MASS", "memoise", "mime", "nlme", "patchwork", "pillar", "pkgconfig", "png", "polyclip", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S7", "sass", "scales", "shades", "stringi", "stringr", "systemfonts", "tibble", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "tweenr", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "publication_ready.Rmd", "filename": "publication_ready.html", "title": "Publication-Ready Output", "engine": "knitr::rmarkdown", "headings": [ "Color-Blind Friendly Palettes", "Custom Color Mapping", "Legend Placement", "Clade Labels", "Taxonomy Quality Report", "Batch Processing", "Reproducibility", "References & Acknowledgments" ], "created": "2026-09-26 16:40:32", "modified": "2026-09-26 16:40:32", "commits": 1 }, { "source": "quick_start.Rmd", "filename": "quick_start.html", "title": "Quick Start: From Tree File to Publication Figure", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Basic Usage", "Adding Titles", "Summarizing Results", "Saving Output", "Taxonomy Quality Check", "References & Acknowledgments" ], "created": "2026-09-26 16:40:32", "modified": "2026-09-26 16:40:32", "commits": 1 }, { "source": "taxonomy_formats.Rmd", "filename": "taxonomy_formats.html", "title": "Supported Taxonomy Label Formats", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Automatic Detection", "Quality Report", "Manual Format Specification", "NCBI Format Handling", "Custom Regex Patterns", "Embedded Format Parsing Strategies", "Custom Taxonomy Levels", "References & Acknowledgments" ], "created": "2026-09-26 16:40:32", "modified": "2026-09-26 16:40:32", "commits": 1 } ], "_score": 3.1760912590556813, "_indexed": false, "_nocasepkg": "rclade", "_universes": [ "cran", "zengzichao" ], "_indexurl": "https://zengzichao.r-universe.dev/Rclade", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-09-26T23:09:07.000Z", "distro": "resolute", "commit": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "fileid": "https://r2.ropensci.org/ea4291d646e2fdf6337b7c1b08e77029996da93c7b25ede2b5687e5714138ee8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36278184931" }, { "r": "4.6.1", "os": "linux", "version": "1.1.5", "date": "2026-09-26T23:08:39.000Z", "distro": "resolute", "commit": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "fileid": "https://r2.ropensci.org/2e41239607a9c4740b587e533b36c8802a15c7302ade224385da64e051e8a21c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36278184931" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.5", "date": "2026-09-26T23:09:28.000Z", "commit": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "fileid": "https://r2.ropensci.org/006023853405f2e5c80ab1ef2cbf48c1966de23ee9ee99f8e8946dc46caebc14", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/36278184931" }, { "r": "4.7.0", "os": "win", "version": "1.1.5", "date": "2026-09-26T23:07:38.000Z", "commit": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "fileid": "https://r2.ropensci.org/c118e0f45588de4bb181b8e625efe069c5b1bc3aa4f76531695357201712c7cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36278184931" }, { "r": "4.6.1", "os": "win", "version": "1.1.5", "date": "2026-09-26T23:07:57.000Z", "commit": "3250326e2e519b87fee1fa12b8921d302ef1a8a5", "fileid": "https://r2.ropensci.org/6b6c505e6f5745656512cacfcdb5811b0656bbc9de6210654466de117e1f6a5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36278184931" } ] }