diff options
| -rw-r--r-- | ChangeLog | 12 | ||||
| -rw-r--r-- | R/set_nd.R | 10 | ||||
| -rw-r--r-- | docs/reference/set_nd.html | 4 | ||||
| -rw-r--r-- | man/set_nd.Rd | 4 | ||||
| -rw-r--r-- | tests/testthat/test_set_nd.R | 2 |
5 files changed, 23 insertions, 9 deletions
@@ -1,3 +1,15 @@ +commit a5503d3e26408f7308a7bf4da617205b93d17422 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-10-10 09:21:46 +0200 + + Fix documentation for set_nd + +commit a5e458ecb33ae87e46b2237174a194f6252a97cf +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-10-10 08:53:30 +0200 + + Finish documentation of set_nd and test it + commit 63df3871a442de4bf47e4d9de1449e7f6ed65b2f Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2019-10-09 19:17:07 +0200 @@ -17,10 +17,10 @@ #' @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 time_zero_nd_value Which value should we use for non-detects or zero values 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, +#' Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, #' 18 December 2014, p. 251 #' @describeIn set_nd Set non-detects in residues series #' @export @@ -56,7 +56,7 @@ set_nd <- function(r, lod, loq = NA, # Handle nd values if (time_zero) { - if (r[1] == "nd") { + if (r[1] %in% c("nd", 0)) { residues_present = FALSE result[1] <- time_zero_nd_value } else { @@ -94,12 +94,12 @@ set_nd <- function(r, lod, loq = NA, return(as.numeric(result)) } } - } if (!residues_in_next) residues_present <- FALSE else residues_present <- TRUE + } else { + residues_present <- TRUE } - } return(as.numeric(result)) } diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html index 75a8fb1..7b0e779 100644 --- a/docs/reference/set_nd.html +++ b/docs/reference/set_nd.html @@ -154,7 +154,7 @@ stop after the first non-detection is to be applied</p></td> </tr> <tr> <th>time_zero_nd_value</th> - <td><p>Which value should we use for non-detects at time zero?</p></td> + <td><p>Which value should we use for non-detects or zero values at time zero?</p></td> </tr> <tr> <th>stop_after_first_nondetect</th> @@ -173,7 +173,7 @@ stop after the first non-detection is to be applied</p></td> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> diff --git a/man/set_nd.Rd b/man/set_nd.Rd index bdbc6d2..085b606 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 at time zero?} +\item{time_zero_nd_value}{Which value should we use for non-detects or zero values at time zero?} \item{stop_after_first_nondetect}{Should we really stop after the first non-detection?} } @@ -59,6 +59,6 @@ set_nd(metabolite, 0.02) } \references{ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251 } diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R index 29087a8..6b73e2d 100644 --- a/tests/testthat/test_set_nd.R +++ b/tests/testthat/test_set_nd.R @@ -17,6 +17,8 @@ test_that("Simple residue series processed as intended", { expect_equal(set_nd(metabolite, 0.02, loq = 0.05), c(NA, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA)) + expect_equal(set_nd(c("nd", 1, 0.2, "nd"), 0.1), c(NA, 1, 0.2, 0.05)) + }) test_that("Simple residue series are processed as in the FOCUS guidance", { |