From 197606de234a936751ac3c1db2e4feb3fa117a92 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jun 2018 02:48:44 +0200 Subject: Rebuild docs with pkgdown 1.1.0 --- docs/authors.html | 35 +- docs/index.html | 51 ++- docs/pkgdown.css | 50 ++- docs/pkgdown.js | 160 ++++---- docs/reference/FOCUS_GW_scenarios_2012.html | 35 +- docs/reference/FOCUS_PELMO_crop_sze_names.html | 35 +- docs/reference/FOCUS_PELMO_crops.html | 35 +- docs/reference/FOCUS_PELMO_location_codes.html | 35 +- docs/reference/FOCUS_Step_12_scenarios.html | 35 +- docs/reference/GUS.html | 37 +- docs/reference/PEC_soil.html | 37 +- docs/reference/PEC_sw_drainage_UK.html | 37 +- docs/reference/PEC_sw_drift.html | 37 +- docs/reference/PEC_sw_exposit_runoff.html | 41 +- docs/reference/PEC_sw_focus.html | 37 +- docs/reference/PEC_sw_sed.html | 37 +- docs/reference/PELMO_path.html | 37 +- docs/reference/PELMO_runs.html | 39 +- docs/reference/SFO_actual_twa.html | 37 +- docs/reference/SSLRC_mobility_classification.html | 37 +- docs/reference/TOXSWA_cwa.html | 35 +- docs/reference/chent_focus_sw.html | 37 +- docs/reference/create_run_list.html | 37 +- docs/reference/drift_data_JKI.html | 37 +- docs/reference/endpoint.html | 37 +- docs/reference/focus_80th.html | 37 +- docs/reference/geomean.html | 37 +- docs/reference/get_flux.html | 37 +- docs/reference/get_interval.html | 37 +- docs/reference/index.html | 448 +++++++++++++--------- docs/reference/max_twa.html | 39 +- docs/reference/one_box-1.png | Bin 15066 -> 15900 bytes docs/reference/one_box-2.png | Bin 14519 -> 15306 bytes docs/reference/one_box-3.png | Bin 28566 -> 30090 bytes docs/reference/one_box.html | 43 ++- docs/reference/perc_runoff_exposit.html | 35 +- docs/reference/perc_runoff_reduction_exposit.html | 35 +- docs/reference/pesticide.txt | 10 + docs/reference/pfm_degradation.html | 37 +- docs/reference/plot.TOXSWA_cwa-1.png | Bin 20867 -> 21899 bytes docs/reference/plot.TOXSWA_cwa-2.png | Bin 20189 -> 21097 bytes docs/reference/plot.TOXSWA_cwa-3.png | Bin 21221 -> 22377 bytes docs/reference/plot.TOXSWA_cwa-4.png | Bin 21595 -> 22788 bytes docs/reference/plot.TOXSWA_cwa-5.png | Bin 14860 -> 16346 bytes docs/reference/plot.TOXSWA_cwa.html | 41 +- docs/reference/plot.one_box-1.png | Bin 15342 -> 16217 bytes docs/reference/plot.one_box-2.png | Bin 31171 -> 32580 bytes docs/reference/plot.one_box-3.png | Bin 35837 -> 37318 bytes docs/reference/plot.one_box.html | 43 ++- docs/reference/read.TOXSWA_cwa.html | 37 +- docs/reference/sawtooth-1.png | Bin 15868 -> 16254 bytes docs/reference/sawtooth-2.png | Bin 35837 -> 37318 bytes docs/reference/sawtooth.html | 41 +- docs/reference/soil_scenario_data_EFSA_2015.html | 35 +- docs/reference/sum_periods.html | 37 +- docs/reference/twa.html | 39 +- 56 files changed, 1599 insertions(+), 536 deletions(-) (limited to 'docs') diff --git a/docs/authors.html b/docs/authors.html index d08c687..0870c21 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -21,13 +21,19 @@ + + + - - - + + + + + + @@ -50,8 +56,12 @@ - pfm + + pfm + 0.4.5 + + @@ -75,15 +91,15 @@ -
-
+
+

Authors

  • -

    Johannes Ranke. Author, maintainer, copyright holder. +

    Johannes Ranke. Author, maintainer, copyright holder.

