From 3e26a8ab76a434c3465ea1db1b4a2a2ff3ea8ec8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 16 May 2017 18:40:25 +0200
Subject: Add TWA concentrations for days > 1, fix link

Now we have seven test calculations for the Step 1 calculator, all
perfectly passing. This provides confidence that this is a
correct reimplementation of the Step 1 part of the Step 1/2 calculator.
---
 R/PEC_sw_focus.R | 31 ++++++++++++++++++++++++-------
 R/PELMO_runs.R   |  2 +-
 2 files changed, 25 insertions(+), 8 deletions(-)

(limited to 'R')

diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R
index 21ed514..c614593 100644
--- a/R/PEC_sw_focus.R
+++ b/R/PEC_sw_focus.R
@@ -15,19 +15,24 @@
 #'   http://esdac.jrc.ec.europa.eu/projects/stepsonetwo
 #' @note The formulas for input to the waterbody via runoff/drainage of the
 #'   parent and subsequent formation of the metabolite in water is not
-#'   documented in the model description coming with the calculator
-#' @note Step 2 is not implemented
+#'   documented in the model description coming with the calculator. As one would
+#'   expecte, this additional input appears to be (as we get the same results)
+#'   calculated by multiplying the application rate with the molar weight
+#'   correction and the formation fraction in water/sediment systems.
+#' @note Step 2 is not implemented.
 #' @export
-#' @param parent A list containing substance specific parameters
+#' @param parent A list containing substance specific parameters, e.g.
+#'   conveniently generated by \code{\link{chent_focus_sw}}.
 #' @param rate The application rate in g/ha. Overriden when
 #'   applications are given explicitly
 #' @param n The number of applications
 #' @param i The application interval
-#' @param met A list containing metabolite specific parameters. If not NULL, 
+#' @param 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.
 #' @param 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 
+#'   of applications via the drift data defined by the
 #'   \code{\link{FOCUS_Step_12_scenarios}}
 #' @param 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
@@ -138,8 +143,20 @@ PEC_sw_focus <- function(parent, rate, n = 1, i = NA,
   PEC[as.character(t_out[-1]), "PECsed"] = PEC_sed_0_part * exp( - k_ws * t_out[-1])
 
   # TWA concentrations
-  PEC["1", "TWAECsw"] = (PEC_sw_0 + PEC["1", "PECsw"]) / 2
-  PEC["1", "TWAECsed"] = (PEC_sed_0 + PEC["1", "PECsed"]) / 2
+  PEC_sw_1 = PEC["1", "PECsw"]
+  PEC_sed_1 = PEC["1", "PECsed"]
+  TWAEC_sw_1 = (PEC_sw_0 + PEC_sw_1) / 2
+  TWAEC_sed_1 = (PEC_sed_0 + PEC_sed_1) / 2
+
+  TWAEC_after = function(TWAEC_1, PEC_1, t) {
+    (TWAEC_1 + PEC_1 * (1 - exp(- k_ws * (t - 1))) / k_ws) / t
+  }
+
+  PEC["1", "TWAECsw"] = TWAEC_sw_1
+  PEC["1", "TWAECsed"] = TWAEC_sed_1
+
+  PEC[as.character(t_out[-1]), "TWAECsw"] = TWAEC_after(TWAEC_sw_1, PEC_sw_1, t_out[-1])
+  PEC[as.character(t_out[-1]), "TWAECsed"] = TWAEC_after(TWAEC_sed_1, PEC_sed_1, t_out[-1])
 
   # Check if PEC_sw_max is above water solubility
   PEC_sw_max = max(PEC[, "PECsw"])
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R
index b152b4d..c0d1266 100644
--- a/R/PELMO_runs.R
+++ b/R/PELMO_runs.R
@@ -26,7 +26,7 @@
 #' @param cores The number of cores to execute PELMO runs in parallel
 #' @param evaluate Should the results be returned?
 #' @param overwrite Should existing run directories be overwritten?
-#' @references PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
+#' @references PELMO.installeR \url{https://pkgdown.jrwb.de/PELMO.installeR}
 #'
 #' Wine \url{https://winehq.org}
 #'
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