Package: Rclade
Title: Automated Deep-Time Phylogenetic Tree Collapsing and
        Visualization
Version: 1.1.5
Authors@R: person("Zeng", "Zichao", email = "zengzichao@sjtu.edu.cn",
                  role = c("aut", "cre"))
Author: Zeng Zichao [aut, cre]
Maintainer: Zeng Zichao <zengzichao@sjtu.edu.cn>
Description: Provides a single-function pipeline for automated
        collapsing and visualization of large phylogenetic trees with
        geological timescales. Automatically parses taxonomic labels
        from multiple formats (GTDB, Silva, NCBI, embedded, custom),
        identifies Most Recent Common Ancestors (MRCAs), assigns
        color-blind-safe palettes, executes batch collapsing with
        automatic nesting-aware ordering, integrates 'deeptime'
        geologic time scales with adaptive time breaks and unit
        switching, and manages smart legend layout. Supports special
        ancestral node identifiers (LUCA, LACA, LBCA) for highlighting
        key nodes in the tree of life. Provides external taxonomy file
        support for trees with incomplete or missing taxonomic labels.
        Features real-time logging with timestamps, step tracking, and
        multiple log levels. Includes comprehensive input validation
        for tree and sequence file formats. Reduces a 60-line manual
        workflow to a single function call while preserving full
        compatibility with the 'ggtree'/'deeptime' ecosystem. The
        visualization pipeline builds on 'ggtree' Yu et al. (2017)
        <doi:10.1111/2041-210X.12628>, 'deeptime' Gearty (2025)
        <doi:10.1080/20964471.2025.2537516>, and 'ape' Paradis and
        Schliep (2019) <doi:10.1093/bioinformatics/bty633>.
License: MIT + file LICENSE
Depends: R (>= 4.1.0)
Imports: ape (>= 5.0), ggtree (>= 4.0.0), deeptime (>= 1.0), ggplot2
        (>= 3.5.0), rlang, stringr (>= 1.5), tidytree (>= 0.4),
        viridisLite
Suggests: treeio (>= 1.0), phangorn (>= 2.0), RColorBrewer, cowplot (>=
        1.1), patchwork (>= 1.1), shiny (>= 1.7), optparse (>= 1.7),
        yaml, vdiffr (>= 1.0), testthat (>= 3.0), knitr, rmarkdown,
        covr, filelock, withr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/testthat/edition: 3
URL: https://github.com/zengzichao/Rclade,
        https://zengzichao.github.io/Rclade/
BugReports: https://github.com/zengzichao/Rclade/issues
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libicu-dev libjpeg-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev
Repository: https://zengzichao.r-universe.dev
Date/Publication: 2026-10-01 13:38:30 UTC
RemoteUrl: https://github.com/zengzichao/rclade
RemoteRef: HEAD
RemoteSha: 9a1a6288be471bd6abfea3e9ad9a3774030985bc
NeedsCompilation: no
Packaged: 2026-10-01 19:54:00 UTC; root