R/nlsBoot1.r

In AMCOOK/FoodHabits: Functions for Food Habits Analysis from BIO Ecosystem Surveys

#' @export

nlsBoot1 <- function (nls, data1,niter = 999,Qlow1, Qhigh1) 
{
  if (!inherits(nls, "nls")) 
    stop("Use only with 'nls' objects")
      data2 <- data1
  fitted1 <- fitted(nls)
  resid1 <- resid(nls)
  var1 <- all.vars(formula(nls)[[2]])
  l1 <- lapply(1:niter, function(i) {
    data2[, var1] <- fitted1 + sample(scale(resid1, scale = FALSE), 
      replace = TRUE)
    nls2 <- try(update(nls, start = as.list(coef(nls)), data = data2), 
      silent = TRUE)
    if (inherits(nls2, "nls")) 
      return(list(coef = coef(nls2), rse = summary(nls2)$sigma))
  })
  if (sum(sapply(l1, is.null)) > niter/2) 
    stop(paste("Procedure aborted: the fit only converged in", 
      round(sum(sapply(l1, is.null))/niter), "% during bootstrapping"))
  tabboot <- sapply(l1[!sapply(l1, is.null)], function(z) z$coef)
  rseboot <- sapply(l1[!sapply(l1, is.null)], function(z) z$rse)
  recapboot <- t(apply(tabboot, 1, quantile, c(0.5, Qlow1, 
    Qhigh1)))
  colnames(recapboot) <- c("Median", Qlow1*100, Qhigh1*100)
  serr <- sum(sapply(l1, is.null))
  if (serr > 0) 
    warning(paste("The fit did not converge", serr, "times during bootstrapping"))
  listboot <- list(coefboot = t(tabboot), rse = rseboot, bootCI = recapboot)
  class(listboot) <- "nlsBoot"
  return(listboot)
}