R/FHtestrcp.default.R

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

FHtestrcp.default <-
function(L, R, group, rho = 0, lambda = 0, alternative, method = NULL,
         methodRule = methodRuleIC1, exact = NULL, permcontrol = permControl(),
         ...)
{
  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)

  cc <- rcp(times,status,rho,lambda)
  names(cc)<-1:length(times)

  if (is.null(method)) method <- methodRule(cc, group, exact)
  method.OK <- (method == "pclt" | method == "exact.mc" | method == "exact.network" | method == "exact.ce")
  if (!method.OK) stop("method not one of: 'pclt', 'exact.mc'. 'exact.network', 'exact.ce'")

  ug <- sort(unique(group))
  k <- length(ug)
  if ((is.numeric(group))&(k>2)) {
  	icalternative <- c("two.sided","less","greater")[alternative == c("different","increasing","decreasing")]
  	icp <- do.call("permTREND", list(x = cc, y = group, alternative=icalternative, method = method,control=permcontrol))
  	}
  else if (!(is.numeric(group))&(k>2)) {
  	icp <- do.call("permKS", list(x = cc, g = group, alternative="two.sided", method = method,control=permcontrol))
  	}
  else {
  	icalternative <- c("two.sided","greater","less")[alternative == c("different","increasing","decreasing")]
  	icp <- do.call("permTS", list(x = cc[group == ug[1]], y = cc[group == ug[2]], alternative=icalternative, method = method,control=permcontrol))
  	}

  out <- list(cc,icp$statistic,icp$p.value,icp$p.conf.int)
  names(out)<-c("scores","statistic","pvalue","p.conf.int")
  out$diff <- aggregate(out$scores,list(group),sum)$x
  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 = ""))

  n <- length(group)
  z <- 1*(matrix(rep(group,k) == rep(ug,each=n),n))
  out$var <- var(out$scores)*((t(z)%*%z) -n*(t(t(colMeans(z)))%*%t(colMeans(z))))

  if ((is.numeric(group))&(k>2)) {
  	out$var <- c(t(ug)%*%out$var%*%ug)
  	out$information <- paste("Trend FH test for right-censored data",sep = "")
  	if (method!="pclt") out$statistic <- (do.call("permTREND", list(x = out$scores, y = group, alternative="two.sided", method = "pclt")))$statistic
  	if (alternative == "increasing") {
  		out$alt.phrase <- paste("Alternative hypothesis: increasing survival functions (higher ", group.name ," implies later event times)", sep = "")
  		}
  	else if (alternative == "decreasing") {
  		out$alt.phrase <- paste("Alternative hypothesis: decreasing survival functions (higher ", group.name, " implies earlier event times)", sep = "")
  		}
  	else {
  		out$alt.phrase <- paste("Alternative hypothesis: survival functions not equal", sep = "")
  		}
  	}
  else if (!(is.numeric(group))&(k>2)) {
  	out$information <- paste("K-sample test for right-censored data",sep = "")
  	if (method!="pclt") out$statistic <- (do.call("permKS", list(x = out$scores, g = group, method = "pclt")))$statistic
  	if (alternative!="different") warning("alternative ignored, group is factor with more than 2 groups")
  	out$alt.phrase <- paste("Alternative hypothesis: survival functions not equal")
  	}
  else {
  	out$var <- out$var[1,1]
  	out$information <- paste("Two-sample test for right-censored data",sep = "")
  	if (method == "pclt") out$statistic <- -out$statistic
  	else {
  		ug <- sort(unique(group))
  		out$statistic <- -(do.call("permTS", list(x = out$scores[group == ug[1]], y = out$scores[group == ug[2]], alternative="two.sided", method = "pclt")))$statistic
  		}
  	if (alternative == "increasing") {
  		out$alt.phrase <- paste("Alternative hypothesis: increasing survival functions (", names(out$n)[2] ," has later event times)", sep = "")
  		}
  	else if (alternative == "decreasing") {
  		out$alt.phrase <- paste("Alternative hypothesis: decreasing survival functions (", names(out$n)[2] ," has earlier event times)", sep = "")
  		}
  	else{
  		out$alt.phrase <- paste("Alternative hypothesis: survival functions not equal", sep = "")
  		}
  	}

  out$information <- paste("\t",out$information,"\n\nParameters: rho=",as.character(rho), ", lambda=",as.character(lambda),"\nDistribution: permutation approach (",sep = "")
  if (method == "pclt") out$information <- paste(out$information,"asymptotic approximation using central limit theorem)",sep = "")
  else if (method == "exact.ce") out$information <- paste(out$information,"exact method using complete enumeration)",sep = "")
  else if (method == "exact.mc") out$information <- paste(out$information,"exact method using Monte Carlo with ",as.character(icp$nmc)," replications)",sep = "")
  else if (method == "exact.network") out$information <- paste(out$information,"exact method using a network algorithm)",sep = "")

  class(out)<-"FHtestrcp"
  out
}