######################################################################################################################
# Compute the log hazard ratio based on non-missing values in the combined sample
EffectSizeEventStat = function(sample.list, parameter) {
# Determine the function call, either to generate the statistic or to return description
call = (parameter[[1]] == "Description")
if (call == FALSE | is.na(call)) {
# Error checks
if (length(sample.list)!=2)
stop("Analysis model: Two samples must be specified in the EffectSizeEventStat statistic.")
if (is.na(parameter[[2]])) method = "Log-Rank"
else {
if (!(parameter[[2]]$method %in% c("Log-Rank", "Cox")))
stop("Analysis model: HazardRatioStat statistic : the method must be Log-Rank or Cox.")
method = parameter[[2]]$method
}
# Outcomes in Sample 1
outcome1 = sample.list[[1]][, "outcome"]
# Remove the missing values due to dropouts/incomplete observations
outcome1.complete = outcome1[stats::complete.cases(outcome1)]
# Observed events in Sample 1 (negation of censoring indicators)
event1 = !sample.list[[1]][, "patient.censor.indicator"]
event1.complete = event1[stats::complete.cases(outcome1)]
# Sample size in Sample 1
n1 = length(outcome1.complete)
# Outcomes in Sample 2
outcome2 = sample.list[[2]][, "outcome"]
# Remove the missing values due to dropouts/incomplete observations
outcome2.complete = outcome2[stats::complete.cases(outcome2)]
# Observed events in Sample 2 (negation of censoring indicators)
event2 = !sample.list[[2]][, "patient.censor.indicator"]
event2.complete = event2[stats::complete.cases(outcome2)]
# Sample size in Sample 2
n2 = length(outcome2.complete)
# Create combined samples of outcomes, censoring indicators (all events are observed) and treatment indicators
outcome = c(outcome1.complete, outcome2.complete)
event = c(event1.complete, event2.complete)
treatment = c(rep(0, n1), rep(1, n2))
# Get the HR
if (method == "Log-Rank"){
surv.test = survival::survdiff(survival::Surv(outcome, event) ~ treatment)
result = -log((surv.test$obs[2]/surv.test$exp[2])/(surv.test$obs[1]/surv.test$exp[1]))
} else if (method == "Cox"){
result = -log(summary(survival::coxph(survival::Surv(outcome, event) ~ treatment))$coef[,"exp(coef)"])
}
}
else if (call == TRUE) {
if (is.na(parameter[[2]])) result = list("Effect size (event)")
else {
result = list("Effect size (event)", "method = ")
}
}
return(result)
}
# End of EffectSizeEventStat
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