Function to set non-detects in residue series

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/process_residues.R
+\name{set_nd}
+\alias{set_nd}
+\alias{set_nd_focus}
+\title{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.}
+\usage{
+set_nd(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA,
+  stop_after_first_nondetect = FALSE)
+
+set_nd_focus(res, 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{stop_after_first_nondetect}{Should we really stop after the first non-detection?}
+}
+\description{
+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.
+}
+\section{Functions}{
+\itemize{
+\item \code{set_nd_focus}: Set non-detects in residues series according to FOCUS rules
+}}
+
+\examples{
+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) p. 75, 76, 131, 132
+}