From e3bc264df69f892e9ad990be22d3ec1b22041daa Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 17 Jun 2020 13:37:59 +0200 Subject: TSCF estimation equations, update docs Briggs et al. (1982) and Dettenmaier et al. (2009) --- ChangeLog | 9 ++ DESCRIPTION | 2 +- NAMESPACE | 1 + R/TSCF.R | 31 ++++ _pkgdown.yml | 1 + docs/404.html | 30 ++-- docs/authors.html | 26 ++-- docs/bootstrap-toc.css | 60 +++++++ docs/bootstrap-toc.js | 159 +++++++++++++++++++ docs/index.html | 28 ++-- docs/pkgdown.css | 121 ++++++++++++++- docs/pkgdown.js | 5 - docs/pkgdown.yml | 3 +- docs/reference/EFSA_GW_interception_2014.html | 53 +++---- docs/reference/EFSA_washoff_2017.html | 53 +++---- docs/reference/FOCUS_GW_scenarios_2012.html | 53 +++---- docs/reference/FOCUS_Step_12_scenarios.html | 36 ++--- docs/reference/TOXSWA_cwa.html | 67 ++++---- docs/reference/TSCF-1.png | Bin 0 -> 24506 bytes docs/reference/TSCF.html | 181 ++++++++++++++++++++++ docs/reference/drift_data_JKI.html | 56 +++---- docs/reference/index.html | 74 ++++++--- docs/reference/perc_runoff_exposit.html | 56 ++++--- docs/reference/perc_runoff_reduction_exposit.html | 56 ++++--- docs/reference/soil_scenario_data_EFSA_2015.html | 53 +++---- docs/reference/soil_scenario_data_EFSA_2017.html | 53 +++---- docs/sitemap.xml | 3 + man/EFSA_GW_interception_2014.Rd | 4 +- man/EFSA_washoff_2017.Rd | 4 +- man/FOCUS_GW_scenarios_2012.Rd | 4 +- man/FOCUS_Step_12_scenarios.Rd | 6 +- man/TOXSWA_cwa.Rd | 9 +- man/TSCF.Rd | 37 +++++ man/drift_data_JKI.Rd | 6 +- man/perc_runoff_exposit.Rd | 6 +- man/perc_runoff_reduction_exposit.Rd | 6 +- man/soil_scenario_data_EFSA_2015.Rd | 6 +- man/soil_scenario_data_EFSA_2017.Rd | 6 +- test.log | 27 ++-- 39 files changed, 1008 insertions(+), 383 deletions(-) create mode 100644 R/TSCF.R create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js create mode 100644 docs/reference/TSCF-1.png create mode 100644 docs/reference/TSCF.html create mode 100644 man/TSCF.Rd diff --git a/ChangeLog b/ChangeLog index fcab6a0..c6701ea 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,12 @@ +commit d81550d0cccae824cc748de48e7fd50ea8d8033a +Author: Johannes Ranke +Date: 2020-04-16 18:02:18 +0200 + + Make na.rm = FALSE the default for geomean() + + This makes more sense and is in line with mean() from base R. Adapt + tests and update docs. + commit 4bc95b3e4aae22e4052e0a4c905a9227c909e2cd Author: Johannes Ranke Date: 2020-02-19 07:49:08 +0100 diff --git a/DESCRIPTION b/DESCRIPTION index 4d471dc..d125af4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,4 +32,4 @@ LazyLoad: yes LazyData: yes Encoding: UTF-8 URL: https://pkdown.jrwb.de/pfm -RoxygenNote: 7.0.2 +RoxygenNote: 7.1.0 diff --git a/NAMESPACE b/NAMESPACE index fffadd7..e24d712 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -26,6 +26,7 @@ export(PEC_sw_sed) export(SFO_actual_twa) export(SSLRC_mobility_classification) export(TOXSWA_cwa) +export(TSCF) export(chent_focus_sw) export(endpoint) export(geomean) diff --git a/R/TSCF.R b/R/TSCF.R new file mode 100644 index 0000000..bfb4c42 --- /dev/null +++ b/R/TSCF.R @@ -0,0 +1,31 @@ +#' Estimation of the transpiration stream concentration factor +#' +#' The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured +#' log Kow for neutral pH must be available in order to apply the Briggs +#' equation. It is not clarified when it can be regarded reliable, but the +#' equation is stated to be produced for non-ionic compounds, suggesting that +#' the compound should not be ionogenic (weak acid/base) +#' or ionic. +#' +#' The Dettenmaier equation is given to show that other views on the subject exist. +#' @references FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. +#' Version 2.2, May 2014 +#' Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake +#' by plant roots. Environ. Sci. Technol 43, 324 - 329 +#' @param log_Kow The decadic logarithm of the octanol-water partition constant +#' @param method Short name of the estimation method. +#' @export +#' @examples +#' plot(TSCF, -1, 5, xlab = "log Kow", ylab = "TSCF", ylim = c(0, 1.1)) +#' TSCF_2 <- function(x) TSCF(x, method = "dettenmaier09") +#' curve(TSCF_2, -1, 5, add = TRUE, lty = 2) +#' legend("topright", lty = 1:2, bty = "n", +#' legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)")) +TSCF <- function(log_Kow, method = c("briggs82", "dettenmaier09")) { + method <- match.arg(method) + TSCF <- switch(method, + briggs82 = 0.784 * exp(- (log_Kow - 1.78)^2 / 2.44), + dettenmaier09 = 11 /( 11 + 2.6^log_Kow) + ) + return(TSCF) +} diff --git a/_pkgdown.yml b/_pkgdown.yml index b40e223..71f3c65 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -19,6 +19,7 @@ reference: - SFO_actual_twa - FOMC_actual_twa - set_nd_nq + - TSCF - title: Predicted environmental concentrations in soil contents: - PEC_soil diff --git a/docs/404.html b/docs/404.html index f42956b..37f381e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -53,7 +57,7 @@ - +
+ +
@@ -115,7 +125,7 @@ Content not found. Please use links in the navbar.
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/authors.html b/docs/authors.html index 05bd9d3..da75377 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -53,7 +57,7 @@ - +
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
    '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
  • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/index.html b/docs/index.html index 2e42649..6ffb312 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,21 +6,21 @@ Utilities for Pesticide Fate Modelling • pfm - - - - + + + + + - - +
    -
    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 6b2cbe1..8b55d14 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -8,23 +8,29 @@ A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm + - + - - + + + + + + + - - + + - + - - + + @@ -32,11 +38,11 @@ - + - + @@ -53,7 +59,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> - +
    -

    Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The soil definitions are from page 46ff. from FOCUS (2012).

    - 
    FOCUS_GW_scenarios_2012
    - + +

    Format

    An object of class list of length 2.

    -

    References

    FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. FOrum for the Co-ordination of pesticde fate models and their USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf

    -

    Examples

    FOCUS_GW_scenarios_2012
    #> $names
@@ -186,17 +188,10 @@ soil definitions are from page 46ff. from FOCUS (2012).
    
 #> 51      Thi     Ck1      6    7.8      32.9    0.18     0.0
 #>
    - @@ -207,7 +202,7 @@ soil definitions are from page 46ff. from FOCUS (2012).

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 77045f1..bbfb592 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ The text file is not included in the package as its licence is not clear." /> - +
    - @@ -309,7 +309,7 @@ The text file is not included in the package as its licence is not clear.

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index cedb023..9f9e3c3 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> - +
    - @@ -259,7 +256,7 @@ for the requested moving window sizes in days.

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/TSCF-1.png b/docs/reference/TSCF-1.png new file mode 100644 index 0000000..efa9e0a Binary files /dev/null and b/docs/reference/TSCF-1.png differ diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html new file mode 100644 index 0000000..b635ba2 --- /dev/null +++ b/docs/reference/TSCF.html @@ -0,0 +1,181 @@ + + + + + + + + +Estimation of the transpiration stream concentration factor — TSCF • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Estimation of the transpiration stream concentration factor

    + + +
    + +
    +

    The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured +log Kow for neutral pH must be available in order to apply the Briggs +equation. It is not clarified when it can be regarded reliable, but the +equation is stated to be produced for non-ionic compounds, suggesting that +the compound should not be ionogenic (weak acid/base) +or ionic.

