ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Computes alpha and beta diversity metrics in a parallel, memory-efficient manner using 'C' and 'pthreads'. Implements 51 classic, compositional, and phylogenetic indices including 'Shannon', 'Bray-Curtis', 'Faith', 'JSD', 'Hellinger', 'Robust Aitchison', and the 'UniFrac' family. Provides random sub-sampling for table rarefaction and parses 'Newick' trees into 'phylo' objects. Integrates with data structures from 'phyloseq', 'rbiom', and other common 'bioinformatics' packages. Algorithms are described in Smith 'et al.' (2026) <doi:10.21105/joss.09777>.

Version:	2.3.1
Depends:	R (≥ 3.6.0)
Imports:	parallel, utils
Suggests:	knitr, Matrix, parallelly, rmarkdown, slam, tinytest
Published:	2026-11-05
DOI:	10.32614/CRAN.package.ecodive
Author:	Daniel P. Smith [aut, cre], Melissa O'Neill [ctb, cph] (PCG random number generator), Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer:	Daniel P. Smith <dansmith01 at gmail.com>
BugReports:	https://github.com/cmmr/ecodive/issues
License:	MIT + file LICENSE
Copyright:	see file COPYRIGHTS
URL:	https://cmmr.github.io/ecodive/, https://github.com/cmmr/ecodive
NeedsCompilation:	yes
Citation:	ecodive citation info
Materials:	README, NEWS
CRAN checks:	ecodive results

Documentation:

Reference manual:	ecodive.html , ecodive.pdf
Vignettes:	Alpha Diversity (source) Beta Diversity (source) Introduction to ecodive (source) Performance Guide (source)

Downloads:

Package source:	ecodive_2.3.1.tar.gz
Windows binaries:	r-devel: ecodive_2.2.6.zip, r-release: ecodive_2.2.6.zip, r-oldrel: ecodive_2.3.1.zip
macOS binaries:	r-release (arm64): ecodive_2.3.1.tgz, r-oldrel (arm64): ecodive_2.3.1.tgz, r-release (x86_64): ecodive_2.3.1.tgz, r-oldrel (x86_64): ecodive_2.3.1.tgz
Old sources:	ecodive archive

Reverse dependencies:

Reverse imports:

mia, rbiom

Linking:

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