From 9851a97ec915ddbfc8357f1a7e2cabae56c89f7d Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 18 Dec 2015 14:45:24 +0100
Subject: Documentation fixes, chents is currently a hard dependency

---
 pkg/R/GUS.R | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

(limited to 'pkg/R/GUS.R')

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")
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