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: 2026-06-04 23:47:27 UTC
RemoteUrl: https://github.com/cmmr/ecodive
RemoteRef: HEAD
RemoteSha: 05cee331bc761fe8b237a2e5a8daa83f8c1abed9
NeedsCompilation: yes
Packaged: 2026-06-24 05:21:27 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>