    +
    + + 
    TSCF(log_Kow, method = c("briggs82", "dettenmaier09"))
    + +

    Arguments

    + + + + + + + + + + +
    log_Kow

    The decadic logarithm of the octanol-water partition constant

    method

    Short name of the estimation method.

    + +

    Details

    + +

    The Dettenmaier equation is given to show that other views on the subject exist.

    +

    References

    + +

    FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. + Version 2.2, May 2014 +Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake +by plant roots. Environ. Sci. Technol 43, 324 - 329

    + +

    Examples

    + 
    plot(TSCF, -1, 5, xlab = "log Kow", ylab = "TSCF", ylim = c(0, 1.1))
    TSCF_2 <- function(x) TSCF(x, method = "dettenmaier09")
+curve(TSCF_2, -1, 5, add = TRUE, lty = 2)
    legend("topright", lty = 1:2, bty = "n",
+  legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)"))
    +
    + +
    + + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown 1.5.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 08d8399..dd78451 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -9,23 +9,29 @@ Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI • pfm + - + - - + + + + + + + - - + + - + - - + + @@ -33,12 +39,12 @@ published by the JKI — drift_data_JKI • pfm + - - + @@ -55,7 +61,7 @@ published by the German Julius-Kühn Institute (JKI)." /> - +
    -

    Deposition from spray drift expressed as percent of the applied dose as published by the German Julius-Kühn Institute (JKI).

    -
    - + +

    Format

    A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late (Obstbau frueh, spaet).

    -

    Source

    JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved @@ -130,7 +133,6 @@ on 2015-06-11

    Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141

    -

    Details

    The data were extracted from the spreadsheet cited below using the R code @@ -146,7 +148,6 @@ these values are used for spray applications with handheld/knapsack equipment (tragbare Spritz- und Sprühgerate).

    Values for non-professional use listed in the JKI spreadsheet were not included.

    -

    Examples

    
@@ -389,19 +390,10 @@ included.
    
 #>       50      0.06                       0.001           NA
 #>
    - @@ -412,7 +404,7 @@ included.

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 0608dd9..944f1f2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -53,7 +57,7 @@ - +
    - @@ -393,7 +427,7 @@ water concentrations

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index a0f723f..38c1f70 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -8,23 +8,29 @@ Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • pfm + - + - - + + + + + + + - - + + - + - - + + @@ -32,10 +38,10 @@ - + - + @@ -52,7 +58,7 @@ - +
    -

    A table of the loss percentages used in Exposit 3 for the twelve different Koc classes

    -
    - + +

    Format

    A data frame with percentage values for the dissolved fraction and the fraction - bound to eroding particles, with Koc classes used as row names

    + bound to eroding particles, with Koc classes used as row names

    Koc_lower_bound

    The lower bound of the Koc class

    dissolved

    The percentage of the applied substance transferred to an adjacent water body in the dissolved phase

    @@ -121,12 +125,11 @@ adjacent water body bound to eroding particles

    - +

    Source

    Excel 3.02 spreadsheet available from https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html

    -

    Examples

    print(perc_runoff_exposit)
    #>              Koc_lower_bound dissolved bound
@@ -143,17 +146,10 @@
 #> >20000-50000           20000     0.014 0.291
 #> >50000                 50000     0.001 0.451
    - @@ -164,7 +160,7 @@
    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index baded1c..947d4c5 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -8,23 +8,29 @@ Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • pfm + - + - - + + + + + + + - - + + - + - - + + @@ -32,10 +38,10 @@ - + - + @@ -52,7 +58,7 @@ - +
    -

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

    - 
    perc_runoff_reduction_exposit
    - + +

    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.

    +from which the values were taken.

    dissolved

    The reduction percentage for the dissolved phase

    bound

    The reduction percentage for the particulate phase

    - +

    Source

    Excel 3.02 spreadsheet available from https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html

    Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.

    -

    Examples

    print(perc_runoff_reduction_exposit)
    #> $`3.02`
@@ -158,17 +161,10 @@ from which the values were taken.
    
 #> 20 m           97.5  97.5
 #>
    - @@ -179,7 +175,7 @@ from which the values were taken.

