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 (>= 4.5.0)
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
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-30 16:34:39 UTC
RemoteUrl: https://github.com/bioc/DiPPER
RemoteRef: HEAD
RemoteSha: 657a071a85192a5ed053ca2c2b554f4ee727757e
NeedsCompilation: yes
Packaged: 2026-10-13 19:42:54 UTC; root
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>