R/FHtestrcc.default.R

In FHtest: Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class

FHtestrcc.default <-
function(L, R, group, rho = 0, lambda = 0, alternative, ...)
{
  if(class(group)[1] == "labelled") group <- as.vector(group)
  if((!is.factor(group))&(!(is.vector(group)&is.numeric(group)))&(!(is.vector(group)&is.character(group)))) stop("group should be a factor, character, or numeric vector")
  call <- match.call(expand.dots =TRUE)
  L.name <- as.character(c(call$L))
  R.name <- as.character(c(call$R))
  group.name <- as.character(c(call$group))
     if ((length(L.name) > 1) | (length(R.name) > 1) | (length(group.name) >
         1)) {
         L.name <- "L"
         R.name <- "R"
         group.name <- "group"
     }
     if ((sum(nchar(L.name)) + sum(nchar(R.name)) + sum(nchar(group.name))) >
         50) {
         L.name <- "L"
         R.name <- "R"
         group.name <- "group"
     }
  if(missing(alternative)||all(alternative!=c("different","increasing","decreasing"))) alternative="different"
  if(sum(L == R)+sum((L<R)&(R == max(R)))!=length(L)) stop("This method needs right-censored data")
  times <- L
  status <- 1*(L == R)
  out<-rcc(times,status,group,rho,lambda)
  out$call <- call
  	out$n = table(group)
  names(out$n)<-paste(group.name,"=",names(out$n),sep="")
  out$data.name <- paste("Data:",paste("{", L.name, ",", R.name, "}", " by ", group.name, sep = ""))
  dif <- t(out$obs-out$exp)
  ug <- sort(unique(group))
  k <- length(ug)
  if ((is.numeric(group))&(k>2)) {
  	out$information <- paste("Trend FH test for right-censored data",sep = "")
  	out$var <- c(t(ug)%*%out$var%*%ug)
  	out$statistic <- c((dif%*%ug)/sqrt(out$var))
  	if (alternative == "increasing") {
  		out$pvalue <- pnorm(out$statistic)
  		out$alt.phrase <- paste("Alternative hypothesis: increasing survival functions (higher ", group.name ," implies later event times)", sep = "")
  	} else if (alternative == "decreasing") {
  		out$pvalue <- 1-pnorm(out$statistic)
  		out$alt.phrase <- paste("Alternative hypothesis: decreasing survival functions (higher ", group.name, " implies earlier event times)", sep = "")
  	} else {
  		out$pvalue <- 2-2*pnorm(abs(out$statistic))
  		out$alt.phrase <- paste("Alternative hypothesis: survival functions not equal", sep = "")
  		}
  	names(out$statistic) <- "Z"
  } else if (!(is.numeric(group))&(k>2)) {
  	out$information <- paste("K-sample test for right-censored data",sep = "")
  	out$statistic= c(dif%*%ginv(out$var)%*%t(dif))
  	if (alternative!="different") warning("alternative ignored, group is factor with more than 2 groups")
  	out$pvalue <- 1 - pchisq(out$statistic,k-1)
  	out$alt.phrase <- paste("Alternative hypothesis: survival functions not equal")
  	names(out$statistic) <- "Chi Square"
  } else {
  	out$var <- out$var[1,1]
  	out$statistic <- dif[2]/sqrt(out$var)
  	out$information <- paste("Two-sample test for right-censored data",sep = "")
  	if (alternative == "increasing") {
  		out$pvalue <- pnorm(out$statistic)
  		out$alt.phrase <- paste("Alternative hypothesis: increasing survival functions (", names(out$n)[2] ," has later event times)", sep = "")
  	} else if (alternative == "decreasing") {
  		out$pvalue <- 1-pnorm(out$statistic)
  		out$alt.phrase <- paste("Alternative hypothesis: decreasing survival functions (", names(out$n)[2] ," has earlier event times)", sep = "")
  	} else{
  		out$pvalue <- 2-2*pnorm(abs(out$statistic))
  		out$alt.phrase <- paste("Alternative hypothesis: survival functions not equal", sep = "")
  	}
  	names(out$statistic) <- "Z"
  }

  out$information <- paste("\t",out$information,"\n\nParameters: rho=",as.character(rho), ", lambda=",as.character(lambda),"\nDistribution: counting process approach",sep = "")
  class(out)<-"FHtestrcc"
  out
}