Package: taxodist 0.6.0

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 lineage retrieval and comparison, clade membership, pairwise and matrix distance calculation, hierarchical clustering, principal coordinates analysis, 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_0.6.0.tar.gz
taxodist_0.6.0.zip(r-4.7-any)taxodist_0.6.0.zip(r-4.6-any)taxodist_0.6.0.zip(r-4.5-any)
taxodist_0.6.0.tgz(r-4.6-any)taxodist_0.6.0.tgz(r-4.5-any)
taxodist_0.6.0.tar.gz(r-4.7-any)taxodist_0.6.0.tar.gz(r-4.6-any)
taxodist_0.6.0.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:

5.32 score 14 scripts 128 downloads 23 exports 24 dependencies

Last updated from:5159a6d5f5. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE164
source / vignettesOK348
linux-releaseNOTE139
macos-releaseNOTE94
macos-oldrelNOTE89
windows-develNOTE73
windows-releaseNOTE74
windows-oldrelNOTE72
wasm-releaseOK118

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
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 | Finding the closest candidates | Focal distances | Clade operations | Testing membership | Filtering taxa | Shared clades and lineage comparison | Clustering, ordination, and visualization | Hierarchical clustering | Principal coordinates analysis | Heatmap | Name resolution and coverage | Cache management | Interpretation and reproducibility | Data source and citation
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
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: 2026-08-06
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 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 taxonomic hierarchy 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