aboutsummaryrefslogtreecommitdiff
path: root/R
diff options
context:
space:
mode:
Diffstat (limited to 'R')
-rw-r--r--R/dimethenamid_2018.R21
-rw-r--r--R/f_time_norm_focus.R24
-rw-r--r--R/mkinds.R3
3 files changed, 40 insertions, 8 deletions
diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R
new file mode 100644
index 00000000..189da618
--- /dev/null
+++ b/R/dimethenamid_2018.R
@@ -0,0 +1,21 @@
+#' Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018
+#'
+#' The datasets were extracted from the active substance evaluation dossier
+#' published by EFSA. Kinetic evaluations shown for these datasets are intended
+#' to illustrate and advance kinetic modelling. The fact that these data and
+#' some results are shown here does not imply a license to use them in the
+#' context of pesticide registrations, as the use of the data may be
+#' constrained by data protection regulations.
+#'
+#' The R code used to create this data object is installed with this package
+#' in the 'dataset_generation' directory. In the code, page numbers are given for
+#' specific pieces of information in the comments.
+#'
+#' @format An [mkindsg] object grouping eight datasets with some meta information
+#' @source Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
+#' Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
+#' Rev. 2 - November 2017
+#' \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211}
+#' @examples
+#' print(dimethenamid_2018)
+"dimethenamid_2018"
diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R
index 66df527e..e7c6f22e 100644
--- a/R/f_time_norm_focus.R
+++ b/R/f_time_norm_focus.R
@@ -11,7 +11,9 @@ utils::globalVariables("D24_2014")
#' @param field_moisture Numeric vector of moisture contents at field capacity
#' (pF2) in \\% w/w
#' @param study_moisture_ref_source Source for the reference value
-#' used to calculate the study moisture
+#' used to calculate the study moisture. If 'auto', preference is given
+#' to a reference moisture given in the meta information, otherwise
+#' the focus soil moisture for the soil class is used
#' @param Q10 The Q10 value used for temperature normalisation
#' @param walker The Walker exponent used for moisture normalisation
#' @param f_na The factor to use for NA values. If set to NA, only factors
@@ -65,7 +67,7 @@ f_time_norm_focus.numeric <- function(object,
#' @rdname f_time_norm_focus
#' @export
f_time_norm_focus.mkindsg <- function(object,
- study_moisture_ref_source = c("meta", "focus"),
+ study_moisture_ref_source = c("auto", "meta", "focus"),
Q10 = 2.58, walker = 0.7, f_na = NA, ...) {
study_moisture_ref_source <- match.arg(study_moisture_ref_source)
@@ -79,11 +81,19 @@ f_time_norm_focus.mkindsg <- function(object,
meta$field_moisture)
}
- if (study_moisture_ref_source == "meta") {
- study_moisture_ref <- meta$study_moisture_ref
+ study_moisture_ref_focus <-
+ focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])]
+
+ if (study_moisture_ref_source == "auto") {
+ study_moisture_ref <- ifelse (is.na(meta$study_ref_moisture),
+ study_moisture_ref_focus,
+ meta$study_ref_moisture)
} else {
- study_moisture_ref <-
- focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])]
+ if (study_moisture_ref_source == "meta") {
+ study_moisture_ref <- meta$study_moisture_ref
+ } else {
+ study_moisture_ref <- study_moisture_ref_focus
+ }
}
if ("study_moisture" %in% names(meta)) {
@@ -99,5 +109,5 @@ f_time_norm_focus.mkindsg <- function(object,
Q10 = Q10, walker = walker, f_na = f_na)
cat("$time_norm was set to\n")
print(object$f_time_norm)
- return(object$f_time_norm)
+ invisible(object$f_time_norm)
}
diff --git a/R/mkinds.R b/R/mkinds.R
index 0e970694..df66ab0f 100644
--- a/R/mkinds.R
+++ b/R/mkinds.R
@@ -140,6 +140,7 @@ mkindsg <- R6Class("mkindsg",
self$f_time_norm <- f_time_norm
if (!missing(meta)) {
+ rownames(meta) <- lapply(ds, function(x) x$title)
self$meta <- meta
}
}
@@ -157,7 +158,7 @@ mkindsg <- R6Class("mkindsg",
print.mkindsg <- function(x, data = FALSE, verbose = data, ...) {
cat("<mkindsg> holding", length(x$ds), "mkinds objects\n")
cat("Title $title: ", x$title, "\n")
- cat("Occurrene of observed compounds $observed_n:\n")
+ cat("Occurrence of observed compounds $observed_n:\n")
print(x$observed_n)
if (any(x$f_time_norm != 1)) {
cat("Time normalisation factors $f_time_norm:\n")

Contact - Imprint