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).
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 |
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/.
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/