Package: ecodive 2.3.0

Daniel P. Smith

ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

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. Parallel and memory-efficient algorithms are described in Smith et al. (2026) <doi:10.21105/joss.09777>.

Authors:Daniel P. Smith [aut, cre], Melissa O'Neill [ctb, cph], Alkek Center for Metagenomics and Microbiome Research [cph, fnd]

ecodive_2.3.0.tar.gz
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ecodive_2.3.0.tgz(r-4.6-x86_64)ecodive_2.3.0.tgz(r-4.6-arm64)ecodive_2.3.0.tgz(r-4.5-x86_64)ecodive_2.3.0.tgz(r-4.5-arm64)
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ecodive_2.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ecodive/json (API)
NEWS

# Install 'ecodive' in R:
install.packages('ecodive', repos = c('https://cmmr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cmmr/ecodive/issues

Pkgdown/docs site:https://cmmr.github.io

Datasets:

On CRAN:

Conda:

8.57 score 7 stars 10 packages 6 scripts 3.4k downloads 58 exports 0 dependencies

Last updated from:e70f237f61. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK129
linux-devel-x86_64OK121
source / vignettesOK152
linux-release-arm64OK111
linux-release-x86_64OK117
macos-release-arm64OK92
macos-release-x86_64OK225
macos-oldrel-arm64OK84
macos-oldrel-x86_64OK200
windows-develOK107
windows-releaseOK87
windows-oldrelOK97
wasm-releaseOK103

Exports:aceaitchisonalpha_divbergerbeta_divbhattacharyyabraybrillouincanberrachao1chebyshevchordclarkdivergenceeuclideanfaithfishergeneralized_unifracgowerhamminghellingerhorninv_simpsonjaccardjensenjsdlist_metricslorentzianmanhattanmargalefmatch_metricmatusitamcintoshmenhinickminkowskimorisitamotykan_cpusnormalized_unifracobservedochiaipsym_chisqrarefyread_treerobust_aitchisonshannonsimpsonsoergelsorensensquared_chisqsquared_chordsquared_euclideansquarestopsoeunweighted_unifracvariance_adjusted_unifracwave_hedgesweighted_unifrac

Dependencies:

Alpha Diversity

Rendered fromadiv.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-01-28
Started: 2025-07-30

Beta Diversity

Rendered frombdiv.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-02-04
Started: 2025-07-30

Introduction to ecodive

Rendered fromecodive.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2025-12-02
Started: 2025-08-01

Performance Guide

Rendered fromperformance.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-02-05
Started: 2025-12-02

Readme and manuals

Help Manual

Help pageTopics
Abundance-based Coverage Estimator (ACE)ace
Aitchison distanceaitchison
Alpha Diversity Wrapper Functionalpha_div
Berger-Parker Indexberger
Beta Diversity Wrapper Functionbeta_div
Bhattacharyya distancebhattacharyya
Bray-Curtis dissimilaritybray
Brillouin Indexbrillouin
Canberra distancecanberra
Chao1 Richness Estimatorchao1
Chebyshev distancechebyshev
Chord distancechord
Clark's divergence distanceclark
Divergencedivergence
Euclidean distanceeuclidean
Example counts matrixex_counts
Example phylogenetic treeex_tree
Faith's Phylogenetic Diversity (PD)faith
Fisher's Alphafisher
Generalized UniFrac (GUniFrac)generalized_unifrac
Gower distancegower
Hamming distancehamming
Hellinger distancehellinger
Horn-Morisita dissimilarityhorn
Inverse Simpson Indexinv_simpson
Jaccard distancejaccard
Jensen-Shannon distancejensen
Jensen-Shannon divergence (JSD)jsd
Find and Browse Available Metricslist_metrics match_metric
Lorentzian distancelorentzian
Manhattan distancemanhattan
Margalef's Richness Indexmargalef
Matusita distancematusita
McIntosh Indexmcintosh
Menhinick's Richness Indexmenhinick
Minkowski distanceminkowski
Morisita dissimilaritymorisita
Motyka dissimilaritymotyka
Number of CPU Coresn_cpus
Normalized Weighted UniFracnormalized_unifrac
Observed Featuresobserved
Otsuka-Ochiai dissimilarityochiai
Probabilistic Symmetric Chi-Squared distancepsym_chisq
Rarefy Observation Countsrarefy
Read a newick formatted phylogenetic tree.read_tree
Robust Aitchison distancerobust_aitchison
Shannon Diversity Indexshannon
Gini-Simpson Indexsimpson
Soergel distancesoergel
Dice-Sorensen dissimilaritysorensen
Squared Chi-Squared distancesquared_chisq
Squared Chord distancesquared_chord
Squared Euclidean distancesquared_euclidean
Squares Richness Estimatorsquares
Topsoe distancetopsoe
Unweighted UniFracunweighted_unifrac
Variance-Adjusted Weighted UniFracvariance_adjusted_unifrac
Wave Hedges distancewave_hedges
Weighted UniFracweighted_unifrac