From 435e07a6f7fd2599d783fd306ee6d9e08acc0c6b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 27 Sep 2019 10:00:15 +0200 Subject: Fix for UK drainage, some EFSA interception and washoff - PEC_sw_drainage_UK() gave results that were a little bit too high for the substances with the highest Koc (>4000), as I used 0.01% instead of 0.008% for them. This must have come from an old vesion of the UK data requirements handbook, at least I do not have another explanation - Add EFSA interception (from 2014 DegT50 guidance) and tier 1 crop wash-off factors (from 2017 PEC soil guidance) for some major arable crops - Update docs --- ChangeLog | 41 ++++ DESCRIPTION | 4 +- GNUmakefile | 2 +- R/EFSA_GW_interception_2014.R | 41 ++++ R/EFSA_washoff_2017.R | 42 ++++ R/PEC_sw_drainage_UK.R | 8 + R/SSLRC_mobility_classification.R | 17 +- _pkgdown.yml | 2 + build.log | 4 +- data/EFSA_GW_interception_2014.RData | Bin 0 -> 352 bytes data/EFSA_washoff_2017.RData | Bin 0 -> 356 bytes docs/404.html | 2 +- docs/README.html | 144 ----------- docs/authors.html | 2 +- docs/index.html | 2 +- docs/jquery.sticky-kit.min.js | 9 - docs/reference/EFSA_GW_interception_2014.html | 198 +++++++++++++++ docs/reference/EFSA_washoff_2017.html | 198 +++++++++++++++ docs/reference/FOCUS_GW_scenarios_2012.html | 2 +- docs/reference/FOCUS_PELMO_crop_sze_names.html | 162 ------------- docs/reference/FOCUS_PELMO_crops.html | 174 ------------- docs/reference/FOCUS_PELMO_location_codes.html | 152 ------------ docs/reference/FOCUS_Step_12_scenarios.html | 2 +- docs/reference/FOMC_actual_twa.html | 2 +- docs/reference/GUS.html | 2 +- docs/reference/PEC_FOMC_accu_rel.html | 2 +- docs/reference/PEC_soil.html | 2 +- docs/reference/PEC_soil_mets.html | 2 +- docs/reference/PEC_sw_drainage_UK.html | 14 +- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_drainage.html | 2 +- docs/reference/PEC_sw_exposit_runoff.html | 2 +- docs/reference/PEC_sw_focus.html | 2 +- docs/reference/PEC_sw_sed.html | 2 +- docs/reference/PELMO_path.html | 157 ------------ docs/reference/PELMO_runs.html | 282 ---------------------- docs/reference/SFO_actual_twa.html | 2 +- docs/reference/SSLRC_mobility_classification.html | 23 +- docs/reference/TOXSWA_cwa.html | 2 +- docs/reference/buffers.html | 137 ----------- docs/reference/chent_focus_sw.html | 2 +- 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docs/reference/plot.one_box-8.png | Bin 12575 -> 0 bytes docs/reference/plot.one_box.html | 2 +- docs/reference/read.TOXSWA_cwa.html | 2 +- docs/reference/sawtooth-6.png | Bin 12575 -> 0 bytes docs/reference/sawtooth.html | 2 +- docs/reference/soil_scenario_data_EFSA_2015.html | 2 +- docs/reference/soil_scenario_data_EFSA_2017.html | 2 +- docs/reference/sum_periods.html | 153 ------------ docs/reference/twa.html | 2 +- docs/sitemap.xml | 6 + man/EFSA_GW_interception_2014.Rd | 48 ++++ man/EFSA_washoff_2017.Rd | 48 ++++ man/PEC_sw_drainage_UK.Rd | 10 + man/SSLRC_mobility_classification.Rd | 13 +- tests/testthat/test_UK_drainage.R | 7 +- 77 files changed, 758 insertions(+), 2042 deletions(-) create mode 100644 R/EFSA_GW_interception_2014.R create mode 100644 R/EFSA_washoff_2017.R create mode 100644 data/EFSA_GW_interception_2014.RData create mode 100644 data/EFSA_washoff_2017.RData delete mode 100644 docs/README.html delete mode 100644 docs/jquery.sticky-kit.min.js create mode 100644 docs/reference/EFSA_GW_interception_2014.html create mode 100644 docs/reference/EFSA_washoff_2017.html delete mode 100644 docs/reference/FOCUS_PELMO_crop_sze_names.html delete mode 100644 docs/reference/FOCUS_PELMO_crops.html delete mode 100644 docs/reference/FOCUS_PELMO_location_codes.html delete mode 100644 docs/reference/PELMO_path.html delete mode 100644 docs/reference/PELMO_runs.html delete mode 100644 docs/reference/buffers.html delete mode 100644 docs/reference/create_run_list.html delete mode 100644 docs/reference/focus_80th.html delete mode 100644 docs/reference/get_flux.html delete mode 100644 docs/reference/get_interval.html delete mode 100644 docs/reference/one_box-4.png delete mode 100644 docs/reference/one_box-8.png delete mode 100644 docs/reference/plot.TOXSWA_cwa-10.png delete mode 100644 docs/reference/plot.TOXSWA_cwa-6.png delete mode 100644 docs/reference/plot.TOXSWA_cwa-8.png delete mode 100644 docs/reference/plot.one_box-4.png delete mode 100644 docs/reference/plot.one_box-8.png delete mode 100644 docs/reference/sawtooth-6.png delete mode 100644 docs/reference/sum_periods.html create mode 100644 man/EFSA_GW_interception_2014.Rd create mode 100644 man/EFSA_washoff_2017.Rd diff --git a/ChangeLog b/ChangeLog index 5e51af7..9e3ad5f 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,44 @@ +commit d28c33cfea96654a883ca869020671346c23568e +Author: Johannes Ranke +Date: 2019-09-27 10:00:15 +0200 + + Fix for UK drainage, add some EFSA interception and washoff + + - PEC_sw_drainage_UK() gave results that were a little bit too high + for the substances with the highest Koc (>4000), as I used 0.01% instead + of 0.008% for them. This must have come from an old vesion of the UK + data requirements handbook, at least I do not have another explanation + + - Added