Package: prevalence 0.4.1

prevalence: Tools for Prevalence Assessment Studies

The prevalence package provides Frequentist and Bayesian methods for prevalence assessment studies. 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 <https://mcmc-jags.sourceforge.io/>.

Authors:Brecht Devleesschauwer [aut, cre], Paul Torgerson [aut], Johannes Charlier [aut], Bruno Levecke [aut], Nicolas Praet [aut], Sophie Roelandt [aut], Suzanne Smit [aut], Pierre Dorny [aut], Dirk Berkvens [aut], Niko Speybroeck [aut]

prevalence_0.4.1.tar.gz
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prevalence.pdf |prevalence.html✨
prevalence/json (API)
NEWS

# Install 'prevalence' in R:
install.packages('prevalence', repos = c('https://brechtdv.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/brechtdv/prevalence/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

On CRAN:

19 exports 2 stars 2.28 score 3 dependencies 8 mentions 37 scripts 304 downloads

Last updated 2 years agofrom:62876ff82c. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 04 2024
R-4.5-winNOTESep 04 2024
R-4.5-linuxNOTESep 04 2024
R-4.4-winNOTESep 04 2024
R-4.4-macNOTESep 04 2024
R-4.3-winOKSep 04 2024
R-4.3-macOKSep 04 2024

Exports:as.matrixautocorr.plotbetaExpertbetaPERTdefine_priordefine_prior2define_xdensplotgelman.plotplotprintpropCIshowsummarytraceplottruePrevtruePrevMultitruePrevMulti2truePrevPools

Dependencies:codalatticerjags

Readme and manuals

Help Manual

Help pageTopics
Tools for prevalence assessment studiesprevalence-package prevalence
Calculate the parameters of a Beta distribution based on expert informationbetaExpert plot.betaExpert print.betaExpert
Calculate the parameters of a Beta-PERT distributionbetaPERT plot.betaPERT print.betaPERT
Methods for Function 'as.matrix' in Package 'prevalence'as.matrix,prev-method as.matrix-methods convert-methods
Definition of 'truePrevMulti' and 'truePrevMulti2' modeldefine_prior define_prior2 define_x
Methods for Function 'plot' in Package 'prevalence'plot,prev,ANY-method plot,prev-method plot-methods
Plotting functions from package 'coda'autocorr.plot,prev-method autocorr.plot-methods densplot,prev-method densplot-methods gelman.plot,prev-method gelman.plot-methods plot-methods-coda traceplot,prev-method traceplot-methods
Class '"prev"'prev-class
Methods for Function 'print' in Package 'prevalence'print,prev-method print-methods
Calculate confidence intervals for prevalences and other proportionspropCI
Methods for Function 'show' in Package 'prevalence'show,prev-method show-methods
Methods for Function 'summary' in Package 'prevalence'summary,prev-method summary-methods
Estimate true prevalence from individuals samplestruePrev
Estimate true prevalence from individuals samples using multiple tests - conditional probability schemetruePrevMulti
Estimate true prevalence from individuals samples using multiple tests - covariance schemetruePrevMulti2
Estimate true prevalence from pooled samplestruePrevPools