From 92d97ba99d7b90d95a67796cb5e68f28f752b70b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 17 Dec 2014 21:39:42 +0100 Subject: Initial commit: R6 class for TOXSWA cwa files --- pkg/man/TOXSWA_cwa.Rd | 55 ++++++++++++++++++++++++++++++++++++++++++++++ pkg/man/plot.TOXSWA_cwa.Rd | 41 ++++++++++++++++++++++++++++++++++ pkg/man/read.TOXSWA_cwa.Rd | 41 ++++++++++++++++++++++++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 pkg/man/TOXSWA_cwa.Rd create mode 100644 pkg/man/plot.TOXSWA_cwa.Rd create mode 100644 pkg/man/read.TOXSWA_cwa.Rd (limited to 'pkg/man') diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd new file mode 100644 index 0000000..73491ce --- /dev/null +++ b/pkg/man/TOXSWA_cwa.Rd @@ -0,0 +1,55 @@ +% 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 +} + -- cgit v1.2.1