set_nd_nq is now in mkin, fix Steps12 bug

If a scenario with a slash "/" was selected in PEC_sw_focus(),
the Step 2 file generated giving an error (path not found) in the
Steps12 calculator, because the scenario name is part of the "compound"
name in this implementation, in order to show it in the list that the
calculator presents.

4 files changed, 37 insertions, 123 deletions

diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index 3ad1ad0..f23423b 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -26,7 +26,7 @@ PEC_sw_focus(
 }
 \arguments{
 \item{parent}{A list containing substance specific parameters, e.g.
-conveniently generated by \code{\link{chent_focus_sw}}.}
+conveniently generated by [chent_focus_sw].}
 
 \item{rate}{The application rate in g/ha. Overriden when
 applications are given explicitly}
@@ -38,20 +38,20 @@ applications are given explicitly}
 \item{comment}{A comment for the input file}
 
 \item{met}{A list containing metabolite specific parameters.  e.g.
-conveniently generated by \code{\link{chent_focus_sw}}.  If not NULL,
+conveniently generated by [chent_focus_sw].  If not NULL,
 the PEC is calculated for this compound, not the parent.}
 
 \item{f_drift}{The fraction of the application rate reaching the waterbody
 via drift. If NA, this is derived from the scenario name and the number
 of applications via the drift data defined by the
-\code{\link{FOCUS_Step_12_scenarios}}}
+[FOCUS_Step_12_scenarios]}
 
 \item{f_rd}{The fraction of the amount applied reaching the waterbody via
 runoff/drainage. At Step 1, it is assumed to be 10%, be it the
 parent or a metabolite}
 
 \item{scenario}{The name of the scenario. Must be one of the scenario
-names given in \code{\link{FOCUS_Step_12_scenarios}}}
+names given in [FOCUS_Step_12_scenarios]}
 
 \item{region}{'n' for Northern Europe or 's' for Southern Europe. If NA, only
 Step 1 PECsw are calculated}
@@ -101,7 +101,7 @@ PEC_sw_focus(dummy_1, 3000, f_drift = 0, overwrite = TRUE, append = FALSE)
 
 # Metabolite
 new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100)
-M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, 
+M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50,
   max_ws = 0, max_soil = 0.5)
 PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1)
 }
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index 3daa1d0..de83ec2 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -49,16 +49,16 @@ for the requested moving window sizes in days.}
 \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$clone()}}
+\item \href{#method-TOXSWA_cwa-new}{\code{TOXSWA_cwa$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()}}
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\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}{
@@ -91,8 +91,8 @@ Create a TOXSWA_cwa object from a file
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-moving_windows"></a>}}
-\if{latex}{\out{\hypertarget{method-moving_windows}{}}}
+\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 `windows` field described above.
 \subsection{Usage}{
@@ -111,8 +111,8 @@ suspended matter will be used.}
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get_events"></a>}}
-\if{latex}{\out{\hypertarget{method-get_events}{}}}
+\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
 threshold value.  The resulting dataframe is stored in the `events`
@@ -133,8 +133,8 @@ suspended matter will be used.}
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-print"></a>}}
-\if{latex}{\out{\hypertarget{method-print}{}}}
+\if{html}{\out{<a id="method-TOXSWA_cwa-print"></a>}}
+\if{latex}{\out{\hypertarget{method-TOXSWA_cwa-print}{}}}
 \subsection{Method \code{print()}}{
 Print a `TOXSWA_cwa` object
 \subsection{Usage}{
@@ -143,8 +143,8 @@ Print a `TOXSWA_cwa` object
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
+\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}{
diff --git a/man/reexports.Rd b/man/reexports.Rd
new file mode 100644
index 0000000..4ae7190
--- /dev/null
+++ b/man/reexports.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reexports.R
+\docType{import}
+\name{reexports}
+\alias{reexports}
+\alias{set_nd_nq}
+\alias{set_nd_nq_focus}
+\title{Objects exported from other packages}
+\keyword{internal}
+\description{
+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}}}
+}}
+
diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd
deleted file mode 100644
index 7135d0d..0000000
--- a/man/set_nd_nq.Rd
+++ /dev/null
@@ -1,103 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/set_nd_nq.R
-\name{set_nd_nq}
-\alias{set_nd_nq}
-\alias{set_nd_nq_focus}
-\title{Set non-detects and unquantified values in residue series without replicates}
-\usage{
-set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
-
-set_nd_nq_focus(
-  res_raw,
-  lod,
-  loq = NA,
-  set_first_sample_nd = TRUE,
-  first_sample_nd_value = 0,
-  ignore_below_loq_after_first_nd = TRUE
-)
-}
-\arguments{
-\item{res_raw}{Character vector of a residue time series, or matrix of
-residue values with rows representing depth profiles for a specific sampling
-time, and columns representing time series of residues at the same depth.
-Values below the limit of detection (lod) have to be coded as "nd", values
-between the limit of detection and the limit of quantification, if any, have
-to be coded as "nq". Samples not analysed have to be coded as "na". All
-values that are not "na", "nd" or "nq" have to be coercible to numeric}
-
-\item{lod}{Limit of detection (numeric)}
-
-\item{loq}{Limit of quantification(numeric). Must be specified if the FOCUS rule to
-stop after the first non-detection is to be applied}
-
-\item{time_zero_presence}{Do we assume that residues occur at time zero?
-This only affects samples from the first sampling time that have been
-reported as "nd" (not detected).}
-
-\item{set_first_sample_nd}{Should the first sample be set to "first_sample_nd_value"
-in case it is a non-detection?}
-
-\item{first_sample_nd_value}{Value to be used for the first sample if it is a non-detection}
-
-\item{ignore_below_loq_after_first_nd}{Should we ignore values below the LOQ after the first
-non-detection that occurs after the quantified values?}
-}
-\value{
-A numeric vector, if a vector was supplied, or a numeric matrix otherwise
-}
-\description{
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015).
-}
-\section{Functions}{
-\itemize{
-\item \code{set_nd_nq_focus}: Set non-detects in residue time series according to FOCUS rules
-}}
-
-\examples{
-# FOCUS (2014) p. 75/76 and 131/132
-parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-set_nd_nq(parent_1, 0.02)
-parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-set_nd_nq(parent_2, 0.02)
-set_nd_nq_focus(parent_2, 0.02, loq = 0.05)
-parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-set_nd_nq(parent_3, 0.02)
-set_nd_nq_focus(parent_3, 0.02, loq = 0.05)
-metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
-set_nd_nq(metabolite, 0.02)
-set_nd_nq_focus(metabolite, 0.02, 0.05)
-#
-# Boesten et al. (2015), p. 57/58
-table_8 <- matrix(
-  c(10, 10, rep("nd", 4),
-    10, 10, rep("nq", 2), rep("nd", 2),
-    10, 10, 10, "nq", "nd", "nd",
-    "nq", 10, "nq", rep("nd", 3),
-    "nd", "nq", "nq", rep("nd", 3),
-    rep("nd", 6), rep("nd", 6)),
-  ncol = 6, byrow = TRUE)
-set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
-table_10 <- matrix(
-  c(10, 10, rep("nd", 4),
-    10, 10, rep("nd", 4),
-    10, 10, 10, rep("nd", 3),
-    "nd", 10, rep("nd", 4),
-    rep("nd", 18)),
-  ncol = 6, byrow = TRUE)
-set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
-}
-\references{
-Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
-J. and Pol, J. W. (2015). Leaching of plant protection products and their
-transformation products; Proposals for improving the assessment of leaching
-to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
-Wageningen UR (University & Research centre)
-
-FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
-  18 December 2014, p. 251
-}