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.

6 files changed, 59 insertions, 28 deletions

diff --git a/ChangeLog b/ChangeLog
index b1eddf2..3297522 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,12 @@
+commit 36036b5901223591e7e21e8b73d8cd1fb034f4cb
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-16 15:43:50 +0200
+
+    Finish the Step 1 calculator including tests
+    
+    Some cleaning up. PELMO facilities do not currently work at my end,
+    as I have no working wine installation on this computer
+
 commit d042f8f06b313e8595087587455daac73d84f17b
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-05-15 20:01:28 +0200
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}
 #'
diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index 22c20c5..656bd6d 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -8,7 +8,8 @@ PEC_sw_focus(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA,
   f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names)
 }
 \arguments{
-\item{parent}{A list containing substance specific parameters}
+\item{parent}{A list containing substance specific parameters, e.g.
+conveniently generated by \code{\link{chent_focus_sw}}.}
 
 \item{rate}{The application rate in g/ha. Overriden when
 applications are given explicitly}
@@ -17,12 +18,13 @@ applications are given explicitly}
 
 \item{i}{The application interval}
 
-\item{met}{A list containing metabolite specific parameters. If not NULL, 
+\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.}
 
 \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 
+of applications via the drift data defined by the
 \code{\link{FOCUS_Step_12_scenarios}}}
 
 \item{f_rd}{The fraction of the amount applied reaching the waterbody via
@@ -42,9 +44,12 @@ this implementation.
 \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
+  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.
 
-Step 2 is not implemented
+Step 2 is not implemented.
 }
 \examples{
 # Parent only
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
index a0d0df8..a86e0fd 100644
--- a/man/PELMO_runs.Rd
+++ b/man/PELMO_runs.Rd
@@ -81,7 +81,7 @@ print(PECgw_2)
 }
 }
 \references{
-PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
+PELMO.installeR \url{https://pkgdown.jrwb.de/PELMO.installeR}
 
 Wine \url{https://winehq.org}
 
diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R
index b067e8f..14045f5 100644
--- a/tests/testthat/test_step_1.R
+++ b/tests/testthat/test_step_1.R
@@ -10,9 +10,9 @@ test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", {
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_1[, "PECsw"]  = c(685.06, 610.32, 543.73, 431.56)
-  PEC_orig_1["1", "TWAECsw"]  = 647.69 # Later TWAEC not implemented
+  PEC_orig_1[, "TWAECsw"]  = c(NA, 647.69, 612.03, 548.76)
   PEC_orig_1[, "PECsed"]  = c(2.36, 2.1, 1.87, 1.49) * 1e3
-  PEC_orig_1["1", "TWAECsed"]  = 2.23e3 # Later TWAEC not implemented
+  PEC_orig_1[, "TWAECsed"]  = c(NA, 2.23e3, 2.11e3, 1.89e3)
 
   expect_equal(res_dummy_1$PEC[1:4, c(1, 2)], PEC_orig_1[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_dummy_1$PEC[1:4, c(3, 4)], PEC_orig_1[, c(3, 4)], tolerance = 10, scale = 1)
@@ -26,9 +26,9 @@ test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", {
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_2[, "PECsw"]  = c(299.89, 290.86, 283.21, 268.50)
-  PEC_orig_2["1", "TWAECsw"]  = 295.38 # Later TWAEC not implemented
+  PEC_orig_2[, "TWAECsw"]  = c(NA, 295.38, 291.20, 283.49)
   PEC_orig_2[, "PECsed"]  = c(319.77, 319.95, 311.53, 295.35)
-  PEC_orig_2["1", "TWAECsed"]  = 319.86 # Later TWAEC not implemented
+  PEC_orig_2[, "TWAECsed"]  = c(NA, 319.86, 317.79, 310.58)
 
   expect_equal(res_dummy_2$PEC[1:4, c(1, 2)], PEC_orig_2[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_dummy_2$PEC[1:4, c(3, 4)], PEC_orig_2[, c(3, 4)], tolerance = 0.01, scale = 1)
@@ -43,9 +43,9 @@ test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", {
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_4[, "PECsw"]  = c(1.82, 1.18, 1.00, 0.70)
-  PEC_orig_4["1", "TWAECsw"]  = 1.50 # Later TWAEC not implemented
+  PEC_orig_4[, "TWAECsw"]  = c(NA, 1.50, 1.29, 1.07)
   PEC_orig_4[, "PECsed"]  = c(10.57, 11.49, 9.66, 6.83)
-  PEC_orig_4["1", "TWAECsed"]  = 11.03 # Later TWAEC not implemented
+  PEC_orig_4[, "TWAECsed"]  = c(NA, 11.03, 10.79, 9.48)
 
