Update docs, use R6 support of roxygen

4 files changed, 37 insertions, 28 deletions

diff --git a/R/GUS.R b/R/GUS.R
index 040857a..32f371c 100644
--- a/R/GUS.R
+++ b/R/GUS.R
@@ -7,7 +7,6 @@
 #' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple
 #' method for assessing pesticide leachability. \emph{Environmental
 #' toxicology and chemistry} \bold{8}(4) 339–57.
-#' @inheritParams endpoint
 #' @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
diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R
index 42cdd35..6521349 100644
--- a/R/TOXSWA_cwa.R
+++ b/R/TOXSWA_cwa.R
@@ -142,35 +142,24 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t
 
 #' R6 class for holding TOXSWA water concentration data and associated statistics
 #'
-#' An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
-#' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}.
+#' @description An R6 class for holding TOXSWA water concentration (cwa) data
+#' and some associated statistics.  like maximum moving window average
+#' concentrations, and dataframes holding the events exceeding specified
+#' thresholds.  Usually, an instance of this class will be generated
+#' by \code{\link{read.TOXSWA_cwa}}.
 #'
-#' @docType class
-#' @importFrom R6 R6Class
 #' @export
 #' @format An \code{\link{R6Class}} generator object.
-#' @field filename Length one character vector.
-#' @field basedir Length one character vector.
+#' @field filename Length one character vector holding the filename.
+#' @field basedir Length one character vector holding the directory where the file came from.
+#' @field zipfile If not null, giving the path to the zip file from which the file was read.
 #' @field segment Length one integer, specifying for which segment the cwa data were read.
+#' @field substance The TOXSWA name of the substance.
 #' @field cwas Dataframe holding the concentrations.
 #' @field events List of dataframes holding the event statistics for each threshold.
 #' @field windows Matrix of maximum time weighted average concentrations (TWAC_max)
 #'   and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
 #'   for the requested moving window sizes in days.
-#' @section Methods:
-#' \describe{
-#'   \item{\code{get_events(threshold, total = FALSE)}}{
-#'         Populate a datataframe with event information for the specified threshold value
-#'         in µg/L. If \code{total = TRUE}, the total concentration including the amount
-#'         adsorbed to suspended matter will be used. The resulting dataframe is stored in the
-#'         \code{events} field of the object.
-#'         }
-#'   \item{\code{moving_windows(windows, total = FALSE)}}{
-#'         Add to the \code{windows} field described above.
-#'         Again, if \code{total = TRUE}, the total concentration including the amount
-#'         adsorbed to suspended matter will be used.
-#'         }
-#' }
 #' @examples
 #' H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
 #'                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
@@ -180,7 +169,6 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t
 #' H_sw_R1_stream$moving_windows(c(7, 21))
 #' print(H_sw_R1_stream)
 #' @keywords data
-
 TOXSWA_cwa <- R6Class("TOXSWA_cwa",
   public = list(
     filename = NULL,
@@ -191,6 +179,15 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
     cwas = NULL,
     windows = NULL,
     events = list(),
+
+    #' @description
+    #' Create a TOXSWA_cwa object from a file
+    #' @param filename The filename
+    #' @param basedir The directory to look in
+    #' @param zipfile Optional path to a zipfile holding the file
+    #' @param segment Either "last" or the number of the segment for which to read the data
+    #' @param substance The TOXSWA substance name (for TOXSWA 4 or higher)
+    #' @param total Should total concentrations be read in? If FALSE, free concentrations are read
     initialize = function(filename, basedir, zipfile = NULL,
                           segment = "last", substance = "parent", total = FALSE) {
       self$filename <- filename
@@ -327,6 +324,12 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
         }
       }
     },
+
+    #' @description
+    #' Add to the `windows` field described above.
+    #' @param windows Window sizes in days
+    #' @param total If TRUE, the total concentration including the amount adsorbed to
+    #' suspended matter will be used.
     moving_windows = function(windows, total = FALSE) {
       window_names = paste(windows, "days")
       n = length(window_names)
@@ -350,6 +353,14 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
       }
       invisible(self)
     },
+
+    #' @description
+    #' Populate a datataframe with event information for the specified
+    #' threshold value.  The resulting dataframe is stored in the `events`
+    #' field of the object.
+    #' @param thresholds Threshold values in µg/L.
+    #' @param total If TRUE, the total concentration including the amount adsorbed to
+    #' suspended matter will be used.
     get_events = function(thresholds, total = FALSE) {
       if (missing(thresholds)) {
         stop("You need to specify at least one threshold concentration in \u03bcg/L")
@@ -397,6 +408,9 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa",
       }
       invisible(self)
     },
+
+    #' @description
+    #' Print a `TOXSWA_cwa` object
     print = function() {
       cat("<TOXSWA_cwa> data from file", self$filename, "segment", self$segment, "\n")
       print(head(self$cwas))
diff --git a/R/drift_data_JKI.R b/R/drift_data_JKI.R
index e44079d..3b02f43 100644
--- a/R/drift_data_JKI.R
+++ b/R/drift_data_JKI.R
@@ -30,7 +30,7 @@
 #' from
 #' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html
 #' on 2015-06-11
-#' 
+#'
 #' Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in
 #' the authorization procedure for plant protection products Mitt. Biol.
 #' Bundesanst. Land- Forstwirtsch. 383, 133-141
@@ -82,6 +82,6 @@
 #'   save(drift_data_JKI, file = "data/drift_data_JKI.RData")
 #' }
 #'
-#' # And this is the resulting data
+#' # And these are the resulting data
 #' drift_data_JKI
 NULL
diff --git a/R/endpoint.R b/R/endpoint.R
index 56a314b..08856f9 100644
--- a/R/endpoint.R
+++ b/R/endpoint.R
@@ -55,7 +55,6 @@ endpoint <- function(chent,
   else return(signif(aggregator(as.numeric(values)), signif))
 }
 
-#' @inheritParams endpoint
 #' @rdname endpoint
 #' @export
 soil_DT50 <- function(chent, aggregator = geomean, signif = 3, 
@@ -68,7 +67,6 @@ soil_DT50 <- function(chent, aggregator = geomean, signif = 3,
   return(ep)
 }
 
-#' @inheritParams endpoint
 #' @rdname endpoint
 #' @export
 soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, 
@@ -79,7 +77,6 @@ soil_Kfoc <- function(chent, aggregator = geomean, signif = 3,
   return(ep)
 }
 
-#' @inheritParams endpoint
 #' @rdname endpoint
 #' @export
 soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) {
@@ -89,7 +86,6 @@ soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) {
   return(ep)
 }
 
-#' @inheritParams endpoint
 #' @rdname endpoint
 #' @param values The values to be returned
 #' @param aggregators A named vector of aggregator functions to be used