Option to thin low TOXSWA PECsw data for plotting

to reduce the file size of plots e.g. as PDF files

3 files changed, 25 insertions, 10 deletions

diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index 7935617..e417094 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -26,7 +26,7 @@ Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_
 \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) 
+and areas under the curve in \u00B5g/day * h (AUC_max_h) or \u00B5g/day * d (AUC_max_d)
 for the requested moving window sizes in days.}
 }}
 
@@ -35,8 +35,8 @@ for the requested moving window sizes in days.}
 \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 
+        in \u00B5g/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)}}{
diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd
index 4e81f91..88e1f37 100644
--- a/man/plot.TOXSWA_cwa.Rd
+++ b/man/plot.TOXSWA_cwa.Rd
@@ -6,7 +6,8 @@
 \usage{
 \method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan",
   "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE,
-  total = FALSE, LC_TIME = "C", ...)
+  threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = "C",
+  ...)
 }
 \arguments{
 \item{x}{The TOXSWA_cwa object to be plotted.}
@@ -18,6 +19,13 @@ the time is given in days relative to the first of January in the first year.}
 
 \item{add}{Should we add to an existing plot?}
 
+\item{threshold_factor}{The factor by which the data have to be lower than the maximum
+in order to get thinned for plotting (see next argument).}
+
+\item{thin_low}{If an integer greater than 1, the data close to zero (smaller than
+1/threshold_factor of the maximum) in the series will be thinned by this factor
+in order to decrease the amount of data that is included in the plots}
+
 \item{total}{Should the total concentration in water be plotted, including substance sorbed
 to suspended matter?}
 
@@ -31,10 +39,17 @@ segment of a TOXSWA surface water body.
 }
 \examples{
 H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                             package = "pfm"))
+  basedir = "SwashProjects/project_H_sw/TOXSWA",
+  zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
 plot(H_sw_D4_pond)
+plot(H_sw_D4_pond, time_column = "t")
+plot(H_sw_D4_pond, time_column = "t_firstjan")
+plot(H_sw_D4_pond, time_column = "t_rel_to_max")
+
+H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+  basedir = "SwashProjects/project_H_sw/TOXSWA",
+  zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
+plot(H_sw_R1_stream, time_column = "t_rel_to_max")
 }
 \author{
 Johannes Ranke
diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd
index f1d5908..28479f2 100644
--- a/man/read.TOXSWA_cwa.Rd
+++ b/man/read.TOXSWA_cwa.Rd
@@ -16,21 +16,21 @@ out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).}
 
 \item{zipfile}{Optional path to a zip file containing the cwa file.}
 
-\item{segment}{The segment for which the data should be read. Either "last", or 
+\item{segment}{The segment for which the data should be read. Either "last", or
 the segment number.}
 
 \item{substance}{For TOXSWA 4 .out files, the default value "parent" leads
 to reading concentrations of the parent compound. Alternatively, the substance
 of interested can be selected by its code name.}
 
-\item{total}{Set this to TRUE in order to read total concentrations as well. This is 
+\item{total}{Set this to TRUE in order to read total concentrations as well. This is
 only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
 files. For .cwa files, the total concentration is always read as well.}
 
 \item{windows}{Numeric vector of width of moving windows in days, for calculating
 maximum time weighted average concentrations and areas under the curve.}
 
-\item{thresholds}{Numeric vector of threshold concentrations in µg/L for
+\item{thresholds}{Numeric vector of threshold concentrations in \u00B5g/L for
 generating event statistics.}
 }
 \value{