R/confbayesx.R

In R2BayesX: Estimate Structured Additive Regression Models with 'BayesX'

confbayesx <-
function(x, parm, level = 0.95, edf, ...)
{
  cn <- colnames(x)
  pnames <- rownames(x)
  if(missing(parm)) 
    parm <- pnames
  else 
    if(is.numeric(parm)) 
      parm <- pnames[parm]
  id <- c(1L:length(pnames))[pnames %in% parm]
  ci <- NULL
  if(any(grepl("t value", cn))) {
    cf <- x[,1L]
    names(cf) <- pnames
    a <- (1 - level)/2
    a <- c(a, 1 - a)
    fac <- qt(a, edf)
    pct <- paste(format(100 * a, trim = TRUE, 
      scientific = FALSE, digits = 3L), "%", sep = "")
    ci <- array(NA, dim = c(length(parm), 2L), 
      dimnames = list(parm, pct))
    ses <- x[id,2L]
    ci[] <- cf[parm] + ses %o% fac
  } else {
    samples <- attr(x, "sample")
    if(!is.null(samples)) {
      colnames(samples) <- rownames(x)
      samples <- samples[,id]
      if(!is.matrix(samples)) {
        samples <- matrix(samples, ncol = 1L)
        colnames(samples) <- parm
      }
      a <- (1 - level)/2
      a <- c(a, 1 - a)
      ci <- t(apply(samples, 2L, quantile, probs = a))
    }
  }

  return(ci)
}