Package: taxodist 0.9.0

taxodist: Taxonomic Hierarchy Distances and Lineage Analysis

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.

Authors:Rodrigo Fonseca Villa [aut, cre]

taxodist_0.9.0.tar.gz
taxodist_0.9.0.zip(r-4.7-any)taxodist_0.9.0.zip(r-4.6-any)taxodist_0.9.0.zip(r-4.5-any)
taxodist_0.9.0.tgz(r-4.6-any)taxodist_0.9.0.tgz(r-4.5-any)
taxodist_0.9.0.tar.gz(r-4.7-any)taxodist_0.9.0.tar.gz(r-4.6-any)
taxodist_0.9.0.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:

5.77 score 2 stars 15 scripts 404 downloads 31 exports 23 dependencies

Last updated from:bdb9906b43. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE178
source / vignettesOK162
linux-releaseNOTE165
macos-releaseNOTE127
macos-oldrelNOTE144
windows-develNOTE103
windows-releaseNOTE92
windows-oldrelNOTE98
wasm-releaseOK91

Exports:cache_infocheck_coverageclear_cacheclosest_relativecompare_bundlescompare_lineagescross_distancesdistance_matrixfilter_cladefocal_distancesget_lineageget_lineage_by_idget_taxonomicon_idis_memberlineage_depthload_cachemrcaread_taxodist_bundlesave_cacheshared_cladestaxo_bundletaxo_clustertaxo_distancetaxo_from_lineagestaxo_heatmaptaxo_ordinatetaxo_pathtaxo_resolvetaxo_searchtaxo_treewrite_taxodist_bundle

Dependencies:askpassclicurlgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangrvestselectrstringistringrsystibbleutf8vctrsxml2

Introduction to taxodist
Overview | What the distance represents | Distance and membership are different | [d(\textit{Tyrannosaurus},\textit{Dinosauria}) | Reproducible packaged examples | Stored lineages | Stored pairwise comparison | Reference distance matrix | Live lineage queries | Retrieving a lineage | Computing a pairwise distance | Finding the MRCA | Inspecting the path between nodes | Working with multiple taxa | Constructing a distance matrix | Distances between two sets of taxa | Finding the closest candidates | Focal distances | Clade operations | Testing membership | Filtering taxa | Shared clades and lineage comparison | Clustering, ordination, and visualization | Hierarchical clustering | Classification trees | Principal coordinates analysis | Heatmap | Name resolution and coverage | Cache management | Interpretation and reproducibility | Data source and citation
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-03-09

Statistical Applications of taxodist
Overview | Inspecting the distance matrix | Hierarchical clustering | Tree representation with ape | Principal coordinates analysis | Taxonomic diversity and distinctness | Mantel test | PERMANOVA | Multivariate dispersion | Complete live workflow | Reporting recommendations | References
Rendered fromstatistical-applications.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-04-21

Methodological Notes and Limitations
Scope | Definition | Ultrametric property | Dependence on the source classification | Ambiguous and missing taxa | Interpretation | Recommended reporting
Rendered frommethodological-notes.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
Started: 2026-08-06

Readme and manuals

Help Manual

Help pageTopics
taxodist: Taxonomic Hierarchy Distances and Lineage Analysistaxodist-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 two taxodist bundlescompare_bundles
Compare lineages of two taxa side by sidecompare_lineages
Compute taxonomic distances between two sets of taxacross_distances
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 a taxodist bundleprint.taxodist_bundle
Print a taxodist bundle comparisonprint.taxodist_bundle_comparison
Print method for taxodist_focal objectsprint.taxodist_focal
Print method for taxodist_path objectsprint.taxodist_path
Print an auditable taxon-resolution tableprint.taxodist_resolution
Print method for taxodist distance resultsprint.taxodist_result
Read a portable taxodist JSON bundleread_taxodist_bundle
Save the taxodist lineage cache to disksave_cache
List all clades shared between two taxashared_clades
Summary method for taxodist_ord objectssummary.taxodist_ord
Create a portable taxodist analysis bundletaxo_bundle
Cluster taxa by taxonomic distancetaxo_cluster
Compute the taxonomic hierarchy distance between two taxataxo_distance
Create an auditable resolution from user-supplied lineagestaxo_from_lineages
Plot a taxonomic heatmaptaxo_heatmap
Ordinate taxa in taxonomic distance spacetaxo_ordinate
Get the taxonomic path between two taxataxo_path
Resolve taxon names in a batch with an auditable resulttaxo_resolve
Search The Taxonomicon for a taxon nametaxo_search
Build a taxonomic tree from lineagestaxo_tree
Reference Taxonomic Dataset (taxobase)taxobase
Write a taxodist bundle as portable JSONwrite_taxodist_bundle