PoolTestR-package: The 'PoolTestR' package.

PoolTestR-packageR Documentation

The 'PoolTestR' package.


This is a package 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. livestock or xenomonitoring). The package was initially conceived as an R-based alternative to the xenomonitoring software, PoolScreen. However, it goes further, allowing for estimates of prevalence to adjusted for hierarchy in sampling frames, and perform flexible (mixed effect) regression analyses. 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.


Angus McLure, Ben O'Neill, Helen Mayfield, Colleen Lau, Brady McPherson (2021). PoolTestR: An R package for estimating prevalence and regression modelling for molecular xenomonitoring and other applications with pooled samples. Environmental Modelling & Software, 145:105158. <DOI:10.1016/j.envsoft.2021.105158>

Stan Development Team (2019). RStan: the R interface to Stan. R package version 2.19.2. https://mc-stan.org

Paul-Christian B├╝rkner (2017). brms: An R Package for Bayesian Multilevel Models Using Stan. Journal of Statistical Software, 80(1), 1-28. <DOI:10.18637/jss.v080.i01>

PoolTestR documentation built on July 1, 2022, 9:06 a.m.