Package: taxodist 0.5.0

taxodist: Taxonomic Distance and Phylogenetic Lineage Computation

Computes phylogenetic distances between any two taxa using hierarchical lineage data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>, a comprehensive curated classification of all life based on Systema Naturae 2000 (Brands, 1989 <http://taxonomicon.taxonomy.nl>). Given any two taxon names, retrieves their full lineages, identifies the most recent common ancestor (MRCA), and computes a dissimilarity index based on lineage depth. Outputs native dist objects, enabling direct integration with the R statistical ecosystem for hierarchical clustering, principal coordinate analysis (PCoA), and multivariate ecological analyses. Supports individual distance queries, pairwise distance matrices, clade filtering, and lineage utilities.

Authors:Rodrigo Fonseca Villa [aut, cre]

taxodist_0.5.0.tar.gz
taxodist_0.5.0.zip(r-4.7)taxodist_0.5.0.zip(r-4.6)taxodist_0.5.0.zip(r-4.5)
taxodist_0.5.0.tgz(r-4.6-any)taxodist_0.5.0.tgz(r-4.5-any)
taxodist_0.5.0.tar.gz(r-4.7-any)taxodist_0.5.0.tar.gz(r-4.6-any)
taxodist_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
taxodist/json (API)

# Install 'taxodist' in R:
install.packages('taxodist', repos = c('https://rodrigosqrt3.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rodrigosqrt3/taxodist/issues

Datasets:

On CRAN:

Conda:

5.07 score 13 scripts 338 downloads 23 exports 24 dependencies

Last updated from:dce8bd0ef6. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE127
source / vignettesOK174
linux-release-x86_64NOTE146
macos-release-arm64NOTE96
macos-oldrel-arm64NOTE132
windows-develNOTE113
windows-releaseNOTE85
windows-oldrelNOTE105
wasm-releaseOK126

Exports:cache_infocheck_coverageclear_cacheclosest_relativecompare_lineagesdistance_matrixfilter_cladefocal_distancesget_lineageget_lineage_by_idget_taxonomicon_idis_memberlineage_depthload_cachemrcasave_cacheshared_cladestaxo_clustertaxo_distancetaxo_heatmaptaxo_ordinatetaxo_pathtaxo_search

Dependencies:askpassclicurlgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6rlangrvestselectrstringistringrsystibbleutf8vctrsxml2

Introduction to taxodist
What is taxodist? | The distance metric | Basic usage | Getting a lineage | Computing distance between two taxa | Finding the most recent common ancestor | Working with multiple taxa | Pairwise distance matrix | Built-in Clustering and Ordination | Hierarchical Clustering | PCoA | Heatmap visualization | Finding the closest relative | Lineage utilities | Comparing lineages side by side | Listing shared clades | Testing clade membership | Filtering a list of taxa by clade | Coverage and caching | Checking coverage before a large run | Caching | Persisting the cache across sessions | A note on lineage depth | Data source and citation
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-06-02
Started: 2026-03-09

Statistical Applications of taxodist
Example dataset: threatened mammals of Brazil | Phylogenetic tree with ape | Taxonomic diversity with vegan | Clarke and Warwick indices (taxondive) | Mantel test with vegan | PERMANOVA with vegan | A complete workflow | References
Rendered fromstatistical-applications.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2026-04-21

Readme and manuals

Help Manual

Help pageTopics
taxodist: Taxonomic Distance and Phylogenetic Lineage Computationtaxodist-package taxodist
Inspect the current taxodist lineage cachecache_info
Check whether a taxon is covered by The Taxonomiconcheck_coverage
Clear the taxodist lineage cacheclear_cache
Find the closest relative of a taxon among a set of candidatesclosest_relative
Compare lineages of two taxa side by sidecompare_lineages
Compute pairwise taxonomic distances for a set of taxadistance_matrix
Filter a vector of taxa to those belonging to a given cladefilter_clade
Compute distances from a focal taxon to a community of taxafocal_distances
Retrieve the full taxonomic lineage of a taxon by nameget_lineage
Retrieve the full taxonomic lineage of a taxonget_lineage_by_id
Find the Taxonomicon ID for a taxon nameget_taxonomicon_id
Test whether one taxon is nested within anotheris_member
Get the lineage depth of a taxonlineage_depth
Load a previously saved taxodist cache from diskload_cache
Compute the most recent common ancestor of two taxamrca
Plot method for taxodist_cluster objectsplot.taxodist_cluster
Plot method for taxodist_ord objectsplot.taxodist_ord
Print method for taxodist_focal objectsprint.taxodist_focal
Print method for taxodist_path objectsprint.taxodist_path
Print method for taxodist distance resultsprint.taxodist_result
Save the taxodist lineage cache to disksave_cache
List all clades shared between two taxashared_clades
Summary method for taxodist_ord objectssummary.taxodist_ord
Cluster taxa by taxonomic distancetaxo_cluster
Compute the phylogenetic distance between two taxataxo_distance
Plot a taxonomic heatmaptaxo_heatmap
Ordinate taxa in taxonomic distance spacetaxo_ordinate
Get the taxonomic path between two taxataxo_path
Search The Taxonomicon for a taxon nametaxo_search
Reference Taxonomic Dataset (taxobase)taxobase