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

## Documentation for package ‘c212’ version 1.0.1

- DESCRIPTION file

## Help Pages

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.