DESCRIPTION

Package: PooledPrevalence
Title: Tools for Implementation and Analysis of Prevalence Studies based Pooled Testing
Type: Package
Version: 1.0.2
Date: 2020-05-15
Authors@R: c(
  person(given = "Angelo",
         family = "D'Ambrosio",
         role = c("aut", "cre"),
         email = "a.dambrosioMD@example.com",
         comment = c(ORCID = "0000-0002-2045-5155")),
  person(given = "Emmanuel",
         family = "Robesyn",
         role = c("ctb", "sad"),
         email = "Emmanuel.Robesyn@ecdc.europa.eu"),
	person(given = "Gianfranco",
         family = "Spiteri",
         role = c("ctb", "sad"),
         email = "Gianfranco.Spiteri@ecdc.europa.eu"),
	person(given = "Angeliki",
         family = "Melidou",
         role = c("sad"),
         email = "Angeliki.Melidou@ecdc.europa.eu")
	)
Description: A set of tools to help design a laboratory based prevalence study harnessing the pooling of laboratory samples to increase resource efficiency.
	The tools provide guidance in choosing the number of samples to pool and the total number of tests to perform, focusing on achieve the maximum estimation performance (low uncertainty and estimation error) while keeping the total amount of tests low.
	In the package there functions to simulate study outcomes, optimize the study design and finally analyze the results of a pooled study to retrieve the relative prevalence estimates.
	The package is based on a Bayesian framework, with the possibility to perform a full hierchical analysis including also uncertainty due to the sensitivity in acquiring the testing material.
	The package was developed in the occasion of the COVID-19 pandemic, but can be utilized in every laboratory based prevalence study. 
	More information about the usage at https://github.com/EU-ECDC/PooledPrevalence and about the methodology at https://www.ecdc.europa.eu/sites/default/files/documents/Methodology-estimating-point-prevalence%20-SARS-CoV-2-infection-pooled-RT-PCR-testing.pdf.
Imports:
    ggplot2,
    stats,
    base,
    dplyr (>= 1.0.0),
    MCMCpack,
    callr,
    broom,
    Rfast,
    magrittr,
    utils,
    partykit,
    stringr,
    scales
License: EUPL
URL: https://github.com/EU-ECDC/PooledPrevalence, https://www.ecdc.europa.eu/sites/default/files/documents/Methodology-estimating-point-prevalence%20-SARS-CoV-2-infection-pooled-RT-PCR-testing.pdf
BugReports: https://github.com/EU-ECDC/PooledPrevalence/issues
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.0
Suggests: 
    testthat