{ "_id": "6a103858acfb0bcc41c9aa67", "Package": "prevalence", "Type": "Package", "Title": "Tools for Prevalence Assessment Studies", "Version": "0.4.1", "Date": "2022-06-03", "Authors@R": "c(person(\"Brecht\", \"Devleesschauwer\",\nrole = c(\"aut\", \"cre\"), email = \"brechtdv@gmail.com\"),\nperson(\"Paul\", \"Torgerson\", role = \"aut\"),\nperson(\"Johannes\", \"Charlier\", role = \"aut\"),\nperson(\"Bruno\", \"Levecke\", role = \"aut\"),\nperson(\"Nicolas\", \"Praet\", role = \"aut\"),\nperson(\"Sophie\", \"Roelandt\", role = \"aut\"),\nperson(\"Suzanne\", \"Smit\", role = \"aut\"),\nperson(\"Pierre\", \"Dorny\", role = \"aut\"),\nperson(\"Dirk\", \"Berkvens\", role = \"aut\"),\nperson(\"Niko\", \"Speybroeck\", role = \"aut\"))", "Author": "Brecht Devleesschauwer [aut, cre], Paul Torgerson [aut],\nJohannes Charlier [aut], Bruno Levecke [aut], Nicolas Praet\n[aut], Sophie Roelandt [aut], Suzanne Smit [aut], Pierre Dorny\n[aut], Dirk Berkvens [aut], Niko Speybroeck [aut]", "Maintainer": "Brecht Devleesschauwer ", "BugReports": "https://github.com/brechtdv/prevalence/issues", "Description": "The prevalence package provides Frequentist and Bayesian\nmethods for prevalence assessment studies. IMPORTANT: the\ntruePrev functions in the prevalence package call on JAGS (Just\nAnother Gibbs Sampler), which therefore has to be available on\nthe user's system. JAGS can be downloaded from\n.", "SystemRequirements": "JAGS (>= 4.0.0) (see\nhttps://mcmc-jags.sourceforge.io/)", "License": "GPL (>= 2)", "URL": "http://prevalence.cbra.be/", "LazyLoad": "yes", "Config/pak/sysreqs": "jags", "Repository": "https://brechtdv.r-universe.dev", "Date/Publication": "2022-06-03 20:53:36 UTC", "RemoteUrl": "https://github.com/brechtdv/prevalence", "RemoteRef": "HEAD", "RemoteSha": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 06:01:22 UTC", "User": "root" }, "MD5sum": "af21ac4fcfac4fc5feb35fa567c3ae5f", "_user": "brechtdv", "_type": "src", "_file": "prevalence_0.4.1.tar.gz", "_fileid": "7bf09824f22b9e890cfe25993e8a6604ed798cd013c6372e6dbd3bc88e39e3ca", "_filesize": 307671, "_sha256": "7bf09824f22b9e890cfe25993e8a6604ed798cd013c6372e6dbd3bc88e39e3ca", "_created": "2026-05-12T06:01:22.000Z", "_published": "2026-05-22T11:04:56.951Z", "_distro": "noble", "_jobs": [ { "job": 77367040624, "time": 108, 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"windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6936817918" } ], "_buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/brechtdv/prevalence", "_commit": { "id": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "author": "Brecht ", "committer": "Brecht ", "message": "correct URLS\n", "time": 1654289616 }, "_maintainer": { "name": "Brecht Devleesschauwer", "email": "brechtdv@gmail.com", "login": "brechtdv", "twitter": "@brechtdv", "uuid": 3698720 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "rjags", "role": "Imports" } ], "_owner": "brechtdv", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "brechtdv", "count": 21, "uuid": 3698720 } ], "_userbio": { "uuid": 3698720, "type": "user", "name": "Brecht" }, "_downloads": { "count": 407, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/prevalence" }, "_mentions": 8, "_devurl": "https://github.com/brechtdv/prevalence", "_searchresults": 52, "_topics": [ "jags", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/prevalence.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/brechtdv/prevalence", "_realowner": "brechtdv", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2013-07-06" }, { "version": "0.2.0", "date": "2013-09-22" }, { "version": "0.3.0", "date": "2014-10-21" }, { "version": "0.4.0", "date": "2015-04-20" }, { "version": "0.4.1", "date": "2022-06-03" } ], "_exports": [ "as.matrix", "autocorr.plot", "betaExpert", "betaPERT", "define_prior", "define_prior2", "define_x", "densplot", "gelman.plot", "plot", "print", "propCI", "show", "summary", "traceplot", "truePrev", "truePrevMulti", "truePrevMulti2", "truePrevPools" ], "_help": [ { "page": "prevalence-package", "title": "Tools for prevalence assessment studies", "topics": [ "prevalence-package", "prevalence" ] }, { "page": "betaExpert", "title": "Calculate the parameters of a Beta distribution based on expert information", "topics": [ "betaExpert", "plot.betaExpert", "print.betaExpert" ] }, { "page": "betaPERT", "title": "Calculate the parameters of a Beta-PERT