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-rw-r--r--pkg/R/GUS.R29
-rw-r--r--pkg/R/endpoint.R3
2 files changed, 21 insertions, 11 deletions
diff --git a/pkg/R/GUS.R b/pkg/R/GUS.R
index 2690f50..8a20561 100644
--- a/pkg/R/GUS.R
+++ b/pkg/R/GUS.R
@@ -5,11 +5,9 @@
#' \deqn{GUS = \log_10 DT50_{soil} (4 - \log_10 K_{oc}}{GUS = log10 DT50soil * (4 - log10 Koc)}
#'
#' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple
-#' method for assessing pesticide leachability. _Environmental
-#' toxicology and chemistry_ *8*(4) 339–57.
+#' method for assessing pesticide leachability. \emph{Environmental
+#' toxicology and chemistry} \bold{8}(4) 339–57.
#' @inheritParams endpoint
-#' @param chent If a chent is given with appropriate information present in its
-#' chyaml field, this information is used, with defaults specified below.
#' @param DT50 Half-life of the chemical in soil. Should be a field
#' half-life according to Gustafson (1989). However, leaching to the sub-soil
#' can not completely be excluded in field dissipation experiments and Gustafson
@@ -20,13 +18,16 @@
#' found and usually described by Freundlich sorption, therefore it is
#' unclear at which reference concentration the Koc should be observed
#' (and if the reference concentration would be in soil or in porewater).
+#' @param chent If a chent is given with appropriate information present in its
+#' chyaml field, this information is used, with defaults specified below.
+#' @param degradation_value Which of the available degradation values should
+#' be used?
#' @param lab_field Should laboratory or field half-lives be used? This
#' defaults to lab in this implementation, in order to avoid
#' double-accounting for mobility. If comparability with the original GUS
#' values given by Gustafson (1989) is desired, non-normalised first-order
#' field half-lives obtained under actual use conditions should be used.
-#' @param degradation_value Which of the available degradation values should
-#' be used?
+#' @param redox Aerobic or anaerobic degradation data
#' @param sorption_value Which of the available sorption values should be used?
#' Defaults to Kfoc as this is what is generally available from the European
#' pesticide peer review process. These values generally use a reference
@@ -34,6 +35,8 @@
#' be Koc values at a concentration of 1 mg/L in the water phase.
#' @param degradation_aggregator Function for aggregating half-lives
#' @param sorption_aggregator Function for aggregation Koc values
+#' @param ... Included in the generic to allow for further arguments later. Therefore
+#' this also had to be added to the specific methods.
#' @return A list with the DT50 and Koc used as well as the resulting score
#' of class GUS_result
#' @author Johannes Ranke
@@ -42,7 +45,7 @@ GUS <- function(...) UseMethod("GUS")
#' @rdname GUS
#' @export
-GUS.numeric <- function(DT50, Koc) {
+GUS.numeric <- function(DT50, Koc, ...) {
score <- log10(DT50) * (4 - log10(Koc))
res <- list(DT50 = DT50, Koc = Koc, score = score)
class(res) <- "GUS_result"
@@ -51,15 +54,16 @@ GUS.numeric <- function(DT50, Koc) {
#' @rdname GUS
#' @export
-GUS.chent <- function(chent, lab_field = "laboratory",
- aerobic = TRUE,
+GUS.chent <- function(chent,
degradation_value = "DT50ref",
+ lab_field = "laboratory",
+ redox = "aerobic",
sorption_value = "Kfoc",
degradation_aggregator = geomean,
sorption_aggregator = geomean,
- digits = 1)
+ ...)
{
- DT50 = soil_DT50(chent, lab_field = lab_field, redox = aerobic,
+ DT50 = soil_DT50(chent, lab_field = lab_field, redox = redox,
value = degradation_value,
aggregator = degradation_aggregator, signif = 5)
Koc = soil_Kfoc(chent, value = sorption_value,
@@ -67,7 +71,10 @@ GUS.chent <- function(chent, lab_field = "laboratory",
GUS.numeric(DT50, Koc)
}
+#' @rdname GUS
#' @export
+#' @param x An object of class GUS_result to be printed
+#' @param digits The number of digits used in the print method
print.GUS_result = function(x, ..., digits = 1) {
cat("GUS: ", round(x$score, digits = 1), "\n")
cat("calculated from DT50 ", x$DT50, " and Koc ", x$Koc, "\n")
diff --git a/pkg/R/endpoint.R b/pkg/R/endpoint.R
index f9b9102..6cc253a 100644
--- a/pkg/R/endpoint.R
+++ b/pkg/R/endpoint.R
@@ -16,6 +16,9 @@
#' usage section is not exclusive
#' @param aggregator The aggregator function. Can be mean,
#' \code{\link{geomean}}, or identity, for example.
+#' @param raw Should the number(s) be returned as stored in the chent
+#' object (could be a character value) to retain original information
+#' about precision?
#' @param signif How many significant digits do we want
#' @return The result from applying the aggregator function to
#' the values converted to a numeric vector, rounded to the

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