EFSA interception (from 2014 DegT50 guidance) and tier 1 + crop wash-off factors (from 2017 PEC soil guidance) for some major + arable crops + + - Updated docs + +commit 803fe13e505960fddccdbd4dcb524715f5eb068d +Author: Johannes Ranke +Date: 2019-09-18 18:18:40 +0200 + + Add url: tag to _pkgdown.yml, typo, update docs + +commit 8deaa29a659630a40e8b11df1fa3ebbbd9ca9e68 +Author: Johannes Ranke +Date: 2019-07-01 08:04:40 +0200 + + Typo + +commit 37a1513d73201dbacc71af3c33a2a2a4e798583c +Author: Johannes Ranke +Date: 2019-06-12 18:15:46 +0200 + + Update of static docs + +commit 5c9dd5c269acc4a6e6e32a7e599afb8f98d8ca36 +Author: Johannes Ranke +Date: 2019-06-12 18:14:46 +0200 + + Documentation fix + commit 069824057caf8e57507852b858a7ecfd8e13e49a Author: Johannes Ranke Date: 2019-05-14 12:41:16 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index db3d51d..1589b14 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.5.6 -Date: 2019-09-18 +Version: 0.5.7 +Date: 2019-09-27 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/GNUmakefile b/GNUmakefile index 76d369e..0d3f38e 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -34,7 +34,7 @@ README.html: README.md pd: roxygen @echo "Building static documentation..." # suppressWarnings to get rid of mbcsToSbcs warnings when plotting the 'µ' character - "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site())' + "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site(lazy=TRUE))' @echo "DONE." $(TGZ): $(pkgfiles) diff --git a/R/EFSA_GW_interception_2014.R b/R/EFSA_GW_interception_2014.R new file mode 100644 index 0000000..15d7835 --- /dev/null +++ b/R/EFSA_GW_interception_2014.R @@ -0,0 +1,41 @@ +#' Subset of EFSA crop interception default values for groundwater modelling +#' +#' @name EFSA_GW_interception_2014 +#' @docType data +#' @source European Food Safety Authority (2014) EFSA Guidance Document for +#' evaluating laboratory and field dissipation studies to obtain DegT50 values +#' of active substances of plant protection products and transformation +#' products of these active substances in soil. \emph{EFSA Journal} +#' \bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 +#' @format A matrix containing interception values, currently only for some selected crops +#' @examples +#' \dontrun{ +#' # This is the code that was used to define the data +#' bbch <- paste0(0:9, "x") +#' crops <- c( +#' "Beans (field + vegetable)", +#' "Peas", +#' "Summer oilseed rape", "Winter oilseed rape", +#' "Tomatoes", +#' "Spring cereals", "Winter cereals") +#' EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), +#' dimnames = list(Crop = crops, BBCH = bbch)) +#' EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- +#' c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) +#' EFSA_GW_interception_2014["Peas", ] <- +#' c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) +#' EFSA_GW_interception_2014["Summer oilseed rape", ] <- +#' c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) +#' EFSA_GW_interception_2014["Winter oilseed rape", ] <- +#' c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) +#' EFSA_GW_interception_2014["Tomatoes", ] <- +#' c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) +#' EFSA_GW_interception_2014["Spring cereals", ] <- +#' c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) +#' EFSA_GW_interception_2014["Winter cereals", ] <- +#' c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) +#' save(EFSA_GW_interception_2014, +#' file = "../data/EFSA_GW_interception_2014.RData") +#' } +#' EFSA_GW_interception_2014 +NULL diff --git a/R/EFSA_washoff_2017.R b/R/EFSA_washoff_2017.R new file mode 100644 index 0000000..450c12e --- /dev/null +++ b/R/EFSA_washoff_2017.R @@ -0,0 +1,42 @@ +#' Subset of EFSA crop washoff default values +#' +#' @name EFSA_washoff_2017 +#' @docType data +#' @source +#' European Food Safety Authority (2017) EFSA guidance document for +#' predicting environmental concentrations of active substances of plant +#' protection products and transformation products of these active substances +#' in soil. \emph{EFSA Journal} \bold{15}(10) 4982 +#' doi:10.2903/j.efsa.2017.4982 +#' @format A matrix containing wash-off factors, currently only for some selected crops +#' @examples +#' \dontrun{ +#' # This is the code that was used to define the data +#' bbch <- paste0(0:9, "x") +#' crops <- c( +#' "Beans (field + vegetable)", +#' "Peas", +#' "Summer oilseed rape", "Winter oilseed rape", +#' "Tomatoes", +#' "Spring cereals", "Winter cereals") +#' EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), +#' dimnames = list(Crop = crops, BBCH = bbch)) +#' EFSA_washoff_2017["Beans (field + vegetable)", ] <- +#' c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) +#' EFSA_washoff_2017["Peas", ] <- +#' c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) +#' EFSA_washoff_2017["Summer oilseed rape", ] <- +#' c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) +#' EFSA_washoff_2017["Winter oilseed rape", ] <- +#' c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) +#' EFSA_washoff_2017["Tomatoes", ] <- +#' c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) +#' EFSA_washoff_2017["Spring