R Observatory: Metrics for ecodive version 2.2.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ecodive

2.2.6Package record

Parallel and Memory-Efficient Ecological Diversity Metrics

1packages depend

18.9Kdownloads / year

98.8%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel P. SmithCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Alkek Center for Metagenomics and Microbiome Research

Computes alpha and beta diversity metrics using concurrent 'C' threads. Metrics include 'UniFrac', Faith's phylogenetic diversity, Bray-Curtis dissimilarity, Shannon diversity index, and many others. Also parses newick trees into 'phylo' objects and rarefies feature tables.

Changes in 2.2.6

When using CLR normalization:
Warns when zeros are detected and pseudocount is NULL.
Then continues with pseudocount <- min(counts[counts>0]) / 2.

Breaking Changes

norm now defaults to "none" instead of "percent".
norm parameter was removed from some beta diversity functions.

From NEWS.md in the release

Install

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

install.packages("ecodive", 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("cmmr/ecodive")

Development version from cmmr/ecodive. 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-ecodive

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-ecodive

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-ecodive

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-devel-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 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.6

READMEYes · 495 wordsVignettesYes · 4 · staticNEWSYes · 100% structured · mentions 2.2.6Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 66 (8 internal)
Examples that run: 100%56 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 11%
Help pages citing references: 74%

Vignettes (4)

How these are measured

Downloads

18.9K

CRAN downloads in the past year

Rank #2,392 · ~52/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.3K30 days

6.8K90 days

18.9K1 year

Compare downloads with other packages →

Also on939 r2u5 autocran11.1K conda_forge

How downloads are counted

Repository

cmmr/ecodive ↗Organization: cmmr

9Stars

0Forks

0Open issues

0Open PRs

5Releases

222Commits

1Commit identities

222 commits · Last activity 2026-10-02 · +12.5% stars, 30d · Default branch at 2.3.0, ahead of CRAN 2.2.6 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-09-30 · 52026-10-08 · 9

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/cmmr/ecodive 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 (1)

Code of conduct

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-06-04 · The repository has a site deploy workflow

pkgdown site last built 2026-06-04

Coverage (1)

Coverage reporting

Show all practicesHide 1 practice

Research and citation (1)

CITATION.cff

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing ecodive adds no packages beyond those that come with R.

Depends (1)

R >= 3.6.0

Imports (2)

parallelutils

LinkingTo (0)

none

Suggests (6)

knitrMatrixparallelly rmarkdown slam testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

2indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

rbiom

How these are counted

Code & Tests

Datasets

People & History

People (3)

Daniel P. Smith

Author, Maintainer since 1.0.0 (2025)

Melissa O'Neill

Contributor, Copyright holder · added in 2.2.6

Author of PCG random number generator

Alkek Center for Metagenomics and Microbiome Research

Copyright holder, Funder

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2.6Latest
record
2026-04-14 · current release · diff ↗
2.2.2
record
2026-01-16 · diff ↗
2.2.1
record
2025-12-12 · diff ↗
2.2.0
record
2025-12-04 · diff ↗
2.1.0
record
2025-09-26 · diff ↗
2.0.0
record
2025-09-21 · diff ↗ ·
removed 3 exports
bray_curtis, kulczynski, weighted_normalized_unifrac

added 40 exports
alpha_div, ace, berger, brillouin, fisher, margalef, mcintosh, menhinick, observed, squares, beta_div, aitchison, bhattacharyya, bray, chebyshev, chord, clark, divergence, hamming, hellinger, horn, jensen, jsd, lorentzian, matusita, minkowski, morisita, motyka, normalized_unifrac, ochiai and 10 more
1.0.0
record
2025-08-22
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-22
Total releases: 7 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 0.6 KB / 2 files
Download size: 205 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ecodive")

Format

Smith, D. P., Alkek Center for Metagenomics and Microbiome Research, & O'Neill, M. (2026). ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics (Version 2.2.6) [Computer software]. https://doi.org/10.32614/CRAN.package.ecodive

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 ecodive version 2.2.6 [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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