Package: ecodive 2.3.0

Daniel P. Smith

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>.

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
ecodive_2.3.0.zip(r-4.7)ecodive_2.3.0.zip(r-4.6)ecodive_2.3.0.zip(r-4.5)
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)
ecodive_2.3.0.tar.gz(r-4.7-arm64)ecodive_2.3.0.tar.gz(r-4.7-x86_64)ecodive_2.3.0.tar.gz(r-4.6-arm64)ecodive_2.3.0.tar.gz(r-4.6-x86_64)
ecodive_2.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ecodive/json (API)

# 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:

8.68 score 8 stars 10 packages 6 scripts 3.8k downloads 58 exports 0 dependencies

Last updated from:05cee331bc. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK136
linux-devel-x86_64OK129
source / vignettesOK166
linux-release-arm64OK121
linux-release-x86_64OK120
macos-release-arm64OK74
macos-release-x86_64OK243
macos-oldrel-arm64OK76
macos-oldrel-x86_64OK331
windows-develOK89
windows-releaseOK89
windows-oldrelOK148
wasm-releaseOK105

Exports:aceaitchisonalpha_divbergerbeta_divbhattacharyyabraybrillouincanberrachao1chebyshevchordclarkdivergenceeuclideanfaithfishergeneralized_unifracgowerhamminghellingerhorninv_simpsonjaccardjensenjsdlist_metricslorentzianmanhattanmargalefmatch_metricmatusitamcintoshmenhinickminkowskimorisitamotykan_cpusnormalized_unifracobservedochiaipsym_chisqrarefyread_treerobust_aitchisonshannonsimpsonsoergelsorensensquared_chisqsquared_chordsquared_euclideansquarestopsoeunweighted_unifracvariance_adjusted_unifracwave_hedgesweighted_unifrac

Dependencies:

Beta Diversity
Introduction | Input Data | Weighted vs Unweighted Metrics | Formulas | Abundance-Based (Weighted) | Presence / Absence (Unweighted) | Phylogenetic | Partial Calculation | References
Rendered frombdiv.Rmdusingknitr::rmarkdown

Last update: 2026-06-04
Started: 2025-07-30

Introduction to ecodive
Introduction | Alpha Diversity | Beta Diversity | Example | Rarefaction | Classic Metrics | Phylogenetic Metrics | Distance Matrices | Performance with Large Datasets
Rendered fromecodive.Rmdusingknitr::rmarkdown

Last update: 2026-06-04
Started: 2025-08-01

Performance Guide
Optimizing ecodive for Large Datasets | The Optimal Input: Compressed Sparse Matrices | Why Sparse Matrices? | rbiom Users | Handling Data Transformations | The Exception: Centered Log-Ratio (CLR) | Summary
Rendered fromperformance.Rmdusingknitr::rmarkdown

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

Alpha Diversity
Input Matrix | Richness Metrics | Diversity Metrics | Dominance Metrics | Phylogenetic Metrics | Formulas | Abundance-based Coverage Estimator (ACE) | Faith's Phylogenetic Diversity (Faith's PD)
Rendered fromadiv.Rmdusingknitr::rmarkdown

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

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