cereals", ] <- +#' c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) +#' EFSA_washoff_2017["Winter cereals", ] <- +#' c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) +#' save(EFSA_washoff_2017, +#' file = "../data/EFSA_washoff_2017.RData") +#' } +#' EFSA_washoff_2017 +NULL diff --git a/R/PEC_sw_drainage_UK.R b/R/PEC_sw_drainage_UK.R index e53f179..3be4c97 100644 --- a/R/PEC_sw_drainage_UK.R +++ b/R/PEC_sw_drainage_UK.R @@ -29,6 +29,14 @@ #' "DFOP", "HS", or "IORE", or an mkinmod object #' @param model_parms A named numeric vector containing the model parameters #' @return The predicted concentration in surface water in µg/L +#' @references HSE's Chemicals Regulation Division (CRD) Active substance +#' PECsw calculations (for UK specific authorisation requests) +#' \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm} +#' accessed 2019-09-27 +#' +#' Drainage PECs Version 1.0 (2015) Spreadsheet published at +#' \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx} +#' accessed 2019-09-27 #' @export #' @author Johannes Ranke #' @examples diff --git a/R/SSLRC_mobility_classification.R b/R/SSLRC_mobility_classification.R index 2f8fb34..602f166 100644 --- a/R/SSLRC_mobility_classification.R +++ b/R/SSLRC_mobility_classification.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015,2018 Johannes Ranke +# Copyright (C) 2015,2018,2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -17,30 +17,39 @@ #' Determine the SSLRC mobility classification for a chemical substance from its Koc #' -#' This implements the method specified in the UK data requirements handbook and was +#' This implements the method specified in the UK data requirements handbook and was #' checked against the spreadsheet published on the CRC website #' #' @param Koc The sorption coefficient normalised to organic carbon in L/kg #' @return A list containing the classification and the percentage of the #' compound transported per 10 mm drain water +#' @references HSE's Chemicals Regulation Division (CRD) Active substance +#' PECsw calculations (for UK specific authorisation requests) +#' \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm} +#' accessed 2019-09-27 +#' +#' Drainage PECs Version 1.0 (2015) Spreadsheet published at +#' \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx} +#' accessed 2019-09-27 #' @export #' @author Johannes Ranke #' @examples #' SSLRC_mobility_classification(100) +#' SSLRC_mobility_classification(10000) SSLRC_mobility_classification <- function(Koc) { if (!is.numeric(Koc) | length(Koc) != 1) stop("Please give a single number") if (is.na(Koc)) { result <- list(NA, NA) } else { - result <- list("Non mobile", 0.01) + result <- list("Non mobile", 0.008) if (Koc < 4000) result <- list("Slightly mobile", 0.02) if (Koc < 1000) result <- list("Slightly mobile", 0.5) if (Koc < 500) result <- list("Moderately mobile", 0.7) if (Koc < 75) result <- list("Mobile", 1.9) if (Koc < 15) result <- list("Very mobile", 1.9) } - names(result) <- c("Mobility classification", + names(result) <- c("Mobility classification", "Percentage drained per mm of drain water") return(result) } diff --git a/_pkgdown.yml b/_pkgdown.yml index b5f7ae7..bec5bf7 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -25,9 +25,11 @@ reference: - soil_scenario_data_EFSA_2015 - soil_scenario_data_EFSA_2017 - PEC_FOMC_accu_rel + - EFSA_washoff_2017 - title: Predicted environmental concentrations in groundwater contents: - FOCUS_GW_scenarios_2012 + - EFSA_GW_interception_2014 - title: Predicted environmental concentrations in surface water contents: - PEC_sw_drift diff --git a/build.log b/build.log index 6f7f78c..e001d03 100644 --- a/build.log +++ b/build.log @@ -7,5 +7,7 @@ Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1/MACRO’ Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1’ Removed empty directory ‘pfm/inst/testdata/SwashProjects’ * looking to see if a ‘data/datalist’ file should be added -* building ‘pfm_0.5.6.tar.gz’ + NB: this package now depends on R (>= 3.5.0) + WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'pfm/data/EFSA_GW_interception_2014.RData' WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'pfm/data/EFSA_washoff_2017.RData' +* building 'pfm_0.5.7.tar.gz' diff --git a/data/EFSA_GW_interception_2014.RData b/data/EFSA_GW_interception_2014.RData new file mode 100644 index 0000000..14fded6 Binary files /dev/null and b/data/EFSA_GW_interception_2014.RData differ diff --git a/data/EFSA_washoff_2017.RData b/data/EFSA_washoff_2017.RData new file mode 100644 index 0000000..699c0c0 Binary files /dev/null and b/data/EFSA_washoff_2017.RData differ diff --git a/docs/404.html b/docs/404.html index d665a2e..8e5e550 100644 --- a/docs/404.html +++ b/docs/404.html @@ -63,7 +63,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/README.html b/docs/README.html deleted file mode 100644 index efdf51f..0000000 --- a/docs/README.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - - - -/home/jranke/git/pfm/README.md • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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/home/jranke/git/pfm/README.md

