R Observatory: Metrics for canaper version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

canaper

1.0.1Package record

Categorical Analysis of Neo- And Paleo-Endemism

0packages dependsuggested by 1

3.8Kdownloads / year

99.1%test coverage

13/13flavors OK

Overview

About

Maintained by Joel H. NittaCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functions to analyze the spatial distribution of biodiversity, in particular categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al (2014) doi:10.1038/ncomms5473. 'canaper' conducts statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species.

Changes in 1.0.1

DOCUMENTATION

Fix installation of dependencies when installing from r-universe repo (https://github.com/ropensci/canaper/commit/774d89f58af8c55dda178fff3d324b2e48b749fd)

Add warning for abundance data, since CANAPE analysis in canaper treats it the same as presence-absence data. Thanks to an anonymous reviewer for the suggestion (https://github.com/ropensci/canaper/commit/143cadee62a9bf3c5256e3d92240c6243bf803e4)

BUG FIXES

Fix internal functions count_higher() and count_lower() that did not distinguish between NA and NA_integer_. Thanks to @hadley (Hadley Wickham) (https://github.com/ropensci/canaper/commit/ff6012d6b817d3ba8765d8c8b009e2818da2ab9f)

OTHER

Remove tidyverse from vignettes and Suggests. Thanks to @hadley for pointing this out. (https://github.com/ropensci/canaper/commit/49aa94b418ad9e85f30e6f751651386674a367d8)

From NEWS.md in the release

Install

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

install.packages("canaper", 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/canaper")

Development version from ropensci/canaper. 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-canaper

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-canaper

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-canaper

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: 4.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-10

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 950 wordsVignettesYes · 3 · staticNEWSYes · 33% structured · mentions 1.0.1Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 19 (1 internal)includes a package overview page
Examples that run: 83%15 run in a plain check · 3 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: 47%

Vignettes (3)

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #8,929 · ~10/day · ~318/mo

Releases R versions

Daily download trend is not available in this view yet.

38430 days

1.1K90 days

3.8K1 year

Compare downloads with other packages →

Also on91 r2u14 autocran

How downloads are counted

Repository

ropensci/canaper ↗Organization: ropensci

9Stars

2Forks

10Open issues

0Open PRs

5Releases

297Commits

7Commit identities

biodiversitycanape

297 commits · Last activity 2023-05-07 · +12.5% stars, 30d · Default branch at 1.0.1.9000, ahead of CRAN 1.0.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-04-07 · 72026-10-02 · 9

How these are measured

PracticesBeta

18 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/ropensci/canaper on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (4)

Code of conduct (inherited from ropensci)Contributing guideIssue templatesPR template

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2022-09-06 · The repository has a site deploy workflow

pkgdown site last built 2023-05-07

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 5 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

codemeta.json

Automation and maintenance (1)

pre-commit

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Installing canaper adds 68 packages (36 with compiled code, 47 MB of source tarballs). Heaviest: sf 9.3 MB, igraph 4.8 MB, s2 2.8 MB.

Depends (1)

R >= 4.1.0

Imports (11)

ape assertr assertthat dplyr future.apply phyloregion progressr purrrstatstibble vegan

LinkingTo (0)

none

Suggests (16)

rmarkdown knitr future tictoc patchwork testthat (>= 3.0.0)stringr magrittr covr picante withr fs readr usethis scales colorBlindness

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

phylospatial

How these are counted

Code & Tests

Datasets

People & History

People (5)

Joel H. Nitta

Author, Maintainer since 1.0.0 (2022)

Wataru Iwasaki

Contributor

Shawn W. Laffan

Contributor, Data contributor

Brent D. Mishler

Contributor, Data contributor

Klaus Schliep

Reviewer

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.1Latest
record
2023-05-05 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.0
record
2022-10-04
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-04
Total releases: 2 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 66 KB / 12 files
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("canaper")

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

It points to 10.5281/zenodo.5094032.

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 canaper version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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