From 584308a7fbf6c7c5eff342b64b451fdaf1af91c6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 29 Sep 2022 17:31:15 +0200 Subject: 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. --- man/set_nd_nq.Rd | 103 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 man/set_nd_nq.Rd (limited to 'man') 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 +} -- cgit v1.2.1