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.">

PoolTestR: Prevalence and Regression for Pool-Tested (Group-Tested) Data (original) (raw)

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.

Version: 0.2.0
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
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)
Suggests: covr
Published: 2024-12-05
DOI: 10.32614/CRAN.package.PoolTestR
Author: Angus McLure ORCID iD [aut, cre], Caitlin Cherryh ORCID iD [ctb]
Maintainer: Angus McLure <angus.mclure at anu.edu.au>
BugReports: https://github.com/AngusMcLure/PoolTestR/issues
License: GPL (≥ 3)
URL: https://github.com/AngusMcLure/PoolTestR
NeedsCompilation: yes
SystemRequirements: GNU make
Language: en-AU
Citation: PoolTestR citation info
Materials: README, NEWS
CRAN checks: PoolTestR results

Documentation:

Downloads:

Linking:

Please use the canonical formhttps://CRAN.R-project.org/package=PoolTestRto link to this page.