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index d5ef9e7..cb3cf14 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -8,23 +8,29 @@ Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm + - + - - + + + + + + + - - + + - + - - + + @@ -32,12 +38,12 @@ - + - + @@ -54,7 +60,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> - +
    -

    Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the scenario and model adjustment factors from p. 15 and p. 17 are included.

    -
    - + +

    Format

    A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. rho is the dry bulk density of the top soil.

    -

    Source

    EFSA (European Food Safety Authority) (2015) @@ -127,7 +130,6 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.

    of active substances of plant protection products and transformation products of these active substances in soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093

    -

    Examples

    if (FALSE) {
@@ -165,17 +167,10 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.
    
 #> CLC     4
 #> CLS     4
    - @@ -186,7 +181,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index f5044e7..7e8044e 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -8,23 +8,29 @@ Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm + - + - - + + + + + + + - - + + - + - - + + @@ -32,12 +38,12 @@ - + - + @@ -54,7 +60,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> - +
    -

    Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included.

    -
    - + +

    Format

    A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. rho is the dry bulk density of the top soil.

    -

    Source

    EFSA (European Food Safety Authority) (2017) @@ -127,7 +130,6 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.

    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

    soil_scenario_data_EFSA_2017
    #>        Zone Country T_arit T_arr Texture  f_om theta_fc   rho f_sce f_mod
@@ -145,17 +147,10 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.
    
 #> CLC Châteaudun  589
 #> CLS    Sevilla  526
    - @@ -166,7 +161,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.1.

