ptw <- function (ref, samp, selected.traces, init.coef = c(0, 1, 0), 
          try = FALSE, warp.type = c("individual", "global"), optim.crit = c("WCC", 
                                                                             "RMS"), mode = c("forward", "backward"), smooth.param = ifelse(try, 
                                                                                                                                            0, 1e+05), trwdth = 20, trwdth.res = trwdth, verbose = FALSE, 
          ...) 
{
  optim.crit <- match.arg(optim.crit)
  warp.type <- match.arg(warp.type)
  mode <- match.arg(mode)
  if (is.vector(ref)) 
    ref <- matrix(ref, nrow = 1)
  if (is.vector(samp)) 
    samp <- matrix(samp, nrow = 1)
  if (nrow(ref) > 1 && nrow(ref) != nrow(samp)) 
    stop("The number of references does not equal the number of samples")
  if (length(dim(ref)) > 2) 
    stop("Reference cannot be an array")
  if (length(dim(samp)) > 2) 
    stop("Sample cannot be an array")
  if (nrow(samp) == 1) 
    warp.type <- "individual"
  r <- nrow(samp)
  if (!missing(selected.traces)) {
    samp <- samp[selected.traces, , drop = FALSE]
    if (nrow(ref) > 1) 
      ref <- ref[selected.traces, , drop = FALSE]
  }
  if (is.vector(init.coef)) 
    init.coef <- matrix(init.coef, nrow = 1)
  if (warp.type == "global") {
    if (nrow(init.coef) != 1) 
      stop("Only one warping function is allowed with global alignment.")
  }
  else {
    if (nrow(init.coef) != nrow(samp)) 
      if (nrow(init.coef) == 1) {
        init.coef <- matrix(init.coef, byrow = TRUE, 
                            nrow = nrow(samp), ncol = length(init.coef))
      }
    else {
      stop("The number of warping functions does not match the number of samples")
    }
  }
  if (warp.type == "individual") {
    w <- matrix(0, nrow(samp), ncol(ref))
    a <- matrix(0, nrow(samp), ncol(init.coef))
    v <- rep(0, nrow(samp))
    warped.sample <- matrix(NA, nrow = nrow(samp), ncol = ncol(samp))
    for (i in 1:nrow(samp)) {
      if (verbose & nrow(samp) > 1) 
        cat(ifelse(nrow(ref) == 1, paste("Warping sample", 
                                         i, "with the reference \n"), paste("Warping sample", 
                                                                            i, "with reference \n", i)))
      if (nrow(ref) == 1) {
        rfrnc <- ref
      }
      else {
        rfrnc <- ref[i, , drop = FALSE]
      }
      quad.res <- pmwarp(rfrnc, samp[i, , drop = FALSE], 
                         optim.crit, init.coef[i, ], try = try, mode = mode, 
                         smooth.param = smooth.param, trwdth = trwdth, 
                         trwdth.res = trwdth.res, ...)
      w[i, ] <- quad.res$w
      a[i, ] <- quad.res$a
      v[i] <- quad.res$v
      warped.sample[i, ] <- c(warp.sample(samp[i, , drop = FALSE], 
                                          w[i, ], mode = mode))
    }
  }
  else {
    if (nrow(ref) == 1) 
      ref <- matrix(ref, nrow = nrow(samp), ncol = ncol(ref), 
                    byrow = TRUE)
    if (verbose) {
      if (nrow(ref) == 1) {
        cat("Simultaneous warping of samples with reference... \n")
      }
      else {
        cat("Simultaneous warping of samples with references... \n")
      }
    }
    quad.res <- pmwarp(ref, samp, optim.crit, c(init.coef), 
                       try = try, mode = mode, smooth.param = smooth.param, 
                       trwdth = trwdth, trwdth.res = trwdth.res, ...)
    w <- t(as.matrix(quad.res$w))
    a <- t(as.matrix(quad.res$a))
    v <- quad.res$v
    warped.sample <- t(warp.sample(samp, w, mode))
  }
  if (verbose) 
    cat("\nFinished.\n")
  result <- list(reference = ref, sample = samp, warped.sample = warped.sample, 
                 warp.coef = a, warp.fun = w, crit.value = v, optim.crit = optim.crit, 
                 mode = mode, warp.type = warp.type)
  class(result) <- "ptw"
  result
}