Package: DiPPER
Title: Differential Prevalence via Probabilistic Estimation in R
Version: 0.99.1
Authors@R: c(
    person(given = "Juho",
           family = "Pelto",
           role = c("aut", "cre"),
           email = "jepelt@utu.fi",
           comment = c(ORCID = "0000-0001-8820-8014")),
    person(given = "Leo",
           family = "Lahti",
           role = "aut",
           email = "leo.lahti@iki.fi",
           comment = c(ORCID = "0000-0001-5537-637X")),
    person(given = "Research Council of Finland",
           role = "fnd",
           comment = "Strategic Research Council, decisions 372345 and 374944")
  )
Description: Implements a Bayesian hierarchical model for differential prevalence 
    analysis, tailored for microbiome studies. The method accommodates both 
    cross-sectional and longitudinal designs, providing finite effect estimates 
    and uncertainty intervals that are naturally adjusted for multiple testing 
    via hierarchical shrinkage. Posterior inference is performed via Markov 
    chain Monte Carlo (MCMC) using 'CmdStan' as the backend.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.6.0)
Imports: instantiate, SummarizedExperiment, TreeSummarizedExperiment,
        stats, utils, ggplot2
Suggests: testthat (>= 3.1.5), knitr, rmarkdown, BiocStyle
SystemRequirements: CmdStan
        (https://mc-stan.org/users/interfaces/cmdstan)
biocViews: Software, Microbiome, Bayesian, Regression,
        DifferentialExpression, Sequencing
URL: https://github.com/jepelt/DiPPER
BugReports: https://github.com/jepelt/DiPPER/issues
Config/roxygen2/version: 8.1.0
Config/testthat/edition: 3
LazyData: false
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DiPPER
git_branch: devel
git_last_commit: 657a071
git_last_commit_date: 2026-09-30
Repository: Bioconductor 3.24
Date/Publication: 2026-10-13
NeedsCompilation: yes
Packaged: 2026-10-13 21:24:55 UTC; biocbuild
Author: Juho Pelto [aut, cre] (ORCID: <https://orcid.org/0000-0001-8820-8014>),
  Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>),
  Research Council of Finland [fnd] (Strategic Research Council,
    decisions 372345 and 374944)
Maintainer: Juho Pelto <jepelt@utu.fi>