    diff --git a/docs/sitemap.xml b/docs/sitemap.xml index b619e4d..0c507b6 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -57,6 +57,9 @@ https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html + + https://pkgdown.jrwb.de/pfm/reference/TSCF.html + https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd index f2e8c1c..2334d7f 100644 --- a/man/EFSA_GW_interception_2014.Rd +++ b/man/EFSA_GW_interception_2014.Rd @@ -4,7 +4,9 @@ \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} +\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 diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd index b1ab30f..e153fbe 100644 --- a/man/EFSA_washoff_2017.Rd +++ b/man/EFSA_washoff_2017.Rd @@ -4,7 +4,9 @@ \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} +\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 diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd index 4529816..53d1d3c 100644 --- a/man/FOCUS_GW_scenarios_2012.Rd +++ b/man/FOCUS_GW_scenarios_2012.Rd @@ -4,7 +4,9 @@ \name{FOCUS_GW_scenarios_2012} \alias{FOCUS_GW_scenarios_2012} \title{A very small subset of the FOCUS Groundwater scenario definitions} -\format{An object of class \code{list} of length 2.} +\format{ +An object of class \code{list} of length 2. +} \usage{ FOCUS_GW_scenarios_2012 } diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd index 0547d61..02963bf 100644 --- a/man/FOCUS_Step_12_scenarios.Rd +++ b/man/FOCUS_Step_12_scenarios.Rd @@ -4,10 +4,12 @@ \name{FOCUS_Step_12_scenarios} \alias{FOCUS_Step_12_scenarios} \title{Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator} -\format{A list containing the scenario names in a character vector called 'names', +\format{ +A list containing the scenario names in a character vector called 'names', the drift percentiles in a matrix called 'drift', interception percentages in a matrix called 'interception' and the runoff/drainage percentages for Step 2 - calculations in a matrix called 'rd'.} + calculations in a matrix called 'rd'. +} \description{ The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear. diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index eb3fe38..6a95a0b 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -4,7 +4,9 @@ \name{TOXSWA_cwa} \alias{TOXSWA_cwa} \title{R6 class for holding TOXSWA water concentration data and associated statistics} -\format{An \code{\link{R6Class}} generator object.} +\format{ +An \code{\link{R6Class}} generator object. +} \description{ An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. @@ -67,6 +69,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{
    }} \if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{TOXSWA_cwa$new( @@ -82,6 +85,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{
    }} \if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-moving_windows}{}}} \subsection{Method \code{moving_windows()}}{ \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{
    }} @@ -90,6 +94,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{
    }} \if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-get_events}{}}} \subsection{Method \code{get_events()}}{ \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{
    }} @@ -98,6 +103,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{
    }} \if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-print}{}}} \subsection{Method \code{print()}}{ \subsection{Usage}{ \if{html}{\out{
    }}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{
    }} @@ -106,6 +112,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{
    }} \if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/TSCF.Rd b/man/TSCF.Rd new file mode 100644 index 0000000..e4cefdc --- /dev/null +++ b/man/TSCF.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TSCF.R +\name{TSCF} +\alias{TSCF} +\title{Estimation of the transpiration stream concentration factor} +\usage{ +TSCF(log_Kow, method = c("briggs82", "dettenmaier09")) +} +\arguments{ +\item{log_Kow}{The decadic logarithm of the octanol-water partition constant} + +\item{method}{Short name of the estimation method.} +} +\description{ +The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured +log Kow for neutral pH must be available in order to apply the Briggs +equation. It is not clarified when it can be regarded reliable, but the +equation is stated to be produced for non-ionic compounds, suggesting that +the compound should not be ionogenic (weak acid/base) +or ionic. +} +\details{ +The Dettenmaier equation is given to show that other views on the subject exist. +} +\examples{ +plot(TSCF, -1, 5, xlab = "log Kow", ylab = "TSCF", ylim = c(0, 1.1)) +TSCF_2 <- function(x) TSCF(x, method = "dettenmaier09") +curve(TSCF_2, -1, 5, add = TRUE, lty = 2) +legend("topright", lty = 1:2, bty = "n", + legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)")) +} +\references{ +FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. + Version 2.2, May 2014 +Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake +by plant roots. Environ. Sci. Technol 43, 324 - 329 +} diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd index 090910f..181eca6 100644 --- a/man/drift_data_JKI.Rd +++ b/man/drift_data_JKI.Rd @@ -5,9 +5,11 @@ \alias{drift_data_JKI} \title{Deposition from spray drift expressed as percent of the applied dose as published by the JKI} -\format{A list currently containing matrices with spray drift percentage +\format{ +A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late -(Obstbau frueh, spaet).