R Observatory: Metrics for APCalign version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

APCalign

2.0.1Package record

Resolving Plant Taxon Names Using the Australian Plant Census

0packages depend

8Kdownloads / year

88.4%test coverage

13/13flavors OK

Overview

About

Maintained by Elizabeth WenkCRAN page ↗GitHub ↗Website ↗Issues ↗

The process of resolving and updating taxon names is necessary when working with biodiversity data. 'APCalign' uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. 'APCalign' also supplies information about the establishment status (i.e. native or introduced) of plant taxa across different states/territories.

Changes in 2.0.1

fuzzy_match() no longer confirms a fuzzy match against a candidate that drops an aff./cf./x qualifier present in the query. Its check_match() confirmation step only compared word positions up to the shorter of query/candidate, so Acacia aff. aneura ("resembles *Acacia aneura*, not confidently identified") could fuzzy-match past its qualifier to the unrelated accepted species Acacia aptaneura instead of being capped at genus rank. A query containing aff, cf, or x as a standalone word now requires the candidate to contain that same token, or the candidate is rejected outright before the coarser word-position check runs; genuine aff./cf.-qualified synonyms and named hybrids that still need fuzzy matching to fix a typo are unaffected.
standardise_taxon_rank() no longer corrupts rank values that are already English, or that merely contain a Latin rank term as a substring. sectio is a literal prefix of its own translation (section) and forma sits inside informal, so replacing either anywhere in the input silently mangled section/subsection/zoosection into sectionn/subsectionn/zoosectionn, and informal/informal group into informl/informl group. Both terms are now matched only as the last word of the value, which still translates the prefixed ranks that need it (subsectio, subforma). APC/APNI rank values are unaffected — the fix changes output only for the zoological and DwC vocabularies, where it was found (traitecoevo/taxonAlign#11).
standardise_names() no longer rewrites affinis to aff. when it is the species epithet of an infraspecific name — that is, when the next word is a rank marker (subsp., var., f., ser., cv. and their unabbreviated or unpunctuated variants). Previously Gomphrena affinis subsp. pilbarensis became Gomphrena aff. subsp. pilbarensis, a name that exists nowhere, so it could only ever align to genus rank. Eight APC/APNI names were affected, three of them currently accepted; all now align at their own rank. A trailing affinis (Acacia affinis) was already left alone and still is. Two hybrid formulas of the form Genus affinis x Genus epithet are still rewritten, and are left for a follow-up.
Fix malformed aligned_reason text for fuzzy genus-level aff./affinis matches (match_06b/06c/06d), which previously appended the date without a separating (.
align_taxa(full = TRUE) no longer leaks the internal identifier_string, identifier_string2 and aligned_name_tmp columns when every name is aligned before the last match step runs. The output is now the documented set of columns in all cases.
native_anywhere_in_australia() now checks for missing taxonomic resources before building the state-origin matrix, so an offline call reports the problem once instead of once per function that gives up. Its native/introduced test also now reads only the state columns, so a taxon whose name contains "native" (e.g. the nativitatis epithets) can no longer be misclassified.
Internal refactor of match_taxa(): the ~54 match steps now share helper functions rather than repeating the same block of code. Alignment output is unchanged.
Internal refactor: the duplicated gsub()-wrapper helper in standardise_names(), strip_names() and strip_names_extra() is now a single shared gsub_perl(), and a redundant nested copy of relevel_taxonomic_status_preferred_order() inside synonyms_for_accepted_names() has been removed in favour of the existing top-level function. Behaviour is unchanged.

From NEWS.md in the release

Install

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

install.packages("APCalign", 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("traitecoevo/APCalign")

Development version from traitecoevo/APCalign. 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-apcalign

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-APCalign

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-APCalign

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: 7.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-13
ERROR13 OK, 1 ERROR2026-03-12
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 645 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 2.0.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 19 (2 internal)includes a package overview page
Examples that run: 31%5 run in a plain check · 11 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 5%

Vignettes (2)

APCalign HTML
updating taxon names HTML

How these are measured

Downloads

8K

CRAN downloads in the past year

Rank #4,716 · ~22/day · ~665/mo

Releases R versions

Daily download trend is not available in this view yet.

75330 days

1.7K90 days

8K1 year

Compare downloads with other packages →

Also on184 r2u67 autocran

How downloads are counted

Repository

traitecoevo/apcalign ↗Organization: traitecoevo

5Stars

7Forks

3Open issues

0Open PRs

18Releases

237Commits

8Commit identities

r-package

237 commits · Last activity 2026-10-14 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 87%
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-25 · 52026-07-07 · 5

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/traitecoevo/apcalign on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-23 · The repository has a site deploy workflow

pkgdown site last built 2026-09-23

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-03-23
Seen in the repository: .claude
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 14 crediting it in the message

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

Review tools

Copilot code review
Commits: at least 1 accepting its review suggestions

Models named in its commits

Claude Sonnet 55 commits · Aug to Sep 2026
Claude Opus 4.84 commits · Jun to Aug 2026
Claude Sonnet 4.63 commits · Mar 2026
Claude Fable 52 commits · Jul to Aug 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing APCalign adds 39 packages (24 with compiled code, 27 MB of source tarballs). Heaviest: stringi 11 MB, arrow 4.2 MB, openssl 1.1 MB.

Depends (1)

R >= 4.1.0

Imports (12)

readr purrr dplyr stringr stringi stringdist crayon httr jsonlite curl arrow rlang

LinkingTo (0)

none

Suggests (8)

janitor tidyr covr knitr rmarkdown kableExtra here testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Author, Contributor

Author, Contributor

Author, Contributor

Contributor

Previously maintained by Daniel Falster (0.1.2 to 1.1.3).

Releases (9)

Pick two releases to compare their code metrics.

2.0.1Latest
record
2026-09-09 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.0
record
2026-03-27 · diff ↗ ·
added 2 exports
clear_cached_resources, synonyms_for_accepted_names
R
R 4.5.0 released · 2025-04-11
1.1.3
record
2025-02-11 · diff ↗
unarchivedReturned to CRAN
2025-01-28
1.1.2
record
2025-01-28 · diff ↗ ·
added 1 export
get_versions
archivedRemoved from CRAN
2025-01-10
issues were not corrected despite reminders
1.1.0
record
2024-08-19 · diff ↗ ·
added 1 export
get_apc_genus_family_lookup
1.0.2
record
2024-08-18 · diff ↗
unarchivedReturned to CRAN
2024-05-30
1.0.1
record
2024-05-30 · diff ↗ ·
added 3 exports
default_version, standardise_taxon_rank, strip_names_extra
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-03-26
policy violation On Internet access
0.1.3
record
2023-11-16 · diff ↗
0.1.2
record
2023-10-11

Show 1 earlier eventHide 1 earlier event

R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-11
Total releases: 9 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 6.1 KB / 1 file
Download size: 3.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("APCalign")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1071/bt24014.

The repository also keeps a CITATION.cff.

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 APCalign version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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