{ "_id": "6ad1116f0edca5be25021880", "Package": "dtametaTMB", "Title": "Diagnostic Test Accuracy Meta-Analysis using Template Model\nBuilder", "Version": "0.1.3.9000", "Authors@R": "c(\nperson(\"Claus\", \"Nowak\",\nemail = \"claus.nowak@donau-uni.ac.at\",\nrole = c(\"aut\", \"cre\"))\n)", "Description": "Fits the hierarchical summary receiver operating\ncharacteristic (HSROC) model of Rutter and Gatsonis (2001)\n, the bivariate binomial-normal model of\nReitsma et al. (2005) , the\nthreshold-based bivariate time-to-event model of Hoyer et al.\n(2018) , and the latent class extensions\nof Liu et al. (2015) for diagnostic\nstudies with an imperfect reference standard. Provides subgroup\nanalyses, HSROC meta-regression, likelihood-ratio tests,\nsummary ROC plots, and coupled forest plots.", "License": "GPL (>= 2)", "URL": "https://github.com/EBME-UWK/dtametaTMB", "BugReports": "https://github.com/EBME-UWK/dtametaTMB/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "LazyData": "true", "Config/roxygen2/version": "8.1.0", "VignetteBuilder": "quarto", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://ebme-uwk.r-universe.dev", "Date/Publication": "2026-10-15 11:48:00 UTC", "RemoteUrl": "https://github.com/ebme-uwk/dtametatmb", "RemoteRef": "HEAD", "RemoteSha": "4534cbe1180cd3dd6e5ceecfec6f3f9a87e136e8", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-15 17:22:13 UTC", "User": "root" }, "Author": "Claus Nowak [aut, cre]", "Maintainer": "Claus Nowak ", "_user": "ebme-uwk", "_type": "src", "_file": "dtametaTMB_0.1.3.9000.tar.gz", "_fileid": 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}, { "page": "fitReitsma", "title": "Fit the Reitsma Model", "topics": [ "fitReitsma" ] }, { "page": "fitReitsmaLCA", "title": "Fit the Reitsma LCA Model", "topics": [ "fitReitsmaLCA" ] }, { "page": "fitReitsmaSubgroup", "title": "Fit the Reitsma Subgroup Model", "topics": [ "fitReitsmaSubgroup" ] }, { "page": "fitReitsmaSubgroupLCA", "title": "Fit the Reitsma Subgroup LCA Model", "topics": [ "fitReitsmaSubgroupLCA" ] }, { "page": "fitReitsmaSubgroupTMB", "title": "Fit the Reitsma Subgroup TMB Model", "topics": [ "fitReitsmaSubgroupTMB" ] }, { "page": "fitReitsmaTMB", "title": "Fit the Reitsma TMB Model", "topics": [ "fitReitsmaTMB" ] }, { "page": "fitRutterGatsonis", "title": "Fit the Rutter and Gatsonis (HSROC) Model", "topics": [ "fitRutterGatsonis" ] }, { "page": "fitRutterGatsonisLCA", "title": "Fit the Rutter and Gatsonis LCA Model", "topics": [ "fitRutterGatsonisLCA" ] }, { "page": "fitRutterGatsonisReg", "title": "Fit the Rutter and Gatsonis Regression Model", "topics": [ 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"forest.ReitsmaSubgroupLCA", "title": "Coupled Forest Plot for Latent Class Diagnostic Test Accuracy Meta-Analysis", "topics": [ "forest.ReitsmaSubgroupLCA" ] }, { "page": "forest.ReitsmaSubgroupTMB", "title": "Coupled Forest Plot for Diagnostic Test Accuracy Meta-Analysis", "topics": [ "forest.ReitsmaSubgroupTMB" ] }, { "page": "forest.RutterGatsonis", "title": "Coupled Forest Plot for Diagnostic Test Accuracy Meta-Analysis", "topics": [ "forest.RutterGatsonis" ] }, { "page": "forest.RutterGatsonisLCA", "title": "Coupled Forest Plot for Latent Class Diagnostic Test Accuracy Meta-Analysis", "topics": [ "forest.RutterGatsonisLCA" ] }, { "page": "forest.RutterGatsonisSubgroup", "title": "Coupled Forest Plot for Diagnostic Test Accuracy Meta-Analysis", "topics": [ "forest.RutterGatsonisSubgroup" ] }, { "page": "forest.RutterGatsonisSubgroupLCA", "title": "Coupled Forest Plot for Latent Class Diagnostic Test Accuracy Meta-Analysis", "topics": [ "forest.RutterGatsonisSubgroupLCA" ] }, { "page": "initHoyerAFT", "title": "Compute Initial Parameter Values for HoyerAFT Models", "topics": [ "initHoyerAFT" ] }, { "page": "logLik.dtametaTMB", "title": "Extract Log-Likelihood from Diagnostic Test Accuracy Models", "topics": [ "logLik.dtametaTMB", "logLik.DTAmodel", "logLik.HoyerAFT", "logLik.Reitsma", "logLik.ReitsmaLCA", "logLik.ReitsmaSubgroup", "logLik.ReitsmaSubgroupLCA", "logLik.ReitsmaSubgroupTMB", "logLik.ReitsmaTMB" ] }, { "page": "pap", "title": "Pap