Add set_nd_nq previously in pfm

pfm depends on mkin anyways, so reexporting set_nd_nq and
set_nd_nq_focus in pfm should provide reasonable continuity.

1 files changed, 103 insertions, 0 deletions

diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd
new file mode 100644
index 00000000..87a3fae1
--- /dev/null
+++ b/man/set_nd_nq.Rd
@@ -0,0 +1,103 @@
+% 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
+}