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-pfm

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The R package pfm provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license. This means:

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This program is free software: you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT
-ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-details.
-
-You should have received a copy of the GNU General Public License along with
-this program. If not, see <http://www.gnu.org/licenses/>
-
-

-Installation

-

You can install the package from github, e.g. using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.

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library(devtools)
-install_github("jranke/pfm", quick = TRUE)
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-
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-Use

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Please refer to the reference.

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-Examples

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One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown here.

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Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown here.

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Developed by Johannes Ranke.

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Site built with pkgdown.

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Subset of EFSA crop interception default values for groundwater modelling

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Subset of EFSA crop interception default values for groundwater modelling

+ +
+ + +

Format

+ +

A matrix containing interception values, currently only for some selected crops

+ +

Source

+ +

European Food Safety Authority (2014) EFSA Guidance Document for +evaluating laboratory and field dissipation studies to obtain DegT50 values +of active substances of plant protection products and transformation +products of these active substances in soil. EFSA Journal +12(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662

+ + +

Examples

+ 
if (FALSE) {
+  # This is the code that was used to define the data
+  bbch <- paste0(0:9, "x")
+  crops <- c(
+    "Beans (field + vegetable)",
+    "Peas",
+    "Summer oilseed rape", "Winter oilseed rape",
+    "Tomatoes",
+    "Spring cereals", "Winter cereals")
+  EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch),
+    dimnames = list(Crop = crops, BBCH = bbch))
+  EFSA_GW_interception_2014["Beans (field + vegetable)", ] <-
+    c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8)
+  EFSA_GW_interception_2014["Peas", ] <-
+    c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85)
+  EFSA_GW_interception_2014["Summer oilseed rape", ] <-
+    c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9)
+  EFSA_GW_interception_2014["Winter oilseed rape", ] <-
+    c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9)
+  EFSA_GW_interception_2014["Tomatoes", ] <-
+    c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5)
+  EFSA_GW_interception_2014["Spring cereals", ] <-
+    c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8)
+  EFSA_GW_interception_2014["Winter cereals", ] <-
+    c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8)
+  save(EFSA_GW_interception_2014,
+    file = "../data/EFSA_GW_interception_2014.RData")
+}
+EFSA_GW_interception_2014
#>                            BBCH
+#> Crop                        0x   1x   2x   3x   4x   5x   6x   7x   8x   9x
+#>   Beans (field + vegetable)  0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80
+#>   Peas                       0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85
+#>   Summer oilseed rape        0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90
+#>   Winter oilseed rape        0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90
+#>   Tomatoes                   0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50
+#>   Spring cereals             0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80
+#>   Winter cereals             0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80
+
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.4.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html new file mode 100644 index 0000000..1f7bce7 --- /dev/null +++ b/docs/reference/EFSA_washoff_2017.html @@ -0,0 +1,198 @@ + + + + + + + + +Subset of EFSA crop washoff default values — EFSA_washoff_2017 • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Subset of EFSA crop washoff default values

+ + +
+ +
+ +

Subset of EFSA crop washoff default values

+ +
+ + +

Format

+ +

A matrix containing wash-off factors, currently only for some selected crops

+ +

Source

+ +

European Food Safety Authority (2017) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. EFSA Journal 15(10) 4982 + doi:10.2903/j.efsa.2017.4982

+ + +

Examples

+ 
if (FALSE) {
+  # This is the code that was used to define the data
+  bbch <- paste0(0:9, "x")
+  crops <- c(
+    "Beans (field + vegetable)",
+    "Peas",
+    "Summer oilseed rape", "Winter oilseed rape",
+    "Tomatoes",
+    "Spring cereals", "Winter cereals")
+  EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch),
+    dimnames = list(Crop = crops, BBCH = bbch))
+  EFSA_washoff_2017["Beans (field + vegetable)", ] <-
+    c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35)
+  EFSA_washoff_2017["Peas", ] <-
+    c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35)
+  EFSA_washoff_2017["Summer oilseed rape", ] <-
+    c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5)
+  EFSA_washoff_2017["Winter oilseed rape", ] <-
+    c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3)
+  EFSA_washoff_2017["Tomatoes", ] <-
+    c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35)
+  EFSA_washoff_2017["Spring cereals", ] <-
+    c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55)
+  EFSA_washoff_2017["Winter cereals", ] <-
+    c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4)
+  save(EFSA_washoff_2017,
+    file = "../data/EFSA_washoff_2017.RData")
+}
+EFSA_washoff_2017
#>                            BBCH
+#> Crop                        0x   1x   2x   3x   4x   5x   6x   7x   8x   9x
+#>   Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35
+#>   Peas                      NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35
+#>   Summer oilseed rape       NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50
+#>   Winter oilseed rape       NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30
+#>   Tomatoes                  NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35
+#>   Spring cereals            NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55
+#>   Winter cereals            NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40
+
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.4.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 90df1b8..6b2cbe1 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -67,7 +67,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> pfm - 0.5.6 + 0.5.7
diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html deleted file mode 100644 index 4612df6..0000000 --- a/docs/reference/FOCUS_PELMO_crop_sze_names.html +++ /dev/null @@ -1,162 +0,0 @@ - - - - - - - - -FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- - - -
- -
-
-
-

FOCUS PELMO crop acronyms used for naming sceneario files

- Source: R/FOCUS_PELMO_data.R - -
- -
- -

A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 -for naming the .sze files located in the FOCUS directory. The crop acronyms -in the file names are sometimes capitalized, sometimes not. The scenario -files used for Beans (field) and Beans (vegetable) are the same.

- -
- - 
FOCUS_PELMO_crop_sze_names
- -

Format

- -

An object of class character of length 25.

- - -

Examples

- 
print(FOCUS_PELMO_crop_sze_names)
#>      app      gra      pot      sug      win      fbe      vbe      bus 
-#> "apples"  "grass" "potato" "sbeets" "wcerea"  "beans"  "beans"  "bushb" 
-#>      cab      car      cit      cot      lin      mai      soi      woi 
-#> "cabbag" "carrot" "citrus" "cotton"  "linse"  "maize" "rapesu" "rapewi" 
-#>      oni      ape      soy      spr      str      sun      tob      tom 
-#> "onions"   "peas"   "soyb" "scerea" "strawb" "sunflo" "tobacc" "tomato" 
-#>      vin 
-#>  "vines"
-
- -
- -
-
-

Developed by Johannes Ranke.

-
- -
-

Site built with pkgdown.

-
- -
-
- - - - - - diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html deleted file mode 100644 index 77b5c01..0000000 --- a/docs/reference/FOCUS_PELMO_crops.html +++ /dev/null @@ -1,174 +0,0 @@ - - - - - - - - -FOCUS PELMO crop names — FOCUS_PELMO_crops • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- - - -
- -
-
-
-

FOCUS PELMO crop names

- Source: R/FOCUS_PELMO_data.R - -
- -
- -

A named character vector with the crop names used in the PELMO 5.5.3 GUI. -For the names, three letter codes were constructed by generally taking the -first three letters in lower case. Only when there is an expression in -parentheses, the first letter of this expression becomes the first letter -in the three letter code, i.e. 'Peas (animals)' has the code ape.

- -
- - 
FOCUS_PELMO_crops
- -

Format

- -

An object of class character of length 25.

