taxodist

0.5.0

Taxonomic Distance and Phylogenetic Lineage Computation

0packages depend

1.4Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Rodrigo Fonseca VillaFirst published 2026-03-245 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("taxodist", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("rodrigosqrt3/taxodist")

Development version from rodrigosqrt3/taxodist. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-taxodist

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-taxodist

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-taxodist

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.14

100.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-05-14
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-29
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-24
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 264 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 4%
Documented parameters: 100%
Return-value docs: 100%
References docs: 6%

Downloads

1.4K

CRAN downloads in the past year

Rank #10,170 · ~4/day · ~118/mo

Releases R versions

Daily download trend is not available in this view yet.

24230 days

1.1K90 days

1.4K1 year

Compare downloads with other packages →

Also on47 r2u34 autocran

Repository

GitHub ↗ rodrigosqrt3/taxodist

0Stars

0Forks

0Open issues

0Open PRs

5Releases

66Commits

1Contributors

License GPL-3.0 · 66 commits · Last activity 2026-06-09

Releases over time

2026-03-11 · 12026-07-07 · 5

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/rodrigosqrt3/taxodist on 2026-07-19.

Continuous integration (1)

GitHub Actions

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (8)

httr rvest stringr purrr cliutilsstatsgraphics

LinkingTo (0)

none

Suggests (8)

testthat mockery knitr rmarkdown xml2 ape vegan webmockr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,138 (65%)Rd 1,062 (22%)Vignettes 648 (13%)

Code characteristics

Object systems

S36

Cyclomatic complexity: 3.0 median / 21 max
Test cases: 148 / 1.14 per code line
System requirements: 1 external

Test coverage

Line coverage

100%

Expression

100.0%

Tests / Examples

100.0% / 0% ex

Functions

31 23 exported

Complexity

4.7 avg / 21 max

Call network

31 nodes / 27 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

31 functions

Function	Cyclo	Coverage
cache_info exp	2	100%
check_coverage exp	1	100%
clear_cache exp	1	100%
closest_relative exp	3	100%
compare_lineages exp	9	100%
distance_matrix exp	10	100%

People & History

People (1)

Maintainer (1)

Rodrigo Fonseca Villa

Author, Maintainer

Authors (1)

Rodrigo Fonseca Villa

Author, Maintainer

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

0.5.0Latest
2026-06-02 · current release · diff ↗
0.4.0
2026-05-25 · diff ↗
0.3.0
2026-05-06 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.0
2026-04-22 · diff ↗
0.1.0
2026-03-24
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-24
Total releases: 5 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 40 KB / 1 file
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

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