Dataset", "topics": [ "pap" ] }, { "page": "plot.HoyerAFT", "title": "Plot Results from a HoyerAFT Model", "topics": [ "plot.HoyerAFT" ] }, { "page": "plot.Reitsma", "title": "Plot Results from a Reitsma Model", "topics": [ "plot.Reitsma" ] }, { "page": "plot.ReitsmaLCA", "title": "Plot Results from a Reitsma LCA Model", "topics": [ "plot.ReitsmaLCA" ] }, { "page": "plot.ReitsmaSubgroup", "title": "Plot Results from a Reitsma Subgroup Model", "topics": [ "plot.ReitsmaSubgroup" ] }, { "page": "plot.ReitsmaSubgroupLCA", "title": "Plot Results from a Reitsma Subgroup LCA Model", "topics": [ "plot.ReitsmaSubgroupLCA" ] }, { "page": "plot.ReitsmaSubgroupTMB", "title": "Plot Results from a Reitsma Subgroup TMB Model", "topics": [ "plot.ReitsmaSubgroupTMB" ] }, { "page": "plot.ReitsmaTMB", "title": "Plot Results from a ReitsmaTMB Model", "topics": [ "plot.ReitsmaTMB" ] }, { "page": "plot.RutterGatsonis", "title": "Plot Results from a Rutter and Gatsonis Model", "topics": [ "plot.RutterGatsonis" ] }, { "page": "plot.RutterGatsonisLCA", "title": "Plot Results from a Rutter and Gatsonis LCA Model", "topics": [ "plot.RutterGatsonisLCA" ] }, { "page": "plot.RutterGatsonisSubgroup", "title": "Plot Results from a Rutter and Gatsonis Subgroup Model", "topics": [ "plot.RutterGatsonisSubgroup" ] }, { "page": "plot.RutterGatsonisSubgroupLCA", "title": "Plot Results from a Rutter and Gatsonis Subgroup LCA Model", "topics": [ "plot.RutterGatsonisSubgroupLCA" ] }, { "page": "print.HoyerAFT", "title": "Print Method for HoyerAFT Objects", "topics": [ "print.HoyerAFT" ] }, { "page": "print.Reitsma", "title": "Print Method for Reitsma Objects", "topics": [ "print.Reitsma" ] }, { "page": "print.ReitsmaLCA", "title": "Print Method for ReitsmaLCA Objects", "topics": [ "print.ReitsmaLCA" ] }, { "page": "print.ReitsmaSubgroup", "title": "Print Method for ReitsmaSubgroup Objects", "topics": [ "print.ReitsmaSubgroup" ] }, { "page": "print.ReitsmaSubgroupLCA", "title": "Print Method for ReitsmaSubgroupLCA Objects", "topics": [ "print.ReitsmaSubgroupLCA" ] }, { "page": "print.ReitsmaSubgroupTMB", "title": "Print Method for ReitsmaSubgroupTMB Objects", "topics": [ "print.ReitsmaSubgroupTMB" ] }, { "page": "print.ReitsmaTMB", "title": "Print Method for ReitsmaTMB Objects", "topics": [ "print.ReitsmaTMB" ] }, { "page": "print.RutterGatsonis", "title": "Print Method for RutterGatsonis Objects", "topics": [ "print.RutterGatsonis" ] }, { "page": "print.RutterGatsonisLCA", "title": "Print Method for RutterGatsonisLCA Objects", "topics": [ "print.RutterGatsonisLCA" ] }, { "page": "print.RutterGatsonisReg", "title": "Print Method for RutterGatsonisReg Objects", "topics": [ "print.RutterGatsonisReg" ] }, { "page": "print.RutterGatsonisSubgroup", "title": "Print Method for RutterGatsonisSubgroup Objects", "topics": [ "print.RutterGatsonisSubgroup" ] }, { "page": "print.RutterGatsonisSubgroupLCA", "title": "Print Method for RutterGatsonisSubgroupLCA Objects", "topics": [ "print.RutterGatsonisSubgroupLCA" ] }, { "page": "print.summary.DTAmodel", "title": "Print a Diagnostic Test Accuracy Model Summary", "topics": [ "print.summary.DTAmodel", "print.summary.HoyerAFT", "print.summary.Reitsma", "print.summary.ReitsmaLCA", "print.summary.ReitsmaSubgroup", "print.summary.ReitsmaSubgroupLCA", "print.summary.ReitsmaSubgroupTMB", "print.summary.ReitsmaTMB", "print.summary.RutterGatsonis", "print.summary.RutterGatsonisLCA", "print.summary.RutterGatsonisReg", "print.summary.RutterGatsonisSubgroup", "print.summary.RutterGatsonisSubgroupLCA" ] }, { "page": "restructure_data", "title": "Construct Interval Data for Threshold-Based Bivariate Time-to-Event Models", "topics": [ "restructure_data" ] }, { "page": "RF", "title": "RF Dataset", "topics": [ "RF" ] }, { "page": "schuetz", "title": "Schuetz Dataset", "topics": [ "schuetz" ] }, { "page": "summary.HoyerAFT", "title": "Summary Method for HoyerAFT Objects", "topics": [ "summary.HoyerAFT" ] }, { "page": "summary.Reitsma", "title": "Summary Method for Reitsma Objects", "topics": [ "summary.Reitsma" ] }, { "page": "summary.ReitsmaLCA", "title": "Summary