- - -

Examples

- 
print(FOCUS_PELMO_crops)
#>                      app                      gra                      pot 
-#>                 "Apples"      "Grass and alfalfa"               "Potatoes" 
-#>                      sug                      win                      fbe 
-#>            "Sugar beets"         "Winter cereals"          "Beans (field)" 
-#>                      vbe                      bus                      cab 
-#>     "Beans (vegetables)"            "Bushberries"                "Cabbage" 
-#>                      car                      cit                      cot 
-#>                "Carrots"                 "Citrus"                 "Cotton" 
-#>                      lin                      mai                      soi 
-#>                "Linseed"                  "Maize" "Oil seed rape (summer)" 
-#>                      woi                      oni                      ape 
-#> "Oil seed rape (winter)"                 "Onions"         "Peas (animals)" 
-#>                      soy                      spr                      str 
-#>               "Soybeans"         "Spring cereals"           "Strawberries" 
-#>                      sun                      tob                      tom 
-#>              "Sunflower"                "Tobacco"               "Tomatoes" 
-#>                      vin 
-#>                  "Vines"
-
- -
- -
-
-

Developed by Johannes Ranke.

-
- -
-

Site built with pkgdown.

-
- -
-
- - - - - - diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html deleted file mode 100644 index c06c729..0000000 --- a/docs/reference/FOCUS_PELMO_location_codes.html +++ /dev/null @@ -1,152 +0,0 @@ - - - - - - - - -Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- - - -
- -
-
-
-

Location codes in FOCUS PELMO

- Source: R/FOCUS_PELMO_data.R - -
- -
- -

A named character vector of one letter location codes used in FOCUS PELMO, -indexed by three letter acronyms.

- -
- - 
FOCUS_PELMO_location_codes
- -

Format

- -

An object of class character of length 9.

- - -

Examples

- 
print(FOCUS_PELMO_location_codes)
#> Cha Ham Jok Kre Oke Pia Por Sev Thi 
-#> "C" "H" "J" "K" "N" "P" "O" "S" "T"
-
- -
- -
-
-

Developed by Johannes Ranke.

-
- -
-

Site built with pkgdown.

-
- -
-
- - - - - - diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 552723f..4eed02f 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -67,7 +67,7 @@ The text file is not included in the package as its licence is not clear." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 38b5f8c..ae6e38c 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 88546fa..b44c120 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -68,7 +68,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html index 68436fb..e4d9bf4 100644 --- a/docs/reference/PEC_FOMC_accu_rel.html +++ b/docs/reference/PEC_FOMC_accu_rel.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 96e2db6..81575f3 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -70,7 +70,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index ce7c6b0..c3b09f4 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 8c55eed..f641773 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -67,7 +67,7 @@ published on the CRC website" /> pfm - 0.5.6 + 0.5.7 @@ -153,6 +153,16 @@ published on the CRC website

The predicted concentration in surface water in µg/L

+

References

+ +

HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm + accessed 2019-09-27

+

Drainage PECs Version 1.0 (2015) Spreadsheet published at + https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx + accessed 2019-09-27

+

Examples

PEC_sw_drainage_UK(150, Koc = 100)
#> [1] 8.076923
@@ -163,6 +173,8 @@ published on the CRC website

  • Arguments
  • Value
    • + +
  • References
  • Examples
    • diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index c1551e2..14ccf79 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -68,7 +68,7 @@ with input via spray drift." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index 641ee7d..1c2deac 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -72,7 +72,7 @@ details, see the discussion of the function arguments below." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index f659bff..30ef975 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -67,7 +67,7 @@ in the worksheet "Konzept Runoff"." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 599b020..1647b19 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -72,7 +72,7 @@ to be used with the FOCUS calculator." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 77e4269..fe65d96 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -69,7 +69,7 @@ PEC calculator" /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html deleted file mode 100644 index a67084c..0000000 --- a/docs/reference/PELMO_path.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - - - -Create a path of run directories as the PELMO GUI does — PELMO_path • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Create a path of run directories as the PELMO GUI does

    - Source: R/PELMO_runs.R - -
    - -
    - -

    Create a path of run directories as the PELMO GUI does

    - -
    - - 
    PELMO_path(psm, crop, scenario = NA)
    - -

    Arguments

    - - - - - - - - - - - - - - -
    psm

    The psm identifier

    crop

    The PELMO crop acronym

    scenario

    The scenario

    - - -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html deleted file mode 100644 index 2a75191..0000000 --- a/docs/reference/PELMO_runs.html +++ /dev/null @@ -1,282 +0,0 @@ - - - - - - - - -Set up runs for FOCUS PELMO — PELMO_runs • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Set up runs for FOCUS PELMO

    - Source: R/PELMO_runs.R - -
    - -
    - -

    Per default, the runs are not only set up but also executed with FOCUS -PELMO, the results are processed and returned. Currently, only FOCUS PELMO -as installed on Linux (or other Unix systems) -using the install_PELMO from the PELMO.installeR package -maintained on github is supported. In such installations, FOCUS PELMO is -installed into the package installation directory of PELMO.installeR -and run using wine.

    - -
    - - 
    PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
-  execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE,
-  overwrite = FALSE)
-
-run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
-  cores = getOption("mc.cores", 2L))
-
-evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")
    - -

    Arguments

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    runs

    A list of lists. Each inner lists has an element named 'psm' -that holds the psm string, and elements named using three letter crop acronyms, -as used in FOCUS_PELMO_crops, -that hold character vectors of three letter scenario acronyms -as used in FOCUS_GW_scenarios_2012.

    psm_dir

    The directory where the psm files are located

    version

    The FOCUS PELMO version

    PELMO_base

    Where the FOCUS PELMO installation is located

    execute

    Should PELMO be executed directly?

    cores

    The number of cores to execute PELMO runs in parallel

    evaluate

    Should the results be returned?

    overwrite

    Should existing run directories be overwritten?

    - -

    Value

    - -

    If evaluate is TRUE, a list of lists of matrices holding the - PEC data.

    - -

    Details

    - -

    As a side effect, an R data file (period_pfm.rda) is generated in each -run directory, holding the results for all FOCUS periods, equivalent to -the period.plm file generated by the FOCUS PELMO GUI.

