R/function.PrevalenceMatching.R

In OptimalCutpoints: Computing Optimal Cutpoints in Diagnostic Tests

function.PrevalenceMatching <-
function(data, marker, status, tag.healthy = 0, direction = c("<", ">"), control = control.cutpoints(), pop.prev, ci.fit = FALSE, conf.level = 0.95, measures.acc) {
	sample.prev <- calculate.sample.prev(data, status, tag.healthy)
	predicted.prev <- measures.acc$Se[,1]*sample.prev+(1-measures.acc$Sp[,1])*(1-sample.prev)
	 
	difference <- abs(sample.prev-predicted.prev)
		 
	cPrevalenceMatching <- measures.acc$cutoffs[which(round(difference,10)==round(min(difference, na.rm = TRUE),10))]
	optimal.difference <- min(difference,na.rm=TRUE)
	  
	optimal.cutoff <- obtain.optimal.measures(cPrevalenceMatching, measures.acc)
	
	res <- list(measures.acc = measures.acc, optimal.cutoff = optimal.cutoff, criterion = difference, optimal.criterion = optimal.difference)
	res
}