R/combine.test.R

In bhklab/survcomp: Performance Assessment and Comparison for Survival Analysis

'combine.test' <-
function(p, weight, method=c("fisher", "z.transform", "logit"), hetero=FALSE, na.rm=FALSE) {
	if(hetero) { stop("function to deal with heterogeneity is not implemented yet!") }
	method <- match.arg(method)
	na.ix <- is.na(p)
	if(any(na.ix) && !na.rm) { stop("missing values are present!") }
	if(all(na.ix)) { return(NA) } ## all p-values are missing
	p <- p[!na.ix]
	k <- length(p)
	if(k == 1) { return(p) }
	if(missing(weight)) { weight <- rep(1, k); }
	switch(method,  
	"fisher"={
		cp <- pchisq(-2 * sum(log(p)), df=2*k, lower.tail=FALSE)
	}, 
	"z.transform"={
		z <- qnorm(p, lower.tail=FALSE)
		cp <- pnorm(sum(weight * z) / sqrt(sum(weight^2)), lower.tail=FALSE)
	}, 
	"logit"={
		tt <- (- sum(log(p / (1 - p)))) / sqrt(k * pi^2 * (5 * k + 2) / (3 * (5 * k + 4)))
		cp <- pt(tt,df=5*k+4, lower.tail=FALSE)
	})
	return(cp)
}