Re: [R] Sensitivy / Specificity and nulls
Maybe you want to check out the prevalence package (http://cran.r-project.org/web/packages/prevalence/index.html), and its development version on GitHub (https://github.com/brechtdv/prevalence/). When you have two tests, and neither can be considered to be a 'gold standard' (ie, SE & SP = 100%), Bayesian latent class approaches can help you to estimate true prevalence, sensitivity and specificity. Brecht Good Day All, I am working with a diagnostic test and comparing the new test to an old test. Normally I would be able to calculate sensitivity and specificity quite easily. However, the 'gold standard' that I am comparing my new diagnostic with is really 'gold-plated' in that sometimes the 'gold standard' fails completely and I have no data from the 'gold standard' but I might have data from the diagnostic test. Of course sometimes my new diagnostic fails but I have data from my 'gold standard' To me this really starts moving towards classification but I cannot seem to find the appropriate calculations. Can someone point me to some web resources to determine the appropriate method to be able to deal with the NULLs ? Resources within the medical realm would be better (because the rest of the folks would understand them better) but not required. -- Devleesschauwer Brecht Doctoral Researcher, MVSc DVM Department of Virology, Parasitology and Immunology Faculty of Veterinary Medicine Ghent University Salisburylaan 133 9820 Merelbeke Belgium Telephone: +32 9 264 7328 Mobile (Belgium): +32 476 365743 Mobile (Nepal): +977 9842 223323 E-mail: brecht.devleesschau...@ugent.be http://users.ugent.be/~bdvleess/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] new package 'prevalence'
Dear list members, A new package, called *prevalence *(version 0.1.0), is now available on CRAN: http://cran.r-project.org/package=prevalence This package provides Frequentist and Bayesian methods useful in prevalence assessment studies. More specifically, the following functions are currently available: * truePrev -- Bayesian estimation of True Prevalence from Apparent Prevalence obtained by testing /individual /samples * truePrevPools -- Bayesian estimation of True Prevalence from Apparent Prevalence obtained by testing /pooled /samples * propCI -- Calculate confidence intervals for a prevalence estimate * betaPERT -- Calculate the parameters of a Beta-PERT distribution * betaExpert -- Calculate the parameters of a Beta distribution based on expert opinion Function 'truePrev' is also implemented in an online Shiny app: http://users.ugent.be/~bdvleess/R/prevalence/shiny/ The development version is on GitHub: https://github.com/brechtdv/prevalence/ Comments and suggestions would be greatly appreciated. Best wishes, Brecht and coauthors. -- Devleesschauwer Brecht Doctoral Researcher, MVSc DVM Department of Virology, Parasitology and Immunology Faculty of Veterinary Medicine Ghent University Salisburylaan 133 9820 Merelbeke Belgium Telephone: +32 9 264 7328 Mobile (Belgium): +32 476 365743 Mobile (Nepal): +977 9842 223323 E-mail:brecht.devleesschau...@ugent.be http://users.ugent.be/~bdvleess/ [[alternative HTML version deleted]] ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
