Update docs with roxygen 8

7 files changed, 100 insertions, 102 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 1e81c59..a266b0c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,4 +26,4 @@ LazyData: true
 Encoding: UTF-8
 URL: https://pkgdown.jrwb.de/pfm, https://github.com/jranke/pfm, http://jranke.github.io/pfm/
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.3.3
+Config/roxygen2/version: 8.0.0
diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd
index 302aa75..0cf01b6 100644
--- a/man/FOCUS_GW_scenarios_2012.Rd
+++ b/man/FOCUS_GW_scenarios_2012.Rd
@@ -1,12 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/FOCUS_GW_scenarios_2012.R
-\docType{data}
 \name{FOCUS_GW_scenarios_2012}
 \alias{FOCUS_GW_scenarios_2012}
 \title{A very small subset of the FOCUS Groundwater scenario definitions}
-\format{
-An object of class \code{list} of length 2.
-}
 \usage{
 FOCUS_GW_scenarios_2012
 }
@@ -22,4 +18,3 @@ FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version
 FOrum for the Co-ordination of pesticde fate models and their USe.
 http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf
 }
-\keyword{datasets}
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index ed4c3f3..bb77eec 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -123,7 +123,7 @@ guidance (2017, p. 14/15) can easily be calculated.
 }
 \note{
 While time weighted average (TWA) concentrations given in the examples
-from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not
+from the EFSA guidance from 2015 (p. 80) can be reproduced, this is not
 true for the TWA concentrations given for the same example in the EFSA guidance
 from 2017 (p. 92).
 
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index 126fed4..8cd9941 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -24,139 +24,142 @@ 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 holding the filename.}
+  \if{html}{\out{<div class="r6-fields">}}
+  \describe{
+    \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 holding the directory where the file came from.}
 
-\item{\code{zipfile}}{If not null, giving the path to the zip file from which the file was read.}
+    \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{segment}}{Length one integer, specifying for which segment the cwa data were read.}
 
-\item{\code{substance}}{The TOXSWA name of the substance.}
+    \item{\code{substance}}{The TOXSWA name of the substance.}
 
-\item{\code{cwas}}{Dataframe holding the concentrations.}
+    \item{\code{cwas}}{Dataframe holding the concentrations.}
 
-\item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
+    \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)
+    \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>}}
+  }
+  \if{html}{\out{</div>}}
 }
 \section{Methods}{
 \subsection{Public methods}{
-\itemize{
-\item \href{#method-TOXSWA_cwa-new}{\code{TOXSWA_cwa$new()}}
-\item \href{#method-TOXSWA_cwa-moving_windows}{\code{TOXSWA_cwa$moving_windows()}}
-\item \href{#method-TOXSWA_cwa-get_events}{\code{TOXSWA_cwa$get_events()}}
-\item \href{#method-TOXSWA_cwa-print}{\code{TOXSWA_cwa$print()}}
-\item \href{#method-TOXSWA_cwa-clone}{\code{TOXSWA_cwa$clone()}}
-}
+  \itemize{
+    \item \href{#method-TOXSWA_cwa-initialize}{\code{TOXSWA_cwa$new()}}
+    \item \href{#method-TOXSWA_cwa-moving_windows}{\code{TOXSWA_cwa$moving_windows()}}
+    \item \href{#method-TOXSWA_cwa-get_events}{\code{TOXSWA_cwa$get_events()}}
+    \item \href{#method-TOXSWA_cwa-print}{\code{TOXSWA_cwa$print()}}
+    \item \href{#method-TOXSWA_cwa-clone}{\code{TOXSWA_cwa$clone()}}
+  }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-TOXSWA_cwa-new"></a>}}
-\if{latex}{\out{\hypertarget{method-TOXSWA_cwa-new}{}}}
-\subsection{Method \code{new()}}{
-Create a TOXSWA_cwa object from a file
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new(
+\if{html}{\out{<a id="method-TOXSWA_cwa-initialize"></a>}}
+\if{latex}{\out{\hypertarget{method-TOXSWA_cwa-initialize}{}}}
+\subsection{\code{TOXSWA_cwa$new()}}{
+  Create a TOXSWA_cwa object from a file
+  \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{</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>}}
+  }
 }
 
