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 (>= 3.4.0)
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: 2024-12-05 01:08:44 UTC; caitlin
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>
Repository: CRAN
Date/Publication: 2024-12-05 05:40:05 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-30 00:32:54 UTC; unix
Archs: PoolTestR.so.dSYM