    - -

    References

    - -

    PELMO.installeR https://pkgdown.jrwb.de/PELMO.installeR

    -

    Wine https://winehq.org

    -

    PELMO test results http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc

    - - -

    Examples

    - 
    # Reproduce the official test results for annual application of Pesticide D
-# to winter cereals at the day before emergence
-runs_1 <- list(
-  list(psm = 'Pesticide_D',
-       win = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")),
-  list(psm = 'Pesticide_D_1_day_pre_em_every_third_year',
-       pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
-time_1 <- system.time(
-  PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
-    cores = 15, overwrite = TRUE)
-)
-print(PECgw_1)
    #> $Pesticide_D
-#> $Pesticide_D$win
-#>     FOCUS DUMMY D
-#> Cha         0.025
-#> Ham         1.621
-#> Jok         0.388
-#> Kre         0.467
-#> Oke         1.608
-#> Pia         0.848
-#> Por         2.386
-#> Sev         0.009
-#> Thi         0.030
-#> 
-#> 
-#> $Pesticide_D_1_day_pre_em_every_third_year
-#> $Pesticide_D_1_day_pre_em_every_third_year$pot
-#>     FOCUS DUMMY D
-#> Cha         0.010
-#> Ham         0.014
-#> Jok         0.009
-#> Kre         0.027
-#> Oke         0.085
-#> Pia         0.051
-#> Por         0.021
-#> Sev         0.000
-#> Thi         0.001
-#> 
-#> 
    # We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
-print(time_1)
    #>        User      System verstrichen 
-#>       0.395       0.093      30.590 
    if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
-  cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
-}
    #> CPU model: AMD Ryzen 7 1700 Eight-Core Processor
    
-# Demonstrate some results with metabolites.
-runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
-                    win = c("Cha", "Ham", "Kre")))
-PECgw_2 <- PELMO_runs(runs_2, psm_dir = system.file("testdata", package = "pfm"),
-  cores = 3, overwrite = TRUE)
-print(PECgw_2)
    #> $Pesticide_D_1_May_every_other_year_mets
-#> $Pesticide_D_1_May_every_other_year_mets$win
-#>     FOCUS DUMMY D      M1    M2
-#> Cha         0.001 126.195 0.000
-#> Ham         0.054  82.196 0.001
-#> Kre         0.103  75.494 0.001
-#> 
-#>
    -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index 1f3a140..1f172c6 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index ddb21de..b0ae939 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -34,7 +34,7 @@ - @@ -67,7 +67,7 @@ checked against the spreadsheet published on the CRC website" /> pfm - 0.5.6 + 0.5.7 @@ -106,7 +106,7 @@ checked against the spreadsheet published on the CRC website" />
    -

    This implements the method specified in the UK data requirements handbook and was +

    This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website

    @@ -127,6 +127,16 @@ checked against the spreadsheet published on the CRC website

    A list containing the classification and the percentage of the compound transported per 10 mm drain water

    +

    References

    + +

    HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm + accessed 2019-09-27

    +

    Drainage PECs Version 1.0 (2015) Spreadsheet published at + https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx + accessed 2019-09-27

    +

    Examples

    SSLRC_mobility_classification(100)
    #> $`Mobility classification`
@@ -134,6 +144,11 @@ checked against the spreadsheet published on the CRC website
    
 #> 
 #> $`Percentage drained per mm of drain water`
 #> [1] 0.7
+#> 
    SSLRC_mobility_classification(10000)
    #> $`Mobility classification`
+#> [1] "Non mobile"
+#> 
+#> $`Percentage drained per mm of drain water`
+#> [1] 0.008
 #>
    diff --git a/docs/reference/buffers.html b/docs/reference/buffers.html deleted file mode 100644 index f04c3d0..0000000 --- a/docs/reference/buffers.html +++ /dev/null @@ -1,137 +0,0 @@ - - - - - - - - -Runoff reduction percentages as used in Exposit — buffers • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Runoff reduction percentages as used in Exposit

    -
    - - -

    A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths

    - - - 
    buffers
    - -

    Format

    - -

    A named list of data frames with reduction percentage values for the -dissolved fraction and the fraction bound to eroding particles, with -vegetated buffer widths as row names. The names of the list items are the Exposit versions -from which the values were taken.

    -
    dissolved

    The reduction percentage for the dissolved phase

    -
    bound

    The reduction percentage for the particulate phase

    -
    - -

    Source

    - -

    Excel 3.01 spreadsheet available from - https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3

    - - -

    Examples

    - 
    print(perc_runoff_reduction_exposit)
    #> $`3.01`
-#>           dissolved bound
-#> No buffer         0     0
-#> 5 m              40    40
-#> 10 m             60    85
-#> 20 m             80    95
-#> 
-#> $`2.0`
-#>   dissolved bound
-#> 1       0.0   0.0
-#> 2      97.5  97.5
-#>
    -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 922c405..324f2fe 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html deleted file mode 100644 index d3c5a97..0000000 --- a/docs/reference/create_run_list.html +++ /dev/null @@ -1,161 +0,0 @@ - - - - - - - - -Create a list of runs that we can traverse — create_run_list • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Create a list of runs that we can traverse

    - Source: R/PELMO_runs.R - -
    - -
    - -

    Create a list of runs that we can traverse

    - -
    - - 
    create_run_list(runs, psm_dir = ".", check_psm_files = FALSE)
    - -

    Arguments

    - - - - - - - - - - - - - - -
    runs

    A list of lists. Each inner lists has an element named 'psm' -that holds the psm string, and elements named using three letter crop acronyms, -as used in FOCUS_PELMO_crops, -that hold character vectors of three letter scenario acronyms -as used in FOCUS_GW_scenarios_2012.

    psm_dir

    The directory where the psm files are located

    check_psm_files

    Should we check if the psm file exists

    - - -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 665cb83..08d8399 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -69,7 +69,7 @@ published by the German Julius-Kühn Institute (JKI)." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 2875b7a..99e407c 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -69,7 +69,7 @@ this function." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html deleted file mode 100644 index 60ecbdd..0000000 --- a/docs/reference/focus_80th.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - - - -Calculate the 80th percentile according to FOCUS guidance — focus_80th • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Calculate the 80th percentile according to FOCUS guidance

    - Source: R/PELMO_runs.R - -
    - -
    - -

    This is nowadays defined as the mean of the 16th and the 17th -highest value. Previously, the 17th highest values was used (FOCUS 2014, p. -18). NaN values need to be set to zero in order to reproduce the -values obtained by PELMO.

