Documentation fixes, chents is currently a hard dependency

9 files changed, 66 insertions, 26 deletions

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index fb9171f..d092444 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.2-4
-Date: 2015-10-15
+Date: 2015-12-18
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", 
                   role = c("aut", "cre", "cph"))
 Description: Utilities for simple calculations of predicted environmental
@@ -12,12 +12,12 @@ Depends:
     R6,
     mkin
 Imports:
-    graphics
-Suggests:
-    testthat,
+    graphics,
     chents
+Suggests:
+    testthat
 License: GPL
 LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
-RoxygenNote: 4.1.1.9001
+RoxygenNote: 5.0.1
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
diff --git a/pkg/man/GUS.Rd b/pkg/man/GUS.Rd
index 5e2c936..33c7364 100644
--- a/pkg/man/GUS.Rd
+++ b/pkg/man/GUS.Rd
@@ -4,18 +4,23 @@
 \alias{GUS}
 \alias{GUS.chent}
 \alias{GUS.numeric}
+\alias{print.GUS_result}
 \title{Groundwater ubiquity score based on Gustafson (1989)}
 \usage{
 GUS(...)
 
-\method{GUS}{numeric}(DT50, Koc)
+\method{GUS}{numeric}(DT50, Koc, ...)
 
-\method{GUS}{chent}(chent, lab_field = "laboratory", aerobic = TRUE,
-  degradation_value = "DT50ref", sorption_value = "Kfoc",
-  degradation_aggregator = geomean, sorption_aggregator = geomean,
-  digits = 1)
+\method{GUS}{chent}(chent, degradation_value = "DT50ref",
+  lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc",
+  degradation_aggregator = geomean, sorption_aggregator = geomean, ...)
+
+\method{print}{GUS_result}(x, ..., digits = 1)
 }
 \arguments{
+\item{...}{Included in the generic to allow for further arguments later. Therefore
+this also had to be added to the specific methods.}
+
 \item{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
@@ -31,14 +36,16 @@ unclear at which reference concentration the Koc should be observed
 \item{chent}{If a chent is given with appropriate information present in its
 chyaml field, this information is used, with defaults specified below.}
 
+\item{degradation_value}{Which of the available degradation values should 
+be used?}
+
 \item{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.}
 
-\item{degradation_value}{Which of the available degradation values should 
-be used?}
+\item{redox}{Aerobic or anaerobic degradation data}
 
 \item{sorption_value}{Which of the available sorption values should be used?
 Defaults to Kfoc as this is what is generally available from the European
@@ -49,6 +56,10 @@ be Koc values at a concentration of 1 mg/L in the water phase.}
 \item{degradation_aggregator}{Function for aggregating half-lives}
 
 \item{sorption_aggregator}{Function for aggregation Koc values}
+
+\item{x}{An object of class GUS_result to be printed}
+
+\item{digits}{The number of digits used in the print method}
 }
 \value{
 A list with the DT50 and Koc used as well as the resulting score
@@ -64,7 +75,7 @@ Johannes Ranke
 }
 \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.
 }
 
diff --git a/pkg/man/endpoint.Rd b/pkg/man/endpoint.Rd
index 6c93022..0ca53b1 100644
--- a/pkg/man/endpoint.Rd
+++ b/pkg/man/endpoint.Rd
@@ -26,6 +26,10 @@ usage section is not exclusive}
 \item{aggregator}{The aggregator function. Can be mean, 
 \code{\link{geomean}}, or identity, for example.}
 
+\item{raw}{Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?}
+
 \item{signif}{How many significant digits do we want}
 }
 \value{
@@ -34,7 +38,6 @@ The result from applying the aggregator function to
   given number of significant digits, or, if raw = TRUE,
   the values as a character value, retaining any implicit
   information on precision that may be present.
-
 }
 \description{
 R6 class objects of class \code{\link{chent}} represent chemical entities
diff --git a/pkg/man/soil_DT50.Rd b/pkg/man/soil_DT50.Rd
index cbec234..89d2883 100644
--- a/pkg/man/soil_DT50.Rd
+++ b/pkg/man/soil_DT50.Rd
@@ -22,6 +22,10 @@ soil_DT50(chent, aggregator = geomean, signif = 3,
 usage section is not exclusive}
 
 \item{redox}{If not NA, are we looking for aerobic or anaerobic data}
+
+\item{raw}{Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?}
 }
 \description{
 Obtain soil DT50
diff --git a/pkg/man/soil_Kfoc.Rd b/pkg/man/soil_Kfoc.Rd
index 3cc67cd..b8c0727 100644
--- a/pkg/man/soil_Kfoc.Rd
+++ b/pkg/man/soil_Kfoc.Rd
@@ -17,6 +17,10 @@ soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc",
 
 \item{value}{The name of the value we want. The list given in the 
 usage section is not exclusive}
+
+\item{raw}{Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?}
 }
 \description{
 Obtain soil Kfoc
diff --git a/pkg/man/soil_N.Rd b/pkg/man/soil_N.Rd
index 9045ea8..9564f82 100644
--- a/pkg/man/soil_N.Rd
+++ b/pkg/man/soil_N.Rd
@@ -13,6 +13,10 @@ soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
 \code{\link{geomean}}, or identity, for example.}
 
 \item{signif}{How many significant digits do we want}
+
+\item{raw}{Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?}
 }
 \description{
 In pesticide fate modelling, this exponent is often called 1/n. Here, in 
diff --git a/pkg/man/soil_sorption.Rd b/pkg/man/soil_sorption.Rd
index 41b8794..5b8bd53 100644
--- a/pkg/man/soil_sorption.Rd
+++ b/pkg/man/soil_sorption.Rd
@@ -16,6 +16,10 @@ soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc =
 \item{aggregators}{A named vector of aggregator functions to be used}
 
 \item{signif}{How many significant digits do we want}
+
+\item{raw}{Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?}
 }
 \description{
 Obtain soil sorption data