R Observatory: Metrics for taxlist version 0.3.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

taxlist

0.3.5

Handling Taxonomic Lists

1packages depend

4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Miguel AlvarezCRAN page ↗GitHub ↗Website ↗Issues ↗

Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (https://www.synbiosys.alterra.nl/turboveg/) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.

Install

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

install.packages("taxlist", 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("ropensci/taxlist")

Development version from ropensci/taxlist. 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-taxlist

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-taxlist

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-taxlist

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.0 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.5

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 0.3.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 47 (10 internal)includes a package overview page
Examples that run: 100%33 run in a plain check
Exported functions with examples: 91%
Documented parameters: 90%
Return-value docs: 87%
Help pages citing references: 4%

Vignettes (1)

Applying taxlist to species lists on diversity records

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #10,102 · ~11/day · ~333/mo

Releases R versions

Daily download trend is not available in this view yet.

39230 days

97590 days

4K1 year

Compare downloads with other packages →

Also on104 r2u8 autocran

How downloads are counted

Repository

ropensci/taxlist ↗Organization: ropensci

13Stars

4Forks

13Open issues

0Open PRs

16Releases

444Commits

23Commit identities

444 commits · Last activity 2026-02-03 · 0% stars, 30d · Default branch at 0.3.6, ahead of CRAN 0.3.5 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-01-24 · 122026-07-07 · 13

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ropensci/taxlist on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Docs source (2)

README.qmdpkgdown

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

VS Code

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing taxlist adds 63 packages (34 with compiled code, 53 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, rcrossref 4.6 MB.

Depends (1)

R >= 4.3

Imports (9)

biblioforeignmethodsstatsstringdist stringi stringrtoolsutils

LinkingTo (0)

none

Suggests (5)

ape knitr rmarkdown taxa testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

taxnames

How these are counted

Code & Tests

Datasets

People & History

People (4)

Miguel Alvarez

Author, Maintainer since 0.1.0 (2017)

Zachary Foster

Contributor · added in 0.1.7

Sam Levin

Reviewer · added in 0.2.0

Margaret Siple

Reviewer · added in 0.2.0

Releases (17)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.5Latest
record
2025-11-28 · current release · diff ↗ ·
added 3 exports
reindex<-, reindex, sort_taxa
R
R 4.5.0 released · 2025-04-11
0.3.0
record
2024-07-03 · diff ↗ ·
removed 1 export
insert_rows

added 4 exports
merge_to_parent, prune_levels, sort_backups, taxlist2df
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.2.4
record
2023-03-12 · diff ↗ ·
added 28 exports
accepted_name<-, basionym<-, change_concept<-, levels<-, levels<-.taxlist, taxon_names<-, taxon_relations<-, taxon_traits<-, taxon_views<-, accepted_name, add_synonym, basionym, delete_name, get_children, get_parents, id_generator, id_solver, levels, merge_taxa, synonyms, tax2traits, taxon_names, taxon_relations, taxon_traits, taxon_views, tnrs, update_name, update_trait
0.2.3
record
2022-09-12 · diff ↗ ·
added 2 exports
df2taxlist, print_name
R
R 4.2.0 released · 2022-04-22
0.2.2
record
2021-07-15 · diff ↗ ·
added 1 export
taxlist2taxmap
R
R 4.1.0 released · 2021-05-18
0.2.1
record
2021-03-29 · diff ↗
0.2.0
record
2020-10-07 · diff ↗
0.1.9
record
2020-05-31 · diff ↗
0.1.8
record
2020-04-29 · diff ↗ ·
added 1 export
taxmap2taxlist
R
R 4.0.0 released · 2020-04-24

Show 11 earlier eventsHide 11 earlier events

0.1.7
record
2020-01-10 · diff ↗ ·
added 5 exports
insert_rows, replace_idx, replace_na, replace_view, replace_x
R
R 3.6.0 released · 2019-04-26
0.1.6
record
2019-01-21 · diff ↗
0.1.5
record
2018-06-29 · diff ↗ ·
added 3 exports
add_parent, add_trait, add_level
0.1.4
record
2018-05-03 · diff ↗ ·
added 2 exports
dissect_name, load_last
R
R 3.5.0 released · 2018-04-23
0.1.3
record
2018-01-05 · diff ↗
0.1.2
record
2017-08-06 · diff ↗
0.1.1
record
2017-07-23 · diff ↗
0.1.0
record
2017-06-15
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-06-15
Total releases: 17 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3
Bundled data: 63 KB / 1 file
Download size: 2.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("taxlist")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for taxlist version 0.3.5 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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