    - -
    - - 
    focus_80th(c_period, old = FALSE)
    - -

    Arguments

    - - - - - - - - - - -
    c_period

    A numeric vector of values to calculate the percentile from

    old

    Should the old calculation method be used (the 17th highest value)?

    - - -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 5775b27..469e12f 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -69,7 +69,7 @@ returns 0 if at least one element of the vector is 0." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html deleted file mode 100644 index 2b138f8..0000000 --- a/docs/reference/get_flux.html +++ /dev/null @@ -1,149 +0,0 @@ - - - - - - - - -Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file

    - Source: R/PELMO_runs.R - -
    - -
    - -

    Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file

    - -
    - - 
    get_flux(chem_file)
    - -

    Arguments

    - - - - - - -
    chem_file

    The full path to a CHEM*.PLM file

    - - -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html deleted file mode 100644 index b6561fb..0000000 --- a/docs/reference/get_interval.html +++ /dev/null @@ -1,153 +0,0 @@ - - - - - - - - -Get the application interval in years from a psm file — get_interval • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Get the application interval in years from a psm file

    - Source: R/PELMO_runs.R - -
    - -
    - -

    Get the application interval in years from a psm file

    - -
    - - 
    get_interval(psm_file, location_code)
    - -

    Arguments

    - - - - - - - - - - -
    psm_file

    The path to the .psm file

    location_code

    The location code

    - - -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index 5c2205a..3d0bc2d 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -67,7 +67,7 @@ https://stackoverflow.com/a/717791" /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/index.html b/docs/reference/index.html index ca8cd18..e1acfc1 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -63,7 +63,7 @@ pfm - 0.5.6 + 0.5.7 @@ -205,6 +205,12 @@

    PEC_FOMC_accu_rel()

    Get the relative accumulation of an FOMC model over multiples of an interval

    + + + +

    EFSA_washoff_2017

    + +

    Subset of EFSA crop washoff default values

    @@ -219,6 +225,12 @@

    FOCUS_GW_scenarios_2012

    A very small subset of the FOCUS Groundwater scenario definitions

    + + + +

    EFSA_GW_interception_2014

    + +

    Subset of EFSA crop interception default values for groundwater modelling

    diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 1078f3e..1d24c2a 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -70,7 +70,7 @@ max_twa." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png deleted file mode 100644 index f7730a4..0000000 Binary files a/docs/reference/one_box-4.png and /dev/null differ diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png deleted file mode 100644 index da3d439..0000000 Binary files a/docs/reference/one_box-8.png and /dev/null differ diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index ebfb872..56d60c0 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index 745d1f1..a0f723f 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 8b1da13..baded1c 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 0154be0..7e4eab1 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/plot.TOXSWA_cwa-10.png b/docs/reference/plot.TOXSWA_cwa-10.png deleted file mode 100644 index 4e5eae3..0000000 Binary files a/docs/reference/plot.TOXSWA_cwa-10.png and /dev/null differ diff --git a/docs/reference/plot.TOXSWA_cwa-6.png b/docs/reference/plot.TOXSWA_cwa-6.png deleted file mode 100644 index c21eacc..0000000 Binary files a/docs/reference/plot.TOXSWA_cwa-6.png and /dev/null differ diff --git a/docs/reference/plot.TOXSWA_cwa-8.png b/docs/reference/plot.TOXSWA_cwa-8.png deleted file mode 100644 index 04e09d6..0000000 Binary files a/docs/reference/plot.TOXSWA_cwa-8.png and /dev/null differ diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 0a69f2e..8ca5b8e 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -67,7 +67,7 @@ segment of a TOXSWA surface water body." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/plot.one_box-4.png b/docs/reference/plot.one_box-4.png deleted file mode 100644 index 06b2cde..0000000 Binary files a/docs/reference/plot.one_box-4.png and /dev/null differ diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png deleted file mode 100644 index 3ff6e8a..0000000 Binary files a/docs/reference/plot.one_box-8.png and /dev/null differ diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 89958c5..d048d22 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -66,7 +66,7 @@ pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index f1d4a47..df84634 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -71,7 +71,7 @@ renamed to ConLiqWatLay in the out file." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png deleted file mode 100644 index 3ff6e8a..0000000 Binary files a/docs/reference/sawtooth-6.png and /dev/null differ diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 050e5eb..c6756a9 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -67,7 +67,7 @@ n and i are disregarded." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 5551d82..d5ef9e7 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -68,7 +68,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index bb898b8..f5044e7 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -68,7 +68,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html deleted file mode 100644 index 45d35c4..0000000 --- a/docs/reference/sum_periods.html +++ /dev/null @@ -1,153 +0,0 @@ - - - - - - - - -Sum up values according to FOCUS periods — sum_periods • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Sum up values according to FOCUS periods

    - Source: R/PELMO_runs.R - -
    - -
    - -

    Sum up values according to FOCUS periods

    - -
    - - 
    sum_periods(annual, interval)
    - -

    Arguments

    - - - - - - - - - - -
    annual

    The annual flux as obtained by get_flux

    interval

    The interval in years

    - - -
    - -
    - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown.

