diff options
| -rw-r--r-- | ChangeLog | 9 | ||||
| -rw-r--r-- | R/PEC_sw_focus.R | 31 | ||||
| -rw-r--r-- | R/PELMO_runs.R | 2 | ||||
| -rw-r--r-- | man/PEC_sw_focus.Rd | 15 | ||||
| -rw-r--r-- | man/PELMO_runs.Rd | 2 | ||||
| -rw-r--r-- | tests/testthat/test_step_1.R | 28 |
6 files changed, 59 insertions, 28 deletions
@@ -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) |