Single line of generated Step12 input file partially validated

2 files changed, 35 insertions, 12 deletions

diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index a5628d7..e9f638d 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -2,11 +2,13 @@
 % Please edit documentation in R/PEC_sw_focus.R
 \name{PEC_sw_focus}
 \alias{PEC_sw_focus}
-\title{Calculate FOCUS Step 1 PEC surface water}
+\title{Calculate PEC surface water at FOCUS Step 1}
 \usage{
-PEC_sw_focus(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA,
-  f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
-  txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)
+PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL,
+  f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
+  region = c("n", "s"), season = c(NA, "of", "mm", "js"),
+  interception = "no interception", txt_file = "pesticide.txt",
+  overwrite = FALSE, append = TRUE)
 }
 \arguments{
 \item{parent}{A list containing substance specific parameters, e.g.
@@ -19,6 +21,8 @@ applications are given explicitly}
 
 \item{i}{The application interval}
 
+\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,
 the PEC is calculated for this compound, not the parent.}
@@ -35,6 +39,15 @@ 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}}}
 
+\item{region}{'n' for Northern Europe or 's' for Southern Europe. If NA, only
+Step 1 PECsw are calculated}
+
+\item{season}{'of' for October to February, 'mm' for March to May, and 'js'
+for June to September. If NA, only step 1 PECsw are calculated}
+
+\item{interception}{One of 'no interception' (default), 'minimal crop cover',
+'average crop cover' or 'full canopy'}
+
 \item{txt_file}{the name, and potentially the full path to the
 Steps.12 input text file to which the specification of the run(s)
 should be written}
@@ -45,11 +58,13 @@ should be written}
 \item{append}{Should the input text file be appended?}
 }
 \description{
-This is reimplementation of Step 1 of the FOCUS Step 1 and 2 calculator
-version 3.2, authored by Michael Klein. Note that results for multiple
+This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+authored by Michael Klein, in R. Note that results for multiple
 applications should be compared to the corresponding results for a
 single application. At current, this is not done automatically in
-this implementation.
+this implementation. Only Step 1 PECs are calculated. However,
+input files are generated that are suitable as input also for Step 2
+to be used with the FOCUS calculator.
 }
 \note{
 The formulas for input to the waterbody via runoff/drainage of the
@@ -63,11 +78,11 @@ Step 2 is not implemented.
 }
 \examples{
 # Parent only
-dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8)
+dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8)
 PEC_sw_focus(dummy_1, 3000, f_drift = 0)
 
 # Metabolite
-new_dummy <- chent_focus_sw(mw = 250, Koc = 100)
+new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100)
 M1 <- chent_focus_sw(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/chent_focus_sw.Rd b/man/chent_focus_sw.Rd
index 945c343..8df01ab 100644
--- a/man/chent_focus_sw.Rd
+++ b/man/chent_focus_sw.Rd
@@ -4,18 +4,26 @@
 \alias{chent_focus_sw}
 \title{Create a chemical compound object for FOCUS Step 1 calculations}
 \usage{
-chent_focus_sw(Koc, DT50_ws = NA, cwsat = 1000, mw = NA, max_soil = 1,
-  max_ws = 1)
+chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA,
+  DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1)
 }
 \arguments{
+\item{name}{Length one character vector containing the name}
+
 \item{Koc}{Partition coefficient between organic carbon and water
 in L/kg.}
 
 \item{DT50_ws}{Half-life in water/sediment systems in days}
 
+\item{DT50_soil}{Half-life in soil in days}
+
+\item{DT50_water}{Half-life in water in days (Step 2)}
+
+\item{DT50_sediment}{Half-life in sediment in days (Step 2)}
+
 \item{cwsat}{Water solubility in mg/L}
 
-\item{mw}{Molar weight in g/mol}
+\item{mw}{Molar weight in g/mol.}
 
 \item{max_soil}{Maximum observed fraction (dimensionless) in soil}