    -
    - -
    -
    - - - - - - diff --git a/docs/reference/twa.html b/docs/reference/twa.html index 016380a..2c21c67 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -68,7 +68,7 @@ is after one window has passed." /> pfm - 0.5.6 + 0.5.7 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 285ffb2..6eff936 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -3,6 +3,12 @@ https://pkgdown.jrwb.de/pfm/index.html + + https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html + + + https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html + https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd new file mode 100644 index 0000000..f2e8c1c --- /dev/null +++ b/man/EFSA_GW_interception_2014.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/EFSA_GW_interception_2014.R +\docType{data} +\name{EFSA_GW_interception_2014} +\alias{EFSA_GW_interception_2014} +\title{Subset of EFSA crop interception default values for groundwater modelling} +\format{A matrix containing interception values, currently only for some selected crops} +\source{ +European Food Safety Authority (2014) EFSA Guidance Document for +evaluating laboratory and field dissipation studies to obtain DegT50 values +of active substances of plant protection products and transformation +products of these active substances in soil. \emph{EFSA Journal} +\bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 +} +\description{ +Subset of EFSA crop interception default values for groundwater modelling +} +\examples{ +\dontrun{ + # This is the code that was used to define the data + bbch <- paste0(0:9, "x") + crops <- c( + "Beans (field + vegetable)", + "Peas", + "Summer oilseed rape", "Winter oilseed rape", + "Tomatoes", + "Spring cereals", "Winter cereals") + EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), + dimnames = list(Crop = crops, BBCH = bbch)) + EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- + c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) + EFSA_GW_interception_2014["Peas", ] <- + c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) + EFSA_GW_interception_2014["Summer oilseed rape", ] <- + c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) + EFSA_GW_interception_2014["Winter oilseed rape", ] <- + c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) + EFSA_GW_interception_2014["Tomatoes", ] <- + c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) + EFSA_GW_interception_2014["Spring cereals", ] <- + c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) + EFSA_GW_interception_2014["Winter cereals", ] <- + c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) + save(EFSA_GW_interception_2014, + file = "../data/EFSA_GW_interception_2014.RData") +} +EFSA_GW_interception_2014 +} diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd new file mode 100644 index 0000000..b1ab30f --- /dev/null +++ b/man/EFSA_washoff_2017.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/EFSA_washoff_2017.R +\docType{data} +\name{EFSA_washoff_2017} +\alias{EFSA_washoff_2017} +\title{Subset of EFSA crop washoff default values} +\format{A matrix containing wash-off factors, currently only for some selected crops} +\source{ +European Food Safety Authority (2017) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. \emph{EFSA Journal} \bold{15}(10) 4982 + doi:10.2903/j.efsa.2017.4982 +} +\description{ +Subset of EFSA crop washoff default values +} +\examples{ +\dontrun{ + # This is the code that was used to define the data + bbch <- paste0(0:9, "x") + crops <- c( + "Beans (field + vegetable)", + "Peas", + "Summer oilseed rape", "Winter oilseed rape", + "Tomatoes", + "Spring cereals", "Winter cereals") + EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), + dimnames = list(Crop = crops, BBCH = bbch)) + EFSA_washoff_2017["Beans (field + vegetable)", ] <- + c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) + EFSA_washoff_2017["Peas", ] <- + c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) + EFSA_washoff_2017["Summer oilseed rape", ] <- + c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) + EFSA_washoff_2017["Winter oilseed rape", ] <- + c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) + EFSA_washoff_2017["Tomatoes", ] <- + c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) + EFSA_washoff_2017["Spring cereals", ] <- + c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) + EFSA_washoff_2017["Winter cereals", ] <- + c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) + save(EFSA_washoff_2017, + file = "../data/EFSA_washoff_2017.RData") +} +EFSA_washoff_2017 +} diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd index edb239e..c9f8ed4 100644 --- a/man/PEC_sw_drainage_UK.Rd +++ b/man/PEC_sw_drainage_UK.Rd @@ -34,6 +34,16 @@ published on the CRC website \examples{ PEC_sw_drainage_UK(150, Koc = 100) } +\references{ +HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm} + accessed 2019-09-27 + + Drainage PECs Version 1.0 (2015) Spreadsheet published at + \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx} + accessed 2019-09-27 +} \author{ Johannes Ranke } diff --git a/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd index c7fd12d..797332b 100644 --- a/man/SSLRC_mobility_classification.Rd +++ b/man/SSLRC_mobility_classification.Rd @@ -14,11 +14,22 @@ A list containing the classification and the percentage of the compound transported per 10 mm drain water } \description{ -This implements the method specified in the UK data requirements handbook and was +This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website } \examples{ SSLRC_mobility_classification(100) +SSLRC_mobility_classification(10000) +} +\references{ +HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm} + accessed 2019-09-27 + + Drainage PECs Version 1.0 (2015) Spreadsheet published at + \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx} + accessed 2019-09-27 } \author{ Johannes Ranke diff --git a/tests/testthat/test_UK_drainage.R b/tests/testthat/test_UK_drainage.R index 859f145..2789819 100644 --- a/tests/testthat/test_UK_drainage.R +++ b/tests/testthat/test_UK_drainage.R @@ -2,7 +2,10 @@ library(pfm) context("UK drainage PEC calculations") test_that("The mobility classification and the drained percentage are correct", { - # Expected results are from the CRD drainage calculator, retrieved 2015-06-11 + # Expected results are from the CRD drainage calculator, retrieved 2019-09-27 + # The last test result was 0.01 when this test was written 2015-06-11. + # I assume that the value of 0.008 was displayed as 0.01 by the spreadsheet + # available at that time expect_equivalent(SSLRC_mobility_classification(1), list("Very mobile", 1.9)) expect_equivalent(SSLRC_mobility_classification(15), list("Mobile", 1.9)) @@ -12,7 +15,7 @@ test_that("The mobility classification and the drained percentage are correct", expect_equivalent(SSLRC_mobility_classification(100), list("Moderately mobile", 0.7)) expect_equivalent(SSLRC_mobility_classification(800), list("Slightly mobile", 0.5)) expect_equivalent(SSLRC_mobility_classification(2000), list("Slightly mobile", 0.02)) - expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.01)) + expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.008)) }) test_that("UK drainflow PECs are correct", { -- cgit v1.2.1