library(Mediana) ################################################################### # Case study 1 # Clinical trial in patients with metastatic colorectal cancer ################################################################### # Number of events parameters event.count.total = c(210, 300) randomization.ratio = c(1,2) # Outcome parameters median.time.placebo = 6 rate.placebo = log(2)/median.time.placebo outcome.placebo = parameters(rate = rate.placebo) median.time.treatment = 9 rate.treatment = log(2)/median.time.treatment outcome.treatment = parameters(rate = rate.treatment) # Data model case.study1.data.model = DataModel() + OutcomeDist(outcome.dist = "ExpoDist") + Event(n.events = event.count.total, rando.ratio = randomization.ratio) + Sample(id = "Placebo", outcome.par = parameters(outcome.placebo)) + Sample(id = "Treatment", outcome.par = parameters(outcome.treatment)) # Analysis model case.study1.analysis.model = AnalysisModel() + Test(id = "Placebo vs treatment", samples = samples("Placebo", "Treatment"), method = "LogrankTest") + Statistic(id = "Hazard Ratio", samples = samples("Placebo", "Treatment"), method = "HazardRatioStat", par = parameters(method = "Cox")) # Evaluation model case.study1.evaluation.model = EvaluationModel() + Criterion(id = "Marginal power", method = "MarginalPower", tests = tests("Placebo vs treatment"), labels = c("Placebo vs treatment"), par = parameters(alpha = 0.025)) + Criterion(id = "Hazard Ratio", method = "MeanSumm", statistics = tests("Hazard Ratio"), labels = c("Average Hazard Ratio")) # Simulation Parameters case.study1.sim.parameters = SimParameters(n.sims = 1000, proc.load = "full", seed = 42938001) # Perform clinical scenario evaluation case.study1.results = CSE(case.study1.data.model, case.study1.analysis.model, case.study1.evaluation.model, case.study1.sim.parameters) summary(case.study1.results) # Reporting case.study1.presentation.model = PresentationModel() + Project(username = "[Mediana's User]", title = "Case study 1", description = "Clinical trial in patients with metastatic colorectal cancer") + Section(by = "outcome.parameter") + Table(by = "event") # Report Generation GenerateReport(presentation.model = case.study1.presentation.model, cse.results = case.study1.results, report.filename = "Case study 1 (survival-type endpoint).docx") # Get the data generated in the CSE case.study1.data.stack = DataStack(data.model = case.study1.data.model, sim.parameters = case.study1.sim.parameters)