R/spearman.ci.R

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

# boot: boot

spearman.ci <-
function(var1,var2,nrep=1000,conf.level=0.95){
  if (length(var1)!=length(var2)) {stop(paste("'",deparse(substitute(var1)),"' and '",
    deparse(substitute(var2)),"' lengths differ",sep=""))}
  data.name <- paste(deparse(substitute(var1))," and ",deparse(substitute(var2)),"\n",nrep," replicates",sep="")
  nul <- as.numeric(row.names(table(c(which(is.na(var1)),which(is.na(var2))))))
  var1.2 <- if(length(nul)>0) {var1[-nul]} else {var1}
  var2.2 <- if(length(nul)>0) {var2[-nul]} else {var2}
  cor.fun <- function(data,ind) {
    as.numeric(suppressWarnings(cor.test(data[ind,1],data[ind,2],method="spearman")$estimate))
  }
  simul <- boot::boot(data.frame(var1.2,var2.2),cor.fun,R=nrep)
  interval <- .ci(simul$t,conf.level=conf.level)
  attr(interval,"conf.level") <- conf.level
  coeff <- as.numeric(suppressWarnings(cor.test(var1,var2,method="spearman")$estimate))
  names(coeff) <- "rho"
  result <- list(method="Spearman's rank correlation",conf.level=conf.level,rep=nrep,data.name=data.name,
    estimate=coeff,conf.int=interval)
  class(result) <- "htest"
  return(result)
}