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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
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(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{
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
}
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