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-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/set_nd_nq.R
-\name{set_nd_nq}
-\alias{set_nd_nq}
-\alias{set_nd_nq_focus}
-\title{Set non-detects and unquantified values in residue series without replicates}
-\usage{
-set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
-
-set_nd_nq_focus(
-  res_raw,
-  lod,
-  loq = NA,
-  set_first_sample_nd = TRUE,
-  first_sample_nd_value = 0,
-  ignore_below_loq_after_first_nd = TRUE
-)
-}
-\arguments{
-\item{res_raw}{Character vector of a residue time series, or matrix of
-residue values with rows representing depth profiles for a specific sampling
-time, and columns representing time series of residues at the same depth.
-Values below the limit of detection (lod) have to be coded as "nd", values
-between the limit of detection and the limit of quantification, if any, have
-to be coded as "nq". Samples not analysed have to be coded as "na". All
-values that are not "na", "nd" or "nq" have to be coercible to numeric}
-
-\item{lod}{Limit of detection (numeric)}
-
-\item{loq}{Limit of quantification(numeric). Must be specified if the FOCUS rule to
-stop after the first non-detection is to be applied}
-
-\item{time_zero_presence}{Do we assume that residues occur at time zero?
-This only affects samples from the first sampling time that have been
-reported as "nd" (not detected).}
-
-\item{set_first_sample_nd}{Should the first sample be set to "first_sample_nd_value"
-in case it is a non-detection?}
-
-\item{first_sample_nd_value}{Value to be used for the first sample if it is a non-detection}
-
-\item{ignore_below_loq_after_first_nd}{Should we ignore values below the LOQ after the first
-non-detection that occurs after the quantified values?}
-}
-\value{
-A numeric vector, if a vector was supplied, or a numeric matrix otherwise
-}
-\description{
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015).
-}
-\section{Functions}{
-\itemize{
-\item \code{set_nd_nq_focus}: Set non-detects in residue time series according to FOCUS rules
-}}
-
-\examples{
-# FOCUS (2014) p. 75/76 and 131/132
-parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-set_nd_nq(parent_1, 0.02)
-parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-set_nd_nq(parent_2, 0.02)
-set_nd_nq_focus(parent_2, 0.02, loq = 0.05)
-parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-set_nd_nq(parent_3, 0.02)
-set_nd_nq_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_nq(metabolite, 0.02)
-set_nd_nq_focus(metabolite, 0.02, 0.05)
-#
-# Boesten et al. (2015), p. 57/58
-table_8 <- matrix(
-  c(10, 10, rep("nd", 4),
-    10, 10, rep("nq", 2), rep("nd", 2),
-    10, 10, 10, "nq", "nd", "nd",
-    "nq", 10, "nq", rep("nd", 3),
-    "nd", "nq", "nq", rep("nd", 3),
-    rep("nd", 6), rep("nd", 6)),
-  ncol = 6, byrow = TRUE)
-set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
-table_10 <- matrix(
-  c(10, 10, rep("nd", 4),
-    10, 10, rep("nd", 4),
-    10, 10, 10, rep("nd", 3),
-    "nd", 10, rep("nd", 4),
-    rep("nd", 18)),
-  ncol = 6, byrow = TRUE)
-set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
-}
-\references{
-Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
-J. and Pol, J. W. (2015). Leaching of plant protection products and their
-transformation products; Proposals for improving the assessment of leaching
-to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
-Wageningen UR (University & Research centre)
-
-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
-}