Package: occumb
Title: Site Occupancy Modeling for Environmental DNA Metabarcoding
Version: 1.3.0
Authors@R: c(
    person("Keiichi", "Fukaya", , "fukayak99@gmail.com", role = c("aut", "cre")),
    person("Ken", "Kellner", role = "cph",
           comment = "summary method for occumbFit class, processing of NIMBLE results, and print method for nimbleSummary class"),
    person("Mika", "Takahashi", , "takahashi.mika@nies.go.jp", role = "aut"),
    person("Martyn", "Plummer", role = "ctb",
           comment = "fixes for JAGS 5.0.0 compatibility"),
    person("Koji", "Makiyama", role = "ctb",
           comment = "option to use NIMBLE"),
    person("Kentaro", "Matsuura", role = "ctb",
           comment = "option to use NIMBLE")
  )
Description: Fits community site occupancy models to environmental DNA
        metabarcoding data collected using spatially-replicated survey
        design. Model fitting results can be used to evaluate and
        compare the effectiveness of species detection to find an
        efficient survey design. Reference: Fukaya et al. (2022)
        <doi:10.1111/2041-210X.13732>, Fukaya and Hasebe (2025)
        <doi:10.1002/1438-390X.12219>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: covr, rmarkdown, spelling, testthat (>= 3.0.0), tibble,
        vdiffr, nimble (>= 1.4.2), coda, parallel, DoE.base
Config/testthat/edition: 3
Imports: stats, methods, graphics, checkmate, crayon, knitr
Collate: 'classes.R' 'fish.R' 'fish_raw.R' 'get_posterior.R' 'gof.R'
        'nimbleSummary.R' 'occumbData.R' 'occumb.R' 'plot.R'
        'predict.R' 'run_nimble.R' 'show.R' 'summary.R' 'utility.R'
        'utils.R'
URL: https://fukayak.github.io/occumb/,
        https://github.com/fukayak/occumb
Depends: jagsUI, R (>= 2.10)
VignetteBuilder: knitr
SystemRequirements: JAGS (http://mcmc-jags.sourceforge.net)
BugReports: https://github.com/fukayak/occumb/issues
Language: en-US
Config/pak/sysreqs: jags
Repository: https://fukayak.r-universe.dev
Date/Publication: 2026-04-04 07:43:16 UTC
RemoteUrl: https://github.com/fukayak/occumb
RemoteRef: HEAD
RemoteSha: 25359166c5539a053955c38133a6707e97454a1c
NeedsCompilation: no
Packaged: 2026-07-03 06:49:23 UTC; root
Author: Keiichi Fukaya [aut, cre],
  Ken Kellner [cph] (summary method for occumbFit class, processing of
    NIMBLE results, and print method for nimbleSummary class),
  Mika Takahashi [aut],
  Martyn Plummer [ctb] (fixes for JAGS 5.0.0 compatibility),
  Koji Makiyama [ctb] (option to use NIMBLE),
  Kentaro Matsuura [ctb] (option to use NIMBLE)
Maintainer: Keiichi Fukaya <fukayak99@gmail.com>