From a5e458ecb33ae87e46b2237174a194f6252a97cf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 10 Oct 2019 08:53:30 +0200 Subject: Finish documentation of set_nd and test it --- R/process_residues.R | 107 -------------------------------------------------- R/set_nd.R | 109 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 109 insertions(+), 107 deletions(-) delete mode 100644 R/process_residues.R create mode 100644 R/set_nd.R (limited to 'R') diff --git a/R/process_residues.R b/R/process_residues.R deleted file mode 100644 index 35d3a4e..0000000 --- a/R/process_residues.R +++ /dev/null @@ -1,107 +0,0 @@ -#' 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. - -#' @param 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 -#' @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 stop_after_first_nondetect Should we really stop after the first non-detection? -#' @references FOCUS (2014) p. 75, 76, 131, 132 -#' @export -#' @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) -set_nd <- function(r, lod, loq = NA, - time_zero = TRUE, time_zero_nd_value = NA, stop_after_first_nondetect = FALSE) -{ - - if (stop_after_first_nondetect & is.na(loq)) { - stop("You need to specify an loq to decide if the curve should be cut off after the first non-detect") - } - - result <- r - - # Handle nq values - if (!missing(loq)) { - nq = 0.5 * (lod + loq) - result[r == "nq"] <- nq - } else { - if (any(r == "nq")) stop("You need to specify lod and loq") - } - - # Handle nd values - if (time_zero) { - if (r[1] == "nd") { - residues_present = FALSE - result[1] <- time_zero_nd_value - } else { - residues_present = TRUE - } - start_i <- 2 - } else { - residues_present <- if (r[1] == "nd") FALSE else TRUE - start_i <- 1 - } - - for (i in start_i:length(r)) { - - # residues_in_next - if (i < length(r)) { - next_value <- r[i + 1] - if (next_value == "nd") residues_in_next = FALSE - else residues_in_next = TRUE - } else { - residues_in_next = FALSE - } - - if (r[i] == "nd") { - if (residues_present | residues_in_next) { - result[i] <- 0.5 * lod - } else { - result[i] <- NA - } - - if (stop_after_first_nondetect) { - if (residues_present & !residues_in_next) { - remaining <- (i + 1):length(r) - if (!any(suppressWarnings(as.numeric(r[remaining])) > loq, na.rm = TRUE)) { - result[remaining] <- NA - return(as.numeric(result)) - } - } - - } - if (!residues_in_next) residues_present <- FALSE - else residues_present <- TRUE - } - - } - return(as.numeric(result)) -} - -#' @describeIn set_nd Set non-detects in residues series according to FOCUS rules -#' @export -set_nd_focus <- function(res, lod, loq = NA, time_zero = TRUE) { - result <- set_nd(res, lod, loq = loq, time_zero = time_zero, - time_zero_nd_value = 0, stop_after_first_nondetect = TRUE) - return(result) -} diff --git a/R/set_nd.R b/R/set_nd.R new file mode 100644 index 0000000..5d98940 --- /dev/null +++ b/R/set_nd.R @@ -0,0 +1,109 @@ +#' 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. + +#' @param 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 +#' @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 Is the first value in the series a time zero value? +#' @param time_zero_nd_value Which value should we use for non-detects at time zero? +#' @param stop_after_first_nondetect Should we really stop after the first non-detection? +#' @references FOCUS (2014) p. 75, 76, 131, 132 +#' @export +#' @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) +set_nd <- function(r, lod, loq = NA, + time_zero = TRUE, time_zero_nd_value = NA, stop_after_first_nondetect = FALSE) +{ + + if (stop_after_first_nondetect & is.na(loq)) { + stop("You need to specify an loq to decide if the curve should be cut off after the first non-detect") + } + + result <- r + + # Handle nq values + if (!missing(loq)) { + nq = 0.5 * (lod + loq) + result[r == "nq"] <- nq + } else { + if (any(r == "nq")) stop("You need to specify lod and loq") + } + + # Handle nd values + if (time_zero) { + if (r[1] == "nd") { + residues_present = FALSE + result[1] <- time_zero_nd_value + } else { + residues_present = TRUE + } + start_i <- 2 + } else { + residues_present <- if (r[1] == "nd") FALSE else TRUE + start_i <- 1 + } + + for (i in start_i:length(r)) { + + # residues_in_next + if (i < length(r)) { + next_value <- r[i + 1] + if (next_value == "nd") residues_in_next = FALSE + else residues_in_next = TRUE + } else { + residues_in_next = FALSE + } + + if (r[i] == "nd") { + if (residues_present | residues_in_next) { + result[i] <- 0.5 * lod + } else { + result[i] <- NA + } + + if (stop_after_first_nondetect) { + if (residues_present & !residues_in_next) { + remaining <- (i + 1):length(r) + if (!any(suppressWarnings(as.numeric(r[remaining])) > loq, na.rm = TRUE)) { + result[remaining] <- NA + return(as.numeric(result)) + } + } + + } + if (!residues_in_next) residues_present <- FALSE + else residues_present <- TRUE + } + + } + return(as.numeric(result)) +} + +#' @describeIn set_nd Set non-detects in residues series according to FOCUS rules +#' @export +set_nd_focus <- function(r, lod, loq = NA, time_zero = TRUE) { + result <- set_nd(r, lod, loq = loq, time_zero = time_zero, + time_zero_nd_value = 0, stop_after_first_nondetect = TRUE) + return(result) +} -- cgit v1.2.1