Residue processing for depth profiles over time

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-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/set_nd.R
-\name{set_nd}
-\alias{set_nd}
-\alias{set_nd_focus}
-\title{Set non-detects in residue series without replicates}
-\usage{
-set_nd(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA,
-  stop_after_first_nondetect = FALSE)
-
-set_nd_focus(r, lod, loq = NA, time_zero = TRUE)
-}
-\arguments{
-\item{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}
-
-\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}{Is the first value in the series a time zero value?}
-
-\item{time_zero_nd_value}{Which value should we use for non-detects at time zero?}
-
-\item{stop_after_first_nondetect}{Should we really stop after the first non-detection?}
-}
-\description{
-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.
-}
-\section{Functions}{
-\itemize{
-\item \code{set_nd}: Set non-detects in residues series
-
-\item \code{set_nd_focus}: Set non-detects in residues 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(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)
-}
-\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
-}