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README.md

prevalence

Travis-CI Build Status CRAN_Status_Badge Cranlogs Downloads

The prevalence package provides Frequentist and Bayesian methods useful in prevalence assessment studies. Several methods are available for estimating True Prevalence (TP) from Apparent Prevalence (AP).

Available functions

propCIDerive confidence intervals for a prevalence estimate
truePrevEstimate TP from AP obtained by testing individual samples with a single test
truePrevMultiEstimate TP from AP obtained by testing individual samples with multiple tests, using a conditional probability scheme
truePrevMulti2Estimate TP from AP obtained by testing individual samples with multiple tests, using a covariance scheme
truePrevPoolsEstimate TP from AP obtained by testing pooled samples
betaPERTCalculate the parameters of a Beta-PERT distribution
betaExpertCalculate the parameters of a Beta distribution based on expert opinion

Install

To download and install the latest released version from CRAN:

install.packages("prevalence")

To download and install the latest development version from GitHub:

devtools::install_github("brechtdv/prevalence")

IMPORTANT: the truePrev functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), which therefore has to be available on the user's system. JAGS can be downloaded from http://mcmc-jags.sourceforge.net/.

More

Function truePrev is also available as an online Shiny application: https://cbra.shinyapps.io/truePrev/

More information and tutorials are available at http://prevalence.cbra.be/

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Tools for prevalence assessment studies

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