} +(Obstbau frueh, spaet). +} \source{ JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd index 3f072df..0bd2827 100644 --- a/man/perc_runoff_exposit.Rd +++ b/man/perc_runoff_exposit.Rd @@ -3,7 +3,8 @@ \name{perc_runoff_exposit} \alias{perc_runoff_exposit} \title{Runoff loss percentages as used in Exposit 3} -\format{A data frame with percentage values for the dissolved fraction and the fraction +\format{ +A data frame with percentage values for the dissolved fraction and the fraction bound to eroding particles, with Koc classes used as row names \describe{ \item{Koc_lower_bound}{The lower bound of the Koc class} @@ -11,7 +12,8 @@ adjacent water body in the dissolved phase} \item{bound}{The percentage of the applied substance transferred to an adjacent water body bound to eroding particles} - }} + } +} \source{ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd index 016f9dd..0aa50c1 100644 --- a/man/perc_runoff_reduction_exposit.Rd +++ b/man/perc_runoff_reduction_exposit.Rd @@ -4,14 +4,16 @@ \name{perc_runoff_reduction_exposit} \alias{perc_runoff_reduction_exposit} \title{Runoff reduction percentages as used in Exposit} -\format{A named list of data frames with reduction percentage values for the +\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. \describe{ \item{dissolved}{The reduction percentage for the dissolved phase} \item{bound}{The reduction percentage for the particulate phase} - }} + } +} \source{ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd index 64c00a8..dfad4aa 100644 --- a/man/soil_scenario_data_EFSA_2015.Rd +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -4,9 +4,11 @@ \name{soil_scenario_data_EFSA_2015} \alias{soil_scenario_data_EFSA_2015} \title{Properties of the predefined scenarios from the EFSA guidance from 2015} -\format{A data frame with one row for each scenario. Row names are the scenario codes, +\format{ +A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} + mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. +} \source{ EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd index aeaacac..f6de290 100644 --- a/man/soil_scenario_data_EFSA_2017.Rd +++ b/man/soil_scenario_data_EFSA_2017.Rd @@ -4,9 +4,11 @@ \name{soil_scenario_data_EFSA_2017} \alias{soil_scenario_data_EFSA_2017} \title{Properties of the predefined scenarios from the EFSA guidance from 2017} -\format{A data frame with one row for each scenario. Row names are the scenario codes, +\format{ +A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} + mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. +} \source{ EFSA (European Food Safety Authority) (2017) EFSA guidance document for predicting environmental concentrations diff --git a/test.log b/test.log index 9dee465..4744951 100644 --- a/test.log +++ b/test.log @@ -3,23 +3,30 @@ Loading required package: R6 Loading required package: mkin Testing pfm ✔ | OK F W S | Context - ⠏ | 0 | Exposit calculations ✔ | 7 | Exposit calculations - ⠏ | 0 | Geometric mean calculation ✔ | 6 | Geometric mean calculation - ⠏ | 0 | Check max_twa for parent mkinfit models against analytical solutions ⠋ | 1 | Check max_twa for parent mkinfit models against analytical solutions ✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [1.9 s] ⠏ | 0 | Simple PEC sediment calculations ✔ | 1 | Simple PEC sediment calculations - ⠏ | 0 | Simple PEC soil calculations ⠙ | 2 | Simple PEC soil calculations ✔ | 17 | Simple PEC soil calculations [0.2 s] + ⠏ | 0 | Simple PEC soil calculations ⠙ | 2 | Simple PEC soil calculations ✔ | 17 | Simple PEC soil calculations [0.3 s] ⠏ | 0 | Simple PEC surface water calculations with drift entry ✔ | 2 | Simple PEC surface water calculations with drift entry - ⠏ | 0 | Processing of residue series ✔ | 11 | Processing of residue series ⠏ | 0 | Actual and time weighted average concentrations for SFO kinetics ✔ | 1 | Actual and time weighted average concentrations for SFO kinetics + ⠏ | 0 | Read and analyse TOXSWA cwa files ⠋ | 1 | Read and analyse TOXSWA cwa files ⠸ | 4 | Read and analyse TOXSWA cwa files ⠼ | 5 | Read and analyse TOXSWA cwa files ⠴ | 6 | Read and analyse TOXSWA cwa files ✖ | 6 1 | Read and analyse TOXSWA cwa files [6.4 s] +──────────────────────────────────────────────────────────────────────────────────────────────────── +test_TOXSWA.R:68: failure: Getting events and moving window analysis works +H_sw_R1_stream$windows has changed from known value recorded in 'H_sw_R1_stream_windows.rds'. +Component "window": Modes: character, numeric +Component "window": Attributes: < target is NULL, current is list > +Component "window": target is character, current is factor +──────────────────────────────────────────────────────────────────────────────────────────────────── + ⠏ | 0 | UK drainage PEC calculations ✔ | 12 | UK drainage PEC calculations + ⠏ | 0 | Exposit calculations ✔ | 7 | Exposit calculations + ⠏ | 0 | Geometric mean calculation ✔ | 6 | Geometric mean calculation + ⠏ | 0 | Check max_twa for parent mkinfit models against analytical solutions ⠋ | 1 | Check max_twa for parent mkinfit models against analytical solutions ✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [2.1 s] + ⠏ | 0 | Processing of residue series ✔ | 11 | Processing of residue series ⠏ | 0 | FOCUS Step 1 calculations ⠹ | 3 | FOCUS Step 1 calculations ✔ | 9 | FOCUS Step 1 calculations [0.1 s] ⠏ | 0 | FOCUS Steps 12 input files ✔ | 8 | FOCUS Steps 12 input files - ⠏ | 0 | Read and analyse TOXSWA cwa files ⠋ | 1 | Read and analyse TOXSWA cwa files ⠸ | 4 | Read and analyse TOXSWA cwa files ⠼ | 5 | Read and analyse TOXSWA cwa files ⠴ | 6 | Read and analyse TOXSWA cwa files ✔ | 7 | Read and analyse TOXSWA cwa files [5.5 s] - ⠏ | 0 | UK drainage PEC calculations ✔ | 12 | UK drainage PEC calculations ══ Results ═════════════════════════════════════════════════════════════════════════════════════════ -Duration: 7.9 s +Duration: 9.3 s -OK: 82 -Failed: 0 +OK: 81 +Failed: 1 Warnings: 0 Skipped: 0 -- cgit v1.2.1