Package: taxodist
Title: Taxonomic Hierarchy Distances and Lineage Analysis
Version: 0.9.0
LazyData: true
Authors@R: person("Rodrigo Fonseca", "Villa", email = "rodrigo03.villa@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0009-0005-2938-2270"))
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Description: Computes distances between taxonomic hierarchy nodes using lineage
    data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>. For
    distinct nodes, distance is defined as the reciprocal of the depth of their
    most recent common ancestor; identical nodes have distance zero. This
    definition yields an ultrametric within each connected hierarchy. Functions
    are provided for auditable name resolution, online or user-supplied lineage
    analysis, clade membership, pairwise, matrix, and cross-set distance
    calculation, classification trees with named clades, hierarchical
    clustering, principal coordinates analysis, portable and comparable JSON
    analysis bundles, and cache management. Distance matrices are returned as
    base R 'dist' objects. The distances represent classification depth rather
    than evolutionary time or phylogenetic branch length.
Language: en-US
License: GPL (>= 3)
URL: https://github.com/rodrigosqrt3/taxodist
BugReports: https://github.com/rodrigosqrt3/taxodist/issues
Encoding: UTF-8
RoxygenNote: 7.3.3
SystemRequirements: internet access for online taxonomy retrieval
Depends: R (>= 4.1.0)
Imports: httr (>= 1.4.0), rvest (>= 1.0.0), stringr (>= 1.4.0), cli (>=
        3.0.0), jsonlite (>= 1.8.0), utils, stats, graphics, tools
Suggests: testthat (>= 3.0.0), mockery, knitr, rmarkdown, xml2, ape,
        vegan
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-10-12 12:34:06 UTC; rodri
Author: Rodrigo Fonseca Villa [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-2938-2270>)
Repository: CRAN
Date/Publication: 2026-10-12 13:30:02 UTC
Built: R 4.6.1; ; 2026-10-12 15:30:07 UTC; unix
