prevalence

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

propCI	Derive confidence intervals for a prevalence estimate
truePrev	Estimate TP from AP obtained by testing individual samples with a single test
truePrevMulti	Estimate TP from AP obtained by testing individual samples with multiple tests, using a conditional probability scheme
truePrevMulti2	Estimate TP from AP obtained by testing individual samples with multiple tests, using a covariance scheme
truePrevPools	Estimate TP from AP obtained by testing pooled samples
betaPERT	Calculate the parameters of a Beta-PERT distribution
betaExpert	Calculate 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")
install.packages("prevalence", repos = c('https://brechtdv.r-universe.dev', 'https://cloud.r-project.org'))

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/