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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-08 09:31:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-08 09:31:35 +0200
commitbc3825ae2d12c18ea3d3caf17eb23c93fef180b8 (patch)
tree112e70a29db2fb35dd624af20f4d400c579b0283 /R
parentc7635af214729d2dc15dd8fbee2ebe6bc64493a4 (diff)
Fix issues for release
Diffstat (limited to 'R')
-rw-r--r--R/nafta.R24
1 files changed, 12 insertions, 12 deletions
diff --git a/R/nafta.R b/R/nafta.R
index 7e5873d8..8a6a519a 100644
--- a/R/nafta.R
+++ b/R/nafta.R
@@ -1,9 +1,9 @@
#' Evaluate parent kinetics using the NAFTA guidance
-#'
+#'
#' The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}}
#' and returns an object of class \code{nafta} that has methods for printing
#' and plotting.
-#'
+#'
#' @param ds A dataframe that must contain one variable called "time" with the
#' time values specified by the \code{time} argument, one column called
#' "name" with the grouping of the observed values, and finally one column of
@@ -23,17 +23,17 @@
#' Pesticides
#' \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation}
#' accessed 2019-02-22
-#'
+#'
#' US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
#' Calculate Representative Half-life Values and Characterizing Pesticide
#' Degradation
#' \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance}
#' @examples
-#'
+#'
#' nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#' print(nafta_evaluation)
#' plot(nafta_evaluation)
-#'
+#'
#' @export
nafta <- function(ds, title = NA, quiet = FALSE, ...) {
if (length(levels(ds$name)) > 1) {
@@ -51,7 +51,7 @@ nafta <- function(ds, title = NA, quiet = FALSE, ...) {
dimnames = list(models, c("DT50", "DT90", "DT50_rep")))
result$distimes["SFO", ] <- distimes[[1]][c(1, 2, 1)]
result$distimes["IORE", ] <- distimes[[2]][c(1, 2, 3)]
- result$distimes["DFOP", ] <- distimes[[3]][c(1, 2, 4)]
+ result$distimes["DFOP", ] <- distimes[[3]][c(1, 2, 5)]
# Get parameters with statistics
result$parameters <- lapply(result$mmkin, function(x) {
@@ -75,13 +75,13 @@ nafta <- function(ds, title = NA, quiet = FALSE, ...) {
return(result)
}
-#' Plot the results of the three models used in the NAFTA scheme.
-#'
+#' Plot the results of the three models used in the NAFTA scheme.
+#'
#' The plots are ordered with increasing complexity of the model in this
#' function (SFO, then IORE, then DFOP).
-#'
+#'
#' Calls \code{\link{plot.mmkin}}.
-#'
+#'
#' @param x An object of class \code{\link{nafta}}.
#' @param legend Should a legend be added?
#' @param main Possibility to override the main title of the plot.
@@ -98,10 +98,10 @@ plot.nafta <- function(x, legend = FALSE, main = "auto", ...) {
}
#' Print nafta objects
-#'
+#'
#' Print nafta objects. The results for the three models are printed in the
#' order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.
-#'
+#'
#' @param x An \code{\link{nafta}} object.
#' @param digits Number of digits to be used for printing parameters and
#' dissipation times.

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