From d81550d0cccae824cc748de48e7fd50ea8d8033a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 16 Apr 2020 18:02:18 +0200
Subject: Make na.rm = FALSE the default for geomean()

This makes more sense and is in line with mean() from base R. Adapt
tests and update docs.
---
 man/TOXSWA_cwa.Rd | 106 +++++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 85 insertions(+), 21 deletions(-)

(limited to 'man/TOXSWA_cwa.Rd')

diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index f073180..eb3fe38 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -5,31 +5,10 @@
 \alias{TOXSWA_cwa}
 \title{R6 class for holding TOXSWA water concentration data and associated statistics}
 \format{An \code{\link{R6Class}} generator object.}
-\usage{
-TOXSWA_cwa
-}
 \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}}.
 }
-\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{
@@ -57,3 +36,88 @@ H_sw_R1_stream$moving_windows(c(7, 21))
 print(H_sw_R1_stream)
 }
 \keyword{data}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{filename}}{Length one character vector.}
+
+\item{\code{basedir}}{Length one character vector.}
+
+\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.}
+
+\item{\code{cwas}}{Dataframe holding the concentrations.}
+
+\item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
+
+\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max)
+and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
+for the requested moving window sizes in days.}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{TOXSWA_cwa$new()}}
+\item \href{#method-moving_windows}{\code{TOXSWA_cwa$moving_windows()}}
+\item \href{#method-get_events}{\code{TOXSWA_cwa$get_events()}}
+\item \href{#method-print}{\code{TOXSWA_cwa$print()}}
+\item \href{#method-clone}{\code{TOXSWA_cwa$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new(
+  filename,
+  basedir,
+  zipfile = NULL,
+  segment = "last",
+  substance = "parent",
+  total = FALSE
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-moving_windows"></a>}}
+\subsection{Method \code{moving_windows()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_events"></a>}}
+\subsection{Method \code{get_events()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-print"></a>}}
+\subsection{Method \code{print()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
-- 
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