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analysis", "topics": [ "ctLongToWide" ] }, { "page": "ctLOO", "title": "K fold cross validation for ctStanFit objects", "topics": [ "ctLOO" ] }, { "page": "ctModel", "title": "Define a ctsem model", "topics": [ "ctModel" ] }, { "page": "ctModelConvertOMX", "title": "Convert an old OpenMx-style ctsem model to the modern ctsem model format.", "topics": [ "ctModelConvertOMX", "ctStanModel" ] }, { "page": "ctModelCoverage_check", "title": "Coverage Check Function", "topics": [ "ctModelCoverage_check" ] }, { "page": "ctModelHigherOrder", "title": "Raise the order of a ctsem type ='omx' model object.", "topics": [ "ctModelHigherOrder" ] }, { "page": "ctModelLatex", "title": "Generate and optionally compile latex equation of subject level ctsem model.", "topics": [ "ctModelLatex" ] }, { "page": "ctModelMatrices", "title": "Matrix view for ctStanModel objects", "topics": [ "ctModelMatrices", "ctModelMatrices<-" ] }, { "page": "ctOptimUncertainty", "title": "Update optimized ctsem uncertainty estimates", "topics": [ "ctOptimUncertainty" ] }, { "page": "ctPlotArray", "title": "Plots three dimensional y values for quantile plots", "topics": [ "ctPlotArray" ] }, { "page": "ctPlotPosterior", "title": "ctPlotPosterior", "topics": [ "ctPlotPosterior", "ctStanPlotPost" ] }, { "page": "ctPoly", "title": "Plots uncertainty bands with shading", "topics": [ "ctPoly" ] }, { "page": "ctPostPredData", "title": "Create a data.table to compare data generated from a ctsem fit with the original data.", "topics": [ "ctPostPredData" ] }, { "page": "ctPostPredict", "title": "Compares model implied density and values to observed, for a ctStanFit object.", "topics": [ "ctPostPredict", "ctStanPostPredict" ] }, { "page": "ctPostPredPlots", "title": "Create diagnostic plots to assess the goodness-of-fit for a ctsem model.", "topics": [ "ctPostPredPlots" ] }, { "page": "ctPredict", "title": "ctPredict", "topics": [ "ctKalman", "ctPredict" ] }, { "page": "ctPredictTIP", "title": "ctPredictTIP", "topics": [ "ctPredictTIP" ] }, { "page": "ctRawParnames", "title": "ctRawParnames", "topics": [ "ctRawParnames", "ctStanParnames" ] }, { "page": "ctResiduals", "title": "Extract Standardized Residuals from a ctsem Fit", "topics": [ "ctResiduals" ] }, { "page": "ctstantestdat", "title": "ctstantestdat", "topics": [ "ctstantestdat" ] }, { "page": "ctstantestfit", "title": "ctstantestfit", "topics": [ "ctstantestfit" ] }, { "page": "ctSubjectPars", "title": "Extract an array of subject specific parameters from a ctStanFit object.", "topics": [ "ctStanSubjectPars", "ctSubjectPars" ] }, { "page": "ctSummaryMatrices", "title": "ctSummaryMatrices", "topics": [ "ctStanContinuousPars", "ctSummaryMatrices" ] }, { "page": "ctTIpredEffects", "title": "Get time independent predictor effect estimates", "topics": [ "ctStanTIpredeffects", "ctTIpredEffects" ] }, { "page": "ctWideNames", "title": "ctWideNames sets default column names for wide ctsem datasets. Primarily intended for internal ctsem usage.", "topics": [ "ctWideNames" ] }, { "page": "ctWideToLong", "title": "ctWideToLong Convert ctsem wide to long format", "topics": [ "ctWideToLong" ] }, { "page": "datastructure", "title": "datastructure", "topics": [ "datastructure" ] }, { "page": "inv_logit", "title": "Inverse logit", "topics": [ "inv_logit" ] }, { "page": "log1p_exp", "title": "log1p_exp", "topics": [ "log1p_exp" ] }, { "page": "longexample", "title": "longexample", "topics": [ "longexample" ] }, { "page": "Oscillating", "title": "Oscillating", "topics": [ "Oscillating" ] }, { "page": "plot.ctKalmanDF", "title": "Plots prediction output from ctPredict.", "topics": [ "plot.ctKalmanDF" ] }, { "page": "plot.ctStanFit", "title": "plot.ctStanFit", "topics": [ "ctStanPlot", "plot.ctStanFit" ] }, { "page": "plot.ctStanModel", "title": "Prior plotting", "topics": [ "plot.ctStanModel" ] }, { "page": "plotctACF", "title": "Plot an approximate continuous-time ACF object from ctACF", "topics": [ "plotctACF" ] }, { "page": "print.summary.ctStanFit", "title": "Print ctStanFit summaries", "topics": [ "print.summary.ctStanFit" ] }, { "page": "sdpcor2cov", "title": "sdcor2cov", "topics": [ "sdpcor2cov" ] }, { "page": "stan_reinitsf", "title": "Quickly initialise stanfit object from model and data", "topics": [ "stan_reinitsf" ] }, { "page": "stan_unconstrainsamples", "title": "Convert samples from a stanfit object to the unconstrained scale", "topics": [ "stan_unconstrainsamples" ] }, { "page": "standatact_specificsubjects", "title": "Adjust standata from ctsem to only use specific subjects", "topics": [ "standatact_specificsubjects" ] }, { "page": "stanoptimis", "title": "Optimize / importance sample a stan or ctStan model.", "topics": [ "stanoptimis" ] }, { "page": "stanWplot", "title": "Runs stan, and plots sampling information while sampling.", "topics": [ "stanWplot" ] }, { "page": "summary.ctEmpiricalBayesFit", "title": "Summarise empirical Bayes subject-wise ctsem fits", "topics": [ "summary.ctEmpiricalBayesFit" ] }, { "page": "summary.ctStanFit", "title": "summary.ctStanFit", "topics": [ "summary.ctStanFit" ] }, { "page": "test_isclose", "title": "Tests if 2 values are close to each other", "topics": [ "test_isclose" ] } ], "_readme": "https://github.com/cran/ctsem/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "cOde", "corpcor", "cpp11", "data.table", "Deriv", "desc", "distributional", "expm", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lattice", "lifecycle", "loo", "magrittr", "MASS", "Matrix", "matrixStats", "mize", "mvtnorm", "numDeriv", "otel", "parallelly", "pillar", "pkgbuild", "pkgconfig", "plyr", "png", "posterior", "processx", "ps", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "rstantools", "S7", "scales", "StanHeaders", "tensorA", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libtbb", "package": "libtbb12", "headers": "libtbb-dev", "source": "onetbb", "version": "2022.3.0-2", "name": "onetbb", "homepage": "https://uxlfoundation.github.io/oneTBB/", "description": "parallelism library for C++ - 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