diff options
| -rw-r--r-- | ChangeLog | 6 | ||||
| -rw-r--r-- | R/set_nd.R | 45 | ||||
| -rw-r--r-- | man/set_nd.Rd | 2 |
3 files changed, 32 insertions, 21 deletions
@@ -1,3 +1,9 @@ +commit a071d46f698397a6c8247e19eceb0fcd5f139056 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-10-10 12:25:42 +0200 + + Fix set_nd for metabolites, handle zero at time zero + commit a5503d3e26408f7308a7bf4da617205b93d17422 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2019-10-10 09:21:46 +0200 @@ -17,7 +17,7 @@ #' @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 or zero values at time zero? +#' @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) Generic Guidance for Estimating Persistence and Degradation #' Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, @@ -51,12 +51,12 @@ set_nd <- function(r, lod, loq = NA, nq = 0.5 * (lod + loq) result[r == "nq"] <- nq } else { - if (any(r == "nq")) stop("You need to specify lod and loq") + if (any(r == "nq", na.rm = TRUE)) stop("You need to specify lod and loq") } # Handle nd values if (time_zero) { - if (r[1] %in% c("nd", 0)) { + if (r[1] %in% c("nd")) { residues_present = FALSE result[1] <- time_zero_nd_value } else { @@ -73,32 +73,37 @@ set_nd <- function(r, lod, loq = NA, # residues_in_next if (i < length(r)) { next_value <- r[i + 1] - if (next_value == "nd") residues_in_next = FALSE + if (is.na(next_value) || 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 (is.na(r[i])) { + residues_present <- FALSE + result[i] <- NA + } else { + 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 (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 + } else { + residues_present <- TRUE } - if (!residues_in_next) residues_present <- FALSE - else residues_present <- TRUE - } else { - residues_present <- TRUE } } return(as.numeric(result)) diff --git a/man/set_nd.Rd b/man/set_nd.Rd index 085b606..cef2705 100644 --- a/man/set_nd.Rd +++ b/man/set_nd.Rd @@ -22,7 +22,7 @@ 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 or zero values at time zero?} +\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?} } |