R Observatory: Metrics for hilldiv3 version 3.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hilldiv3

3.1.1Package record

Integral Analysis of Diversity Based on Hill Numbers

0packages depend

285downloads / year

79.4%test coverage

13/13flavors OK

Overview

About

Maintained by Antton AlberdiCRAN page ↗GitHub ↗Website ↗Issues ↗

Measures and compares the diversity of biological communities (e.g. tables of operational taxonomic units (OTUs), amplicon sequence variants (ASVs) or metagenome-assembled genomes (MAGs)) based on Hill numbers, in a unified framework for neutral, phylogenetic and functional diversity measurement, diversity partitioning, (dis)similarity measurement, diversity profiles, evenness, redundancy and attribution of Hill power-sum weight to taxa and sets. The statistical framework encompasses richness, Shannon and Simpson diversity, Faith's phylogenetic diversity (PD), Rao's quadratic entropy and Sorensen- and UniFrac-type dissimilarities, all grounded in a single Hill-number framework. Methods are described in Jost (2007) doi:10.1890/06-1736.1, Chao et al. (2010) doi:10.1098/rstb.2010.0272, Chiu et al. (2014) doi:10.1890/12-0960.1 and reviewed in Alberdi & Gilbert (2019) doi:10.1111/1755-0998.13014. Optional import adapters interoperate with the Bioconductor packages 'phyloseq', 'SummarizedExperiment' and 'TreeSummarizedExperiment', which are available from https://bioconductor.org.

Changes in 3.1.1

Documentation only: links in the README to CONTRIBUTING.md, CODE_OF_CONDUCT.md and CITATION.cff now use absolute URLs, fixing the invalid file URI note raised by the CRAN incoming checks.

From NEWS.md in the release

Install

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

install.packages("hilldiv3", 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("alberdilab/hilldiv3")

Development version from alberdilab/hilldiv3. Installs pak first if it is not already available.

# 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-hilldiv3

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-hilldiv3

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: 2.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK6 OK2026-10-07

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.1.1

READMEYes · 773 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 3.1.1Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 19 (2 internal)includes a package overview page
Examples that run: 100%15 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 11%

Vignettes (1)

Getting started with hilldiv3 HTML

How these are measured

Downloads

285

CRAN downloads in the past year

Rank #25,334 · ~1/day · ~24/mo

hilldiv3 Releases R versions

Daily download trend is not available in this view yet.

28530 days

28590 days

2851 year

Compare downloads with other packages →

How downloads are counted

Repository

alberdilab/hilldiv3 ↗Organization: alberdilab

0Stars

1Forks

0Open issues

0Open PRs

2Releases

39Commits

1Commit identities

License file reads as GPL-3.0 · 39 commits · Last activity 2026-10-08

Responsiveness

not measured

Releases over time

2026-10-07 · 12026-10-08 · 2

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/alberdilab/hilldiv3 on 2026-10-11.

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 (3)

Code of conductContributing guideIssue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-08 · The repository has a site deploy workflow

pkgdown site last built 2026-10-08, before release 3.1.1 (2026-10-16)

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrLint workflow

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing hilldiv3 adds 5 packages (5 with compiled code, 4.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, ape 1.4 MB, rlang 766 KB.

Depends (1)

R >= 4.1.0

Imports (8)

ape cligrDevicesgraphicsmethodsrlangstatsutils

LinkingTo (0)

none

Suggests (14)

clusterfurrr future ggplot2 knitr patchwork phyloseq progressr rmarkdown SummarizedExperiment testthat (>= 3.0.0)tibble TreeSummarizedExperiment vegan

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 (1)

Antton Alberdi

Author, Maintainer since 3.0.0 (2026)

Releases (2)

Pick two releases to compare their code metrics.

3.1.1Latest
record
2026-10-16 · current release · diff ↗ ·
added 1 export
hillshare
3.0.0
record
2026-10-06 ·
3 days in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-03 21:57 to 2026-10-06 15:36 UTC, in 13 readings.
R
R 4.6.0 released · 2026-04-24

Across CRAN, the median accepted release of the past year spent 15 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-10-06
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.7 KB / 3 files
Download size: 68 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hilldiv3")

Format

Alberdi, A. (2026). hilldiv3: Integral Analysis of Diversity Based on Hill Numbers (Version 3.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.hilldiv3

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 hilldiv3 version 3.1.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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