Package: PoolTestR
Title: Prevalence and Regression for Pool-Tested (Group-Tested) Data
Version: 0.2.0
Authors@R: c(
    person("Angus", "McLure", , "angus.mclure@anu.edu.au", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2551-3059")),
    person("Caitlin", "Cherryh", role = "ctb",
           comment = c(ORCID = "0000-0001-6146-4376"))
  )
Description: An easy-to-use tool for working with presence/absence
        tests on 'pooled' or 'grouped' samples. The primary application
        is for estimating prevalence of a marker in a population based
        on the results of tests on pooled specimens.  This sampling
        method is often employed in surveillance of rare conditions in
        humans or animals (e.g. molecular xenomonitoring). The package
        was initially conceived as an R-based alternative to the
        molecular xenomonitoring software, 'PoolScreen'
        <https://sites.uab.edu/statgenetics/software/>. However, it
        goes further, allowing for estimates of prevalence to be
        adjusted for hierarchical sampling frames, and perform flexible
        mixed-effect regression analyses (McLure et al. Environmental
        Modelling and Software.  <DOI:10.1016/j.envsoft.2021.105158>).
        The package is currently in early stages, however more features
        are planned or in the works: e.g. adjustments for imperfect
        test specificity/sensitivity, functions for helping with
        optimal experimental design, and functions for spatial
        modelling.
License: GPL (>= 3)
URL: https://github.com/AngusMcLure/PoolTestR
BugReports: https://github.com/AngusMcLure/PoolTestR/issues
Depends: R (>= 4.1.0)
Imports: brms, dplyr, lme4 (>= 1.1-35.1), methods, progress, Rcpp (>=
        0.12.0), RcppParallel (>= 5.0.1), rlang, rstan (>= 2.26.0),
        rstantools (>= 2.3.1.1), stats, stringr, tibble
Suggests: covr
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.26.0), StanHeaders (>=
        2.26.0)
Biarch: true
Encoding: UTF-8
Language: en-AU
LazyData: true
RoxygenNote: 7.3.2
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2026-10-29 10:03:29 UTC; root
Author: Angus McLure [aut, cre]
        (<https://orcid.org/0000-0003-2551-3059>), Caitlin Cherryh
        [ctb] (<https://orcid.org/0000-0001-6146-4376>)
Maintainer: Angus McLure <angus.mclure@anu.edu.au>
Config/pak/sysreqs: make
Repository: https://cran.r-universe.dev
Date/Publication: 2024-12-05 05:40:05 UTC
RemoteUrl: https://github.com/cran/PoolTestR
RemoteRef: HEAD
RemoteSha: 83703761eae0cb481939cc542a34f22e113bb46b