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. --- R/set_nd_nq.R | 164 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 164 insertions(+) create mode 100644 R/set_nd_nq.R (limited to 'R') diff --git a/R/set_nd_nq.R b/R/set_nd_nq.R new file mode 100644 index 00000000..37b9a894 --- /dev/null +++ b/R/set_nd_nq.R @@ -0,0 +1,164 @@ +#' Set non-detects and unquantified values in residue series without replicates +#' +#' 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). +#' +#' @param 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 +#' @param lod Limit of detection (numeric) +#' @param loq Limit of quantification(numeric). Must be specified if the FOCUS rule to +#' stop after the first non-detection is to be applied +#' @param 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). +#' @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) +#' @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 +#' @return A numeric vector, if a vector was supplied, or a numeric matrix otherwise +#' @export +#' @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) +set_nd_nq <- function(res_raw, lod, loq = NA, time_zero_presence = FALSE) { + if (!is.character(res_raw)) { + stop("Please supply a vector or a matrix of character values") + } + if (is.vector(res_raw)) { + was_vector <- TRUE + res_raw <- as.matrix(res_raw) + } else { + was_vector <- FALSE + if (!is.matrix(res_raw)) { + stop("Please supply a vector or a matrix of character values") + } + } + nq <- 0.5 * (loq + lod) + nda <- 0.5 * lod # not detected but adjacent to detection + res_raw[res_raw == "nq"] <- nq + + if (!time_zero_presence) { + for (j in 1:ncol(res_raw)) { + if (res_raw[1, j] == "nd") res_raw[1, j] <- "na" + } + } + res_raw[res_raw == "na"] <- NA + + not_nd_na <- function(value) !(grepl("nd", value) | is.na(value)) + + for (i in 1:nrow(res_raw)) { + for (j in 1:ncol(res_raw)) { + if (!is.na(res_raw[i, j]) && res_raw[i, j] == "nd") { + if (i > 1) { # check earlier sample in same layer + if (not_nd_na(res_raw[i - 1, j])) res_raw[i, j] <- "nda" + } + if (i < nrow(res_raw)) { # check later sample + if (not_nd_na(res_raw[i + 1, j])) res_raw[i, j] <- "nda" + } + if (j > 1) { # check above sample at the same time + if (not_nd_na(res_raw[i, j - 1])) res_raw[i, j] <- "nda" + } + if (j < ncol(res_raw)) { # check sample below at the same time + if (not_nd_na(res_raw[i, j + 1])) res_raw[i, j] <- "nda" + } + } + } + } + res_raw[res_raw == "nda"] <- nda + res_raw[res_raw == "nd"] <- NA + + result <- as.numeric(res_raw) + dim(result) <- dim(res_raw) + dimnames(result) <- dimnames(res_raw) + if (was_vector) result <- as.vector(result) + return(result) +} + +#' @describeIn set_nd_nq Set non-detects in residue time series according to FOCUS rules +#' @param set_first_sample_nd Should the first sample be set to "first_sample_nd_value" +#' in case it is a non-detection? +#' @param first_sample_nd_value Value to be used for the first sample if it is a non-detection +#' @param ignore_below_loq_after_first_nd Should we ignore values below the LOQ after the first +#' non-detection that occurs after the quantified values? +#' @export +set_nd_nq_focus <- function(res_raw, lod, loq = NA, + set_first_sample_nd = TRUE, first_sample_nd_value = 0, + ignore_below_loq_after_first_nd = TRUE) +{ + + if (!is.vector(res_raw)) stop("FOCUS rules are only specified for one-dimensional time series") + + if (ignore_below_loq_after_first_nd & is.na(loq)) { + stop("You need to specify an LOQ") + } + + n <- length(res_raw) + if (ignore_below_loq_after_first_nd) { + for (i in 3:n) { + if (!res_raw[i - 2] %in% c("na", "nd")) { + if (res_raw[i - 1] == "nd") { + res_remaining <- res_raw[i:n] + res_remaining_unquantified <- ifelse(res_remaining == "na", TRUE, + ifelse(res_remaining == "nd", TRUE, + ifelse(res_remaining == "nq", TRUE, + ifelse(suppressWarnings(as.numeric(res_remaining)) < loq, TRUE, FALSE)))) + res_remaining_numeric <- suppressWarnings(as.numeric(res_remaining)) + res_remaining_below_loq <- ifelse(res_remaining == "nq", TRUE, + ifelse(!is.na(res_remaining_numeric) & res_remaining_numeric < loq, TRUE, FALSE)) + if (all(res_remaining_unquantified)) { + res_raw[i:n] <- ifelse(res_remaining_below_loq, "nd", res_remaining) + } + } + } + } + } + + result <- set_nd_nq(res_raw, lod = lod, loq = loq) + + if (set_first_sample_nd) { + if (res_raw[1] == "nd") result[1] <- first_sample_nd_value + } + + return(result) +} -- cgit v1.2.1