-\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-TOXSWA_cwa-moving_windows"></a>}}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-moving_windows}{}}}
-\subsection{Method \code{moving_windows()}}{
-Add to the \code{windows} field described above.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{windows}}{Window sizes in days}
-
-\item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to
+\subsection{\code{TOXSWA_cwa$moving_windows()}}{
+  Add to the \code{windows} field described above.
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{windows}}{Window sizes in days}
+      \item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to
 suspended matter will be used.}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
-\if{html}{\out{</div>}}
-}
-}
+
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-TOXSWA_cwa-get_events"></a>}}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-get_events}{}}}
-\subsection{Method \code{get_events()}}{
-Populate a datataframe with event information for the specified
+\subsection{\code{TOXSWA_cwa$get_events()}}{
+  Populate a datataframe with event information for the specified
 threshold value.  The resulting dataframe is stored in the \code{events}
 field of the object.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{thresholds}}{Threshold values in µg/L.}
-
-\item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{TOXSWA_cwa$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{</div>}}
-}
-}
+
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-TOXSWA_cwa-print"></a>}}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-print}{}}}
-\subsection{Method \code{print()}}{
-Print a \code{TOXSWA_cwa} object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}}
+\subsection{\code{TOXSWA_cwa$print()}}{
+  Print a \code{TOXSWA_cwa} object
+  \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-TOXSWA_cwa-clone"></a>}}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-clone}{}}}
-\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$clone(deep = FALSE)}\if{html}{\out{</div>}}
+\subsection{\code{TOXSWA_cwa$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>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{deep}}{Whether to make a deep clone.}
-}
-\if{html}{\out{</div>}}
-}
-}
 }
diff --git a/man/max_twa.Rd b/man/max_twa.Rd
index 2bba22f..2b0b136 100644
--- a/man/max_twa.Rd
+++ b/man/max_twa.Rd
@@ -19,7 +19,7 @@ for finding the maximum. It is therefore recommended to check this using
 \code{max_twa}.
 }
 \details{
-The method working directly on fitted \link[mkin:mkinfit]{mkin::mkinfit} objects uses the
+The method working directly on fitted \link[mkin:mkinfit]{mkinfit} objects uses the
 equations given in the PEC soil section of the FOCUS guidance and is restricted
 SFO, FOMC and DFOP models and to the parent compound
 }
diff --git a/man/one_box.Rd b/man/one_box.Rd
index 83a9fe0..16f4859 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -19,10 +19,10 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 \item{x}{When numeric, this is the half-life to be used for an exponential
 decline. When a character string specifying a parent decline model is given
 e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters.
-If x is an \link[mkin:mkinfit]{mkin::mkinfit} object, the decline is calculated from this
+If x is an \link[mkin:mkinfit]{mkinfit} object, the decline is calculated from this
 object.}
 
-\item{ini}{The initial amount. If x is an \link[mkin:mkinfit]{mkin::mkinfit} object, and
+\item{ini}{The initial amount. If x is an \link[mkin:mkinfit]{mkinfit} object, and
 ini is 'model', the fitted initial concentrations are used. Otherwise, ini
 must be numeric. If it has length one, it is used for the parent and
 initial values of metabolites are zero, otherwise, it must give values for
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 4ae7190..a5d8677 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -12,6 +12,6 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{mkin}{\code{\link[mkin]{set_nd_nq}}, \code{\link[mkin:set_nd_nq]{set_nd_nq_focus}}}
+  \item{mkin}{\code{\link[mkin:set_nd_nq]{set_nd_nq()}}, \code{\link[mkin:set_nd_nq_focus]{set_nd_nq_focus()}}}
 }}