Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)

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Documentation for package ‘c212’ version 0.98

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c212-package Methods for the Detection of Safety Signals in Randomised Controlled Trials using Groupings.
c212.1a Implementation of the Berry and Berry Three-Level Hierarchical Model without Point-Mass.
c212.1a.interim A Two or Three-Level Hierarchical Body-system based Model for interim analysis without Point-Mass.
c212.BB Implementation of the Berry and Berry Three-Level Hierarchical Model.
c212.BB.interim A Two or Three-Level Hierarchical Body-system based Model for interim analysis with Point-Mass.
c212.BH Implementation of Benjamini-Hochberg procedure for False Discovery Rate control
c212.BH.adjust.pvals Benjamini-Hochberg procedure adjusted p-values
c212.bin.test Plot Raw Adverse Event Incidence Data
c212.BONF Implementation of Bonferroni correction for error control
c212.convergence.diag Convergence Diagnostics of the Simulation
c212.DFDR Implementation of the Double False Discovery Rate for controlling the False Discovery Rate.
c212.err.cntrl Implementaion of Group Bonferroni-Hochberg procedure for control of the False Discovery Rate
c212.FDR.data Fisher Test p-values for End of Trial Data Clinical Data
c212.fisher.test Fisher Exact Test
c212.GBH Implementaion of Group Bonferroni-Hochberg procedure for control of the False Discovery Rate
c212.gen.initial.values Generate a template simulation initial values.
c212.global.sim.params Generate a template for the individual model parameter simulation control parameters.
c212.hyper.params Generate a template for the individual model parameter simulation control parameters.
c212.interim.1a.hier2 A Two-Level Hierarchical Body-system based Model for interim analysis without Point-Mass.
c212.interim.1a.hier3 A Three-Level Hierarchical Body-system based Model for interim analysis without Point-Mass.
c212.interim.BB.hier2 A Three-Level Hierarchical Body-system based Model for interim analysis with Point-Mass.
c212.interim.BB.hier3 A Three-Level Hierarchical Body-system based Model for interim analysis with Point-Mass.
c212.interim.MLE Poisson Maximum Likelihood Estimator
c212.LSL Implementaion of the least-slope estimator estimator (LSL) for the proportion of true null hypotheses.
c212.monitor.samples Generate a template for choosing which samples to monitor.
c212.NOADJ Unadjusted test of multiple hypotheses.
c212.plot.eot.data Plot Adverse Event Incidence Data
c212.plot.interim.data Plot Adverse Event Count Data for a Body-system by Interval
c212.plot.samples Plot Posterior Distribution
c212.pointmass.weights Generate a template for the point-mass weightings.
c212.print.convergence.summary Print a Summary of the Convergence Diagnostics of the Simulation
c212.print.summary.stats Print the Summary Statistics of Posterior Distributions
c212.ptheta Reports the posterior probability that theta (the increase in the log-odds) is greater than zero for each Adverse Event
c212.sim.control.params Generate a template for the individual model parameter simulation control parameters.
c212.ssBH Implementation of Subset Benjamini-Hochberg for False Discover Rate control
c212.summary.stats Summary Statistics for the Posterior Distributions in the model.
c212.trial.data End of Trial Data Clinical Data for Adverse Event Incidence
c212.trial.interval.data1 Interim analysis trial data.
c212.trial.interval.data2 Interim analysis trial data.
c212.TST Implementaion of the two-stage estimator (TST) for the proportion of true null hypotheses.