PoolTestR: Prevalence and Regression for Pool-Tested (Group-Tested) Data
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: |
0.1.3 |
| Depends: |
R (≥ 3.4.0) |
| Imports: |
dplyr, methods, Rcpp (≥ 0.12.0), rstan (≥ 2.18.1), rstantools (≥ 2.0.0), brms, stats, lme4, stringr, progress |
| LinkingTo: |
BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0) |
| Published: |
2022-07-01 |
| DOI: |
10.32614/CRAN.package.PoolTestR |
| Author: |
Angus McLure 
[aut, cre] |
| Maintainer: |
Angus McLure <angus.mclure at anu.edu.au> |
| BugReports: |
https://github.com/AngusMcLure/PoolTestR |
| 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:
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