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: |
0.2.0 |
| 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 
[aut, cre],
Caitlin Cherryh
[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:
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