Package: ecodive
Type: Package
Title: Parallel and Memory-Efficient Ecological Diversity Metrics
Version: 2.3.0
Authors@R: c(
    person(
      "Daniel P.", "Smith",
      email   = "dansmith01@gmail.com",
      role    = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-2479-2044")),
    person(
      "Melissa", "O'Neill",
      role    = c("ctb", "cph"),
      comment = "PCG random number generator"),
    person(
      "Alkek Center for Metagenomics and Microbiome Research", 
      role = c("cph", "fnd") ))
Description: 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>.
URL: https://cmmr.github.io/ecodive/, https://github.com/cmmr/ecodive
BugReports: https://github.com/cmmr/ecodive/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/Needs/website: rmarkdown
Config/testthat/edition: 3
Imports: parallel, utils
Suggests: knitr, Matrix, parallelly, rmarkdown, slam, tinytest
VignetteBuilder: knitr
Repository: https://cmmr.r-universe.dev
Date/Publication: 2026-10-02 18:18:22 UTC
RemoteUrl: https://github.com/cmmr/ecodive
RemoteRef: HEAD
RemoteSha: 1621defb3ab8fcc2101b90a41506c1336ebe29d3
NeedsCompilation: yes
Packaged: 2026-10-02 18:56:32 UTC; root
Author: Daniel P. Smith [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2479-2044>),
  Melissa O'Neill [ctb, cph] (PCG random number generator),
  Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>