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-#' Set non-detects in residue series without replicates
-#'
-#' Sets non-detects directly before or directly after detects to NA. Values between
-#' lod and loq are set to their mean value if an loq is specified.
-#' If 'time_zero' is set to TRUE, the residue series is assumed to start with time
-#' zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
-#' set_nd_focus variant, this is zero, otherwise this argument has NA as default
-#' value.
-#' If stopping after the first non-detection is requested, as in in the FOCUS
-#' variant of the function, an loq has to be specified in order to decide
-#' if any later detections are above the loq.
-#'
-#' @param r A character vector of sequential residues without replicates, with
-#' non-detects specified as 'nd' and unquantified values above the limit of
-#' detection specified as 'nq', otherwise coercible to numeric
-#' @param lod Limit of detection (numeric)
-#' @param loq Limit of quantification(numeric). Must be specified if the FOCUS rule to
-#' stop after the first non-detection is to be applied
-#' @param time_zero Is the first value in the series a time zero value?
-#' @param time_zero_nd_value Which value should we use for non-detects at time zero?
-#' @param stop_after_first_nondetect Should we really stop after the first non-detection?
-#' @references FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-#'   Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
-#'   18 December 2014, p. 251
-#' @describeIn set_nd Set non-detects in residues series
-#' @export
-#' @examples
-#' # FOCUS (2014) p. 75/76 and 131/132
-#' parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-#' set_nd(parent_1, 0.02)
-#' parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-#' set_nd(parent_2, 0.02)
-#' set_nd_focus(parent_2, 0.02, loq = 0.05)
-#' parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-#' set_nd(parent_3, 0.02)
-#' set_nd_focus(parent_3, 0.02, loq = 0.05)
-#' metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
-#' set_nd(metabolite, 0.02)
-set_nd <- function(r, lod, loq = NA,
-  time_zero = TRUE, time_zero_nd_value = NA, stop_after_first_nondetect = FALSE)
-{
-
-  if (stop_after_first_nondetect & is.na(loq)) {
-    stop("You need to specify an loq to decide if the curve should be cut off after the first non-detect")
-  }
-
-  result <- r
-
-  # Handle nq values
-  if (!missing(loq)) {
-    nq = 0.5 * (lod + loq)
-    result[r == "nq"] <- nq
-  } else {
-    if (any(r == "nq", na.rm = TRUE)) stop("You need to specify lod and loq")
-  }
-
-  #  Handle nd values
-  if (time_zero) {
-    if (r[1] %in% c("nd")) {
-      residues_present = FALSE
-      result[1] <- time_zero_nd_value
-    } else {
-      residues_present = TRUE
-    }
-    start_i <- 2
-  } else {
-    residues_present <- if (r[1] == "nd") FALSE else TRUE
-    start_i <- 1
-  }
-
-  for (i in start_i:length(r)) {
-
-    # residues_in_next
-    if (i < length(r)) {
-      next_value <- r[i + 1]
-      if (is.na(next_value) || next_value == "nd") residues_in_next = FALSE
-      else residues_in_next = TRUE
-    } else {
-      residues_in_next = FALSE
-    }
-
-    if (is.na(r[i])) {
-      residues_present <- FALSE
-      result[i] <- NA
-    } else {
-      if (r[i] == "nd") {
-        if (residues_present | residues_in_next) {
-          result[i] <- 0.5 * lod
-        } else {
-          result[i] <- NA
-        }
-
-        if (stop_after_first_nondetect) {
-          if (residues_present & !residues_in_next) {
-            remaining <- (i + 1):length(r)
-            if (!any(suppressWarnings(as.numeric(r[remaining])) > loq, na.rm = TRUE)) {
-              result[remaining] <- NA
-              return(as.numeric(result))
-            }
-          }
-        }
-        if (!residues_in_next) residues_present <- FALSE
-        else residues_present <- TRUE
-      } else {
-        residues_present <- TRUE
-      }
-    }
-  }
-  return(as.numeric(result))
-}
-
-#' @describeIn set_nd Set non-detects in residues series according to FOCUS rules
-#' @export
-set_nd_focus <- function(r, lod, loq = NA, time_zero = TRUE) {
-  result <- set_nd(r, lod, loq = loq, time_zero = time_zero,
-    time_zero_nd_value = 0, stop_after_first_nondetect = TRUE)
-  return(result)
-}