Method for ReitsmaLCA Objects", "topics": [ "summary.ReitsmaLCA" ] }, { "page": "summary.ReitsmaSubgroup", "title": "Summary Method for ReitsmaSubgroup Objects", "topics": [ "summary.ReitsmaSubgroup" ] }, { "page": "summary.ReitsmaSubgroupLCA", "title": "Summary Method for ReitsmaSubgroupLCA Objects", "topics": [ "summary.ReitsmaSubgroupLCA" ] }, { "page": "summary.ReitsmaSubgroupTMB", "title": "Summary Method for ReitsmaSubgroupTMB Objects", "topics": [ "summary.ReitsmaSubgroupTMB" ] }, { "page": "summary.ReitsmaTMB", "title": "Summary Method for ReitsmaTMB Objects", "topics": [ "summary.ReitsmaTMB" ] }, { "page": "summary.RutterGatsonis", "title": "Summary Method for RutterGatsonis Objects", "topics": [ "summary.RutterGatsonis" ] }, { "page": "summary.RutterGatsonisLCA", "title": "Summary Method for RutterGatsonisLCA Objects", "topics": [ "summary.RutterGatsonisLCA" ] }, { "page": "summary.RutterGatsonisReg", "title": "Summary Method for RutterGatsonisReg Objects", "topics": [ "summary.RutterGatsonisReg" ] }, { "page": "summary.RutterGatsonisSubgroup", "title": "Summary Method for RutterGatsonisSubgroup Objects", "topics": [ "summary.RutterGatsonisSubgroup" ] }, { "page": "summary.RutterGatsonisSubgroupLCA", "title": "Summary Method for RutterGatsonisSubgroupLCA Objects", "topics": [ "summary.RutterGatsonisSubgroupLCA" ] }, { "page": "tub", "title": "Tub Dataset", "topics": [ "tub" ] }, { "page": "vcov.dtametaTMB", "title": "Extract Variance-Covariance Matrix", "topics": [ "vcov.dtametaTMB", "vcov.DTAmodel", "vcov.Reitsma", "vcov.ReitsmaLCA", "vcov.ReitsmaSubgroup", "vcov.ReitsmaSubgroupLCA" ] } ], "_readme": "https://github.com/ebme-uwk/dtametatmb/raw/HEAD/README.md", "_rundeps": [ "backports", "boot", "broom", "cli", "colorspace", "cowplot", "cpp11", "Deriv", "doBy", "dplyr", "farver", "forecast", "forestploter", "fracdiff", "generics", "ggplot2", "glmmTMB", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "mgcv", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "purrr", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "RTMB", "S7", "sandwich", "scales", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "TMB", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "dtametaTMB.qmd", "filename": "dtametaTMB.pdf", "title": "Introduction to dtametaTMB", "engine": "quarto::html", "headings": [ "How do I load the package?", "Which model should I use?", "Validation", "How do I use the Reitsma model?", "$$\\begin", "How do I get a summary plot of the Reitsma model?", "How do I get a coupled forest plot?", "How do I export results to RevMan?", "How do I fit the Reitsma model using the custom TMB backend?", "An example illustrating numerical behaviour near the boundary", "How do I use the Rutter and Gatsonis model?", "How do I get a summary plot of the Rutter and Gatsonis model?", "How do I simplify the models via parameter constraints?", "How do I use the Hoyer model?", "Which distributions does dtametaTMB support?", "Weibull distribution", "Log-normal distribution", "Log-logistic distribution", "Random effects structure", "Censoring mechanism", "How do I compute sensitivities and specificities?", "How do I interpret test direction?", "In a nutshell", "How do I fit the Hoyer model?", "How do I get a summary plot of the Hoyer model?", "How do I fit the Hoyer model to the FeNO dataset?", "How does testdirection=\"less\" work?", "How does fitHoyer work internally? -- Optional advanced workflow", "Step 1: How do we restructure the data set?", "Step 2: How do we get initial values?", "Step 3: How do we fit the model?", "References" ], "created": "2026-07-01 04:21:35", "modified": "2026-10-11 09:13:46", "commits": 23 }, { "source": "LCA.qmd", "filename": "LCA.pdf", "title": "Latent Class Meta-Analysis", "engine": "quarto::html", "headings": [ "What are latent class models?", "Which latent class models does dtametaTMB support?", "What is conditional independence?", "How do latent class models work?", "How do we model disease prevalence?", "$$\\text{logit}(\\pi_i)", "How do we model the index test? 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