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
Roxygen: list(markdown = TRUE)
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
Config/pak/sysreqs: libicu-dev libxml2-dev libssl-dev
Repository: https://rodrigosqrt3.r-universe.dev
Date/Publication: 2026-10-12 12:11:14 UTC
RemoteUrl: https://github.com/rodrigosqrt3/taxodist
RemoteRef: HEAD
RemoteSha: bdb9906b43f34ec35586414e484e4a0cbff1d0ea
NeedsCompilation: no
Packaged: 2026-10-12 16:20:30 UTC; root
Author: Rodrigo Fonseca Villa [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-2938-2270>)