Update docs, use R6 support of roxygen

1 files changed, 54 insertions, 22 deletions

diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index 6a95a0b..3daa1d0 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
-\docType{class}
 \name{TOXSWA_cwa}
 \alias{TOXSWA_cwa}
 \title{R6 class for holding TOXSWA water concentration data and associated statistics}
@@ -8,26 +7,12 @@
 An \code{\link{R6Class}} generator object.
 }
 \description{
-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}}.
+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}}.
 }
-\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",
@@ -41,12 +26,16 @@ print(H_sw_R1_stream)
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
 \describe{
-\item{\code{filename}}{Length one character vector.}
+\item{\code{filename}}{Length one character vector holding the filename.}
+
+\item{\code{basedir}}{Length one character vector holding the directory where the file came from.}
 
-\item{\code{basedir}}{Length one character vector.}
+\item{\code{zipfile}}{If not null, giving the path to the zip file from which the file was read.}
 
 \item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.}
 
+\item{\code{substance}}{The TOXSWA name of the substance.}
+
 \item{\code{cwas}}{Dataframe holding the concentrations.}
 
 \item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
@@ -71,6 +60,7 @@ for the requested moving window sizes in days.}
 \if{html}{\out{<a id="method-new"></a>}}
 \if{latex}{\out{\hypertarget{method-new}{}}}
 \subsection{Method \code{new()}}{
+Create a TOXSWA_cwa object from a file
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new(
   filename,
@@ -82,29 +72,71 @@ for the requested moving window sizes in days.}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{filename}}{The filename}
+
+\item{\code{basedir}}{The directory to look in}
+
+\item{\code{zipfile}}{Optional path to a zipfile holding the file}
+
+\item{\code{segment}}{Either "last" or the number of the segment for which to read the data}
+
+\item{\code{substance}}{The TOXSWA substance name (for TOXSWA 4 or higher)}
+
+\item{\code{total}}{Should total concentrations be read in? If FALSE, free concentrations are read}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-moving_windows"></a>}}
 \if{latex}{\out{\hypertarget{method-moving_windows}{}}}
 \subsection{Method \code{moving_windows()}}{
+Add to the `windows` field described above.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{windows}}{Window sizes in days}
+
+\item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to
+suspended matter will be used.}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-get_events"></a>}}
 \if{latex}{\out{\hypertarget{method-get_events}{}}}
 \subsection{Method \code{get_events()}}{
+Populate a datataframe with event information for the specified
+threshold value.  The resulting dataframe is stored in the `events`
+field of the object.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{thresholds}}{Threshold values in µg/L.}
+
+\item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to
+suspended matter will be used.}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-print"></a>}}
 \if{latex}{\out{\hypertarget{method-print}{}}}
 \subsection{Method \code{print()}}{
+Print a `TOXSWA_cwa` object
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}}
 }