distribution", "topics": [ "betaPERT", "plot.betaPERT", "print.betaPERT" ] }, { "page": "convert-methods", "title": "Methods for Function 'as.matrix' in Package 'prevalence'", "topics": [ "as.matrix,prev-method", "as.matrix-methods", "convert-methods" ] }, { "page": "define", "title": "Definition of 'truePrevMulti' and 'truePrevMulti2' model", "topics": [ "define_prior", "define_prior2", "define_x" ] }, { "page": "plot-methods", "title": "Methods for Function 'plot' in Package 'prevalence'", "topics": [ "plot,prev,ANY-method", "plot,prev-method", "plot-methods" ] }, { "page": "plot-methods-coda", "title": "Plotting functions from package 'coda'", "topics": [ "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" ] }, { "page": "prev-class", "title": "Class '\"prev\"'", "topics": [ "prev-class" ] }, { "page": "print-methods", "title": "Methods for Function 'print' in Package 'prevalence'", "topics": [ "print,prev-method", "print-methods" ] }, { "page": "propCI", "title": "Calculate confidence intervals for prevalences and other proportions", "topics": [ "propCI" ] }, { "page": "show-methods", "title": "Methods for Function 'show' in Package 'prevalence'", "topics": [ "show,prev-method", "show-methods" ] }, { "page": "summary-methods", "title": "Methods for Function 'summary' in Package 'prevalence'", "topics": [ "summary,prev-method", "summary-methods" ] }, { "page": "truePrev", "title": "Estimate true prevalence from individuals samples", "topics": [ "truePrev" ] }, { "page": "truePrevMulti", "title": "Estimate true prevalence from individuals samples using multiple tests - conditional probability scheme", "topics": [ "truePrevMulti" ] }, { "page": "truePrevMulti2", "title": "Estimate true prevalence from individuals samples using multiple tests - covariance scheme", "topics": [ "truePrevMulti2" ] }, { "page": "truePrevPools", "title": "Estimate true prevalence from pooled samples", "topics": [ "truePrevPools" ] } ], "_readme": "https://github.com/brechtdv/prevalence/raw/HEAD/README.md", "_rundeps": [ "coda", "lattice", "rjags" ], "_sysdeps": [ { "shlib": 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It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary." }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 4.619093330626743, "_indexed": true, "_nocasepkg": "prevalence", "_universes": [ "brechtdv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.1", "date": "2026-05-12T06:03:32.000Z", "distro": "noble", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "2dbfaf451d8e9c390d45f14a602106a30367ad004c43958ba6190e1c44464d97", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.6.0", "os": "linux", "version": "0.4.1", "date": "2026-05-12T06:03:45.000Z", "distro": "noble", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "59da534d3b171439d9f06e4ac0d0416c5847e06b5ed621a80489c98879698981", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.5.3", "os": "mac", "version": "0.4.1", "date": "2026-05-12T06:04:17.000Z", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "75e46de946d46b1385097f610fa4b992ac66d105a1e0b152edb53cb5465179ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.6.0", "os": "mac", "version": "0.4.1", "date": "2026-05-12T06:03:45.000Z", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "69c8855c9c32c0eeef7005c49ae952885d30ba61fdfff4a33b0ced9c5c1ee606", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.7.0", "os": "win", "version": "0.4.1", "date": "2026-05-12T06:02:48.000Z", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "127cc4efacf9d164307bd53eb48fb419ea414601a48a26623322037f6f77ef2f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.5.3", "os": "win", "version": "0.4.1", "date": "2026-05-12T06:02:48.000Z", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "338c2f5c49ddf5b73aa9fb6935105ad99d7f359e3d7ed69a662162ffeeaf8635", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.6.0", "os": "win", "version": "0.4.1", "date": "2026-05-12T06:02:41.000Z", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "c5732e085008956c27b795cfa54d95c5eb5b3313d6390e6fe76e005c54de21a4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.1", "date": "2026-05-22T11:04:36.000Z", "commit": "62876ff82cc889aababb8fb208453e8c56f4d1fc", "fileid": "4634b0ce3a10f3a776dcbd8265a9a9470f6d8e1894cc27885fea58bff7ef5f89", "status": "success", "buildurl": "https://github.com/r-universe/brechtdv/actions/runs/25716420880" } ] }