   expect_equal(res_dummy_4$PEC[1:4, c(1, 2)], PEC_orig_4[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_dummy_4$PEC[1:4, c(3, 4)], PEC_orig_4[, c(3, 4)], tolerance = 0.01, scale = 1)
@@ -60,9 +60,9 @@ test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", {
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_5[, "PECsw"]  = c(61.60, 59.45, 59.10, 58.41)
-  PEC_orig_5["1", "TWAECsw"]  = 60.53 # Later TWAEC not implemented
+  PEC_orig_5[, "TWAECsw"]  = c(NA, 60.53, 59.90, 59.33)
   PEC_orig_5[, "PECsed"]  = c(500.78, 511.28, 508.29, 502.35)
-  PEC_orig_5["1", "TWAECsed"]  = 506.03 # Later TWAEC not implemented
+  PEC_orig_5[, "TWAECsed"]  = c(NA, 506.03, 507.90, 506.61)
 
   expect_equal(res_dummy_5$PEC[1:4, c(1, 2)], PEC_orig_5[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_dummy_5$PEC[1:4, c(3, 4)], PEC_orig_5[, c(3, 4)], tolerance = 0.01, scale = 1)
@@ -77,9 +77,9 @@ test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", {
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_7[, "PECsw"]  = c(626.99, 601.13, 586.43, 558.10)
-  PEC_orig_7["1", "TWAECsw"]  = 614.06 # Later TWAEC not implemented
+  PEC_orig_7[, "TWAECsw"]  = c(NA, 614.06, 603.90, 588.03)
   PEC_orig_7[, "PECsed"]  = c(3.0, 3.01, 2.93, 2.79) * 1e3
-  PEC_orig_7["1", "TWAECsed"]  = 3.01e3 # Later TWAEC not implemented
+  PEC_orig_7[, "TWAECsed"]  = c(NA, 3.01e3, 2.99e3, 2.92e3)
 
   expect_equal(res_dummy_7$PEC[1:4, c(1, 2)], PEC_orig_7[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_dummy_7$PEC[1:4, c(3, 4)], PEC_orig_7[, c(3, 4)], tolerance = 10, scale = 1)
@@ -95,9 +95,9 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced"
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_M1[, "PECsw"]  = c(62.5, 62.07, 61.64, 60.79)
-  PEC_orig_M1["1", "TWAECsw"]  = 62.28 # Later TWAEC not implemented
+  PEC_orig_M1[, "TWAECsw"]  = c(NA, 62.28, 62.07, 61.64)
   PEC_orig_M1[, "PECsed"]  = c(31.25, 31.03, 30.82, 30.40)
-  PEC_orig_M1["1", "TWAECsed"]  = 31.14 # Later TWAEC not implemented
+  PEC_orig_M1[, "TWAECsed"]  = c(NA, 31.14, 31.03, 30.82)
 
   expect_equal(res_M1$PEC[1:4, c(1, 2)], PEC_orig_M1[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_M1$PEC[1:4, c(3, 4)], PEC_orig_M1[, c(3, 4)], tolerance = 0.01, scale = 1)
@@ -110,9 +110,9 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced"
     dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
 
   PEC_orig_M2[, "PECsw"]  = c(64.34, 63.78, 63.34, 62.47)
-  PEC_orig_M2["1", "TWAECsw"]  = 64.06 # Later TWAEC not implemented
+  PEC_orig_M2[, "TWAECsw"]  = c(NA, 64.06, 63.81, 63.36)
   PEC_orig_M2[, "PECsed"]  = c(31.25, 31.89, 31.67, 31.23)
-  PEC_orig_M2["1", "TWAECsed"]  = 31.57 # Later TWAEC not implemented
+  PEC_orig_M2[, "TWAECsed"]  = c(NA, 31.57, 31.68, 31.56)
 
   expect_equal(res_M2$PEC[1:4, c(1, 2)], PEC_orig_M2[, c(1, 2)], tolerance = 0.01, scale = 1)
   expect_equal(res_M2$PEC[1:4, c(3, 4)], PEC_orig_M2[, c(3, 4)], tolerance = 0.01, scale = 1)