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c212 (version 0.98)

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

Description

Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class. This work was supported by the Engineering and Physical Sciences Research Council (UK) (EPSRC) [award reference 1521741] and Frontier Science (Scotland) Ltd. The package title c212 is in reference to the original Engineering and Physical Sciences Research Council (UK) funded project which was named CASE 2/12.

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Version

Install

install.packages('c212')

Monthly Downloads

644

Version

0.98

License

GPL (>= 2)

Maintainer

Raymond Carragher

Last Published

September 8th, 2020

Functions in c212 (0.98)

c212.err.cntrl

Implementaion of Group Bonferroni-Hochberg procedure for control of the False Discovery Rate
c212.1a.interim

A Two or Three-Level Hierarchical Body-system based Model for interim analysis without Point-Mass.
c212.bin.test

Plot Raw Adverse Event Incidence Data
c212.BB.interim

A Two or Three-Level Hierarchical Body-system based Model for interim analysis with Point-Mass.
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.FDR.data

Fisher Test p-values for End of Trial Data Clinical Data
c212.fisher.test

Fisher Exact Test
c212.BB

Implementation of the Berry and Berry Three-Level Hierarchical Model.
c212.convergence.diag

Convergence Diagnostics of the Simulation
c212.hyper.params

Generate a template for the individual model parameter simulation control parameters.
c212.interim.BB.hier2

A Three-Level Hierarchical Body-system based Model for interim analysis with Point-Mass.
c212.interim.1a.hier3

A Three-Level Hierarchical Body-system based Model for interim analysis without Point-Mass.
c212.plot.eot.data

Plot Adverse Event Incidence Data
c212.monitor.samples

Generate a template for choosing which samples to monitor.
c212.NOADJ

Unadjusted test of multiple hypotheses.
c212.print.summary.stats

Print the Summary Statistics of Posterior Distributions
c212.LSL

Implementaion of the least-slope estimator estimator (LSL) for the proportion of true null hypotheses.
c212.ptheta

Reports the posterior probability that theta (the increase in the log-odds) is greater than zero for each Adverse Event
c212.plot.interim.data.rd

Plot Adverse Event Count Data for a Body-system by Interval
c212.interim.1a.hier2

A Two-Level Hierarchical Body-system based Model for interim analysis without Point-Mass.
c212.gen.initial.values

Generate a template simulation initial values.
c212.TST

Implementaion of the two-stage estimator (TST) for the proportion of true null hypotheses.
c212.trial.interval.data2

Interim analysis trial data.
c212.trial.interval.data1

Interim analysis trial data.
c212.plot.samples

Plot Posterior Distribution
c212.trial.data

End of Trial Data Clinical Data for Adverse Event Incidence
c212.ssBH

Implementation of Subset Benjamini-Hochberg for False Discover Rate control
c212.interim.BB.hier3

A 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.global.sim.params

Generate a template for the individual model parameter simulation control parameters.
c212.sim.control.params

Generate a template for the individual model parameter simulation control parameters.
c212.interim.MLE

Poisson Maximum Likelihood Estimator
c212.summary.stats

Summary Statistics for the Posterior Distributions in the model.
c212.BH.adjust.pvals

Benjamini-Hochberg procedure adjusted p-values
c212.BONF

Implementation of Bonferroni correction for error control
c212.DFDR

Implementation of the Double False Discovery Rate for controlling the False Discovery Rate.
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.GBH

Implementaion of Group Bonferroni-Hochberg procedure for control of the False Discovery Rate