3 files changed, 137 insertions, 0 deletions
diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd
new file mode 100644
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+++ b/pkg/man/TOXSWA_cwa.Rd
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+% Generated by roxygen2 (4.1.0): 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 cwa concentration data and associated statistics}
+\format{An \code{\link{R6Class}} generator object.}
+\usage{
+TOXSWA_cwa
+}
+\description{
+An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}.
+}
+\section{Fields}{
+
+\describe{
+\item{\code{filename}}{Length one character vector.}
+
+\item{\code{basedir}}{Length one character vector.}
+
+\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.}
+
+\item{\code{cwas}}{Dataframe holding the concentrations.}
+
+\item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
+
+\item{\code{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",
+                                 system.file("testdata/SwashProjects/project_H_sw/TOXSWA",
+                                             package = "pfm"))
+H_sw_R1_stream$get_events(c(2, 10))
+}
+\keyword{data}
+
diff --git a/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd
new file mode 100644
index 0000000..7f841b7
--- /dev/null
+++ b/pkg/man/plot.TOXSWA_cwa.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/TOXSWA_cwa.R
+\name{plot.TOXSWA_cwa}
+\alias{plot.TOXSWA_cwa}
+\title{Plot TOXSWA surface water concentrations}
+\usage{
+\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan"),
+  xlab = "default", ylab = "default", add = FALSE, total = FALSE,
+  LC_TIME = "C", ...)
+}
+\arguments{
+\item{x}{The TOXSWA_cwa object to be plotted.}
+
+\item{time_column}{What should be used for the time axis. If "t_firstjan" is chosen,
+the time is given in days relative to the first of January in the first year.}
+
+\item{xlab,ylab}{Labels for x and y axis.}
+
+\item{add}{Should we add to an existing plot?}
+
+\item{total}{Should the total concentration in water be plotted, including substance sorbed
+to suspended matter?}
+
+\item{LC_TIME}{Specification of the locale used to format dates}
+
+\item{...}{Further arguments passed to \code{plot} if we are not adding to an existing plot}
+}
+\description{
+Plot TOXSWA hourly concentrations of a chemical substance in a specific
+segment of a segment of a TOXSWA surface water body.
+}
+\examples{
+H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 system.file("testdata/SwashProjects/project_H_sw/TOXSWA",
+                                             package = "pfm"))
+plot(H_sw_D4_pond)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd
new file mode 100644
index 0000000..bb00dcd
--- /dev/null
+++ b/pkg/man/read.TOXSWA_cwa.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/TOXSWA_cwa.R
+\name{read.TOXSWA_cwa}
+\alias{read.TOXSWA_cwa}
+\title{Read TOXSWA surface water concentrations}
+\usage{
+read.TOXSWA_cwa(filename, basedir = ".", segment = "last", windows = c(7,
+  21), thresholds = NULL)
+}
+\arguments{
+\item{filename}{The filename of the cwa file.}
+
+\item{basedir}{The full path to the directory where the cwa file resides.}
+
+\item{segment}{The segment for which the data should be read. Either "last", or
+the segment number.}
+
+\item{windows}{Numeric vector of width of moving windows for calculating
+time weighted average concentrations and areas under the curve.}
+
+\item{thresholds}{Numeric vector of threshold concentrations in µg/L for
+generating event statistics.}
+}
+\value{
+An instance of an R6 object of class
+\code{\link{TOXSWA_cwa}}.
+}
+\description{
+Read TOXSWA hourly concentrations of a chemical substance in a specific
+segment of a TOXSWA surface water body. Per default, the data for the last
+segment are imported.
+}
+\examples{
+H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 system.file("testdata/SwashProjects/project_H_sw/TOXSWA",
+                                             package = "pfm"))
+}
+\author{
+Johannes Ranke
+}
+