@@ -105,5 +121,8 @@
+ + + diff --git a/docs/index.html b/docs/index.html index 5b977a6..1558e8a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,8 @@ Utilities for Pesticide Fate Modelling • pfm - - + + @@ -29,8 +29,12 @@ - pfm + + pfm + 0.4.5 +
+
@@ -58,18 +69,18 @@

pfm

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:

-
This program is free software: you can redistribute it and/or modify it under
+
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
+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
+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/>

+this program. If not, see <http://www.gnu.org/licenses/>

Installation

@@ -92,13 +103,29 @@ this program. If not, see <http://www.gnu.org/license
@@ -113,5 +140,7 @@ this program. If not, see <http://www.gnu.org/license + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 181fe63..6ca2f37 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -1,13 +1,32 @@ -/* Sticker footer */ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + body > .container { display: flex; - padding-top: 60px; - min-height: calc(100vh); + height: 100%; flex-direction: column; + + padding-top: 60px; } body > .container .row { - flex: 1; + flex: 1 0 auto; } footer { @@ -16,6 +35,7 @@ footer { border-top: 1px solid #e5e5e5; color: #666; display: flex; + flex-shrink: 0; } footer p { margin-bottom: 0; @@ -38,6 +58,12 @@ img { max-width: 100%; } +/* Typographic tweaking ---------------------------------*/ + +.contents h1.page-header { + margin-top: calc(-60px + 1em); +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -68,7 +94,7 @@ a.anchor { .contents h1, .contents h2, .contents h3, .contents h4 { padding-top: 60px; - margin-top: -60px; + margin-top: -40px; } /* Static header placement on mobile devices */ @@ -108,7 +134,6 @@ a.anchor { /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} -.ref-index h2 {font-size: 20px;} .ref-index td {vertical-align: top;} .ref-index .alias {width: 40%;} @@ -192,3 +217,16 @@ a.sourceLine:hover { .hasCopyButton:hover button.btn-copy-ex { visibility: visible; } + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} + +/* vertical spacing after htmlwidgets */ +.html-widget { + margin-bottom: 10px; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 64b20df..de9bd72 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,94 +1,110 @@ -$(function() { - - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(function() { + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + + $('body').scrollspy({ + target: '#sidebar', + offset: 60 }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + var path = paths(links[i].pathname); + + var length = prefix_length(cur_path, path); + if (length > max_length) { + max_length = length; + pos = i; + } + } - var cur_path = paths(location.pathname); - $("#navbar ul li a").each(function(index, value) { - if (value.text == "Home") - return; - if (value.getAttribute("href") === "#") - return; - - var path = paths(value.pathname); - if (is_prefix(cur_path, path)) { - // Add class to parent
  • , and enclosing
  • if in dropdown - var menu_anchor = $(value); + // Add class to parent
  • , and enclosing
  • if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); menu_anchor.parent().addClass("active"); menu_anchor.closest("li.dropdown").addClass("active"); } }); -}); -function paths(pathname) { - var pieces = pathname.split("/"); - pieces.shift(); // always starts with / + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } - var end = pieces[pieces.length - 1]; - if (end === "index.html" || end === "") - pieces.pop(); - return(pieces); -} + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(0); -function is_prefix(needle, haystack) { - if (needle.length > haystack.lengh) - return(false); + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 1 : 0); + } - for (var i = 0; i < haystack.length; i++) { - if (needle[i] != haystack[i]) - return(false); - } + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } - return(true); -} + return(haystack.length); + } -/* Clipboard --------------------------*/ + /* Clipboard --------------------------*/ -function changeTooltipMessage(element, msg) { - var tooltipOriginalTitle=element.getAttribute('data-original-title'); - element.setAttribute('data-original-title', msg); - $(element).tooltip('show'); - element.setAttribute('data-original-title', tooltipOriginalTitle); -} + function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); + } -if(Clipboard.isSupported()) { - $(document).ready(function() { - var copyButton = ""; + if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = ""; - $(".examples").addClass("hasCopyButton"); + $(".examples, div.sourceCode").addClass("hasCopyButton"); - // Insert copy buttons: - $(copyButton).prependTo(".hasCopyButton"); + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); - // Initialize tooltips: - $('.btn-copy-ex').tooltip({container: 'body'}); + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); - // Initialize clipboard: - var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { - text: function(trigger) { - return trigger.parentNode.textContent; - } - }); + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); - clipboardBtnCopies.on('success', function(e) { - changeTooltipMessage(e.trigger, 'Copied!'); - e.clearSelection(); - }); + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); - clipboardBtnCopies.on('error', function() { - changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); }); - }); -} - + } +})(window.jQuery || window.$) diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 8b3ee87..3402035 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> - pfm + + pfm + 0.4.5 + + @@ -79,16 +95,20 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> -
    +

    A very small subset of the FOCUS Groundwater scenario definitions

    + Source: R/FOCUS_GW_scenarios_2012.R +
    +

    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
    @@ -191,5 +211,8 @@ soil definitions are from page 46ff. from FOCUS (2012).

    + + + diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html index 954a707..9297f2a 100644 --- a/docs/reference/FOCUS_PELMO_crop_sze_names.html +++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ files used for Beans (field) and Beans (vegetable) are the same." /> - pfm + + pfm + 0.4.5 +
    +
    @@ -81,18 +97,22 @@ files used for Beans (field) and Beans (vegetable) are the same." /> -
    +

    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
    @@ -135,5 +155,8 @@ files used for Beans (field) and Beans (vegetable) are the same.

    + + + diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html index 81783ba..2393e41 100644 --- a/docs/reference/FOCUS_PELMO_crops.html +++ b/docs/reference/FOCUS_PELMO_crops.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -57,8 +63,12 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> - pfm + + pfm + 0.4.5 +
    +
    @@ -82,12 +98,15 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> -
    +

    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 @@ -95,6 +114,7 @@ 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
    @@ -147,5 +167,8 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape.
    + + + diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html index 31084b8..d601243 100644 --- a/docs/reference/FOCUS_PELMO_location_codes.html +++ b/docs/reference/FOCUS_PELMO_location_codes.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ indexed by three letter acronyms." /> - pfm + + pfm + 0.4.5 +
    +
    @@ -79,16 +95,20 @@ indexed by three letter acronyms." /> -
    +

    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
    @@ -125,5 +145,8 @@ indexed by three letter acronyms.

    + + + diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 9bd7165..294846d 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ The text file is not included in the package as its licence is not clear." /> - pfm + + pfm + 0.4.5 +
    +
    @@ -79,16 +95,20 @@ The text file is not included in the package as its licence is not clear." /> -
    +

    Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

    + Source: R/FOCUS_Step_12_scenarios.R +
    +

    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.

    +

    Format

    @@ -294,5 +314,8 @@ The text file is not included in the package as its licence is not clear.

    + + + diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 98bed51..3fa93c9 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -21,18 +21,24 @@ + + + - - - + + + + + + @@ -55,8 +61,12 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> - pfm + + pfm + 0.4.5 +
    +
    @@ -80,17 +96,21 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> -
    +

    Groundwater ubiquity score based on Gustafson (1989)

    + Source: R/GUS.R +
    +

    The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

    + 
    GUS(...)
 
@@ -105,7 +125,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$
    
 # S3 method for GUS_result
 print(x, ..., digits = 1)
    -

    Arguments

    +

    Arguments

    @@ -219,5 +239,8 @@ Johannes Ranke + + + diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index a706729..65c8519 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> - pfm + + pfm + 0.4.5 + + @@ -81,18 +97,22 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> -
    +

    Calculate predicted environmental concentrations in soil

    + Source: R/PEC_soil.R +
    +

    This is a basic calculation of a contaminant concentration in bulk soil based on complete, instantaneous mixing. If an interval is given, an attempt is made at calculating a long term maximum concentration using the concepts layed out for example in the PPR panel opinion (EFSA 2012).

    + 
    PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
   PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA,
@@ -100,7 +120,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012).
    
   Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default",
   "EFSA_2015"), porewater = FALSE)
    -

    Arguments

    +

    Arguments

    @@ -276,5 +296,8 @@ Johannes Ranke + + + diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 7ad2c12..6eb042e 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ published on the CRC website" /> - pfm + + pfm + 0.4.5 + + @@ -79,21 +95,25 @@ published on the CRC website" /> -
    +

    Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

    + Source: R/PEC_sw_drainage_UK.R +
    +

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

    + 
    PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL,
   soil_DT50 = NULL, model = NULL, model_parms = NULL)
    -

    Arguments

    +

    Arguments

    @@ -164,5 +184,8 @@ Johannes Ranke + + + diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index 6a567fe..fa9a968 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -21,18 +21,24 @@ + + + - - - + + + + + + @@ -55,8 +61,12 @@ with input via spray drift." /> - pfm + + pfm + 0.4.5 + + @@ -80,23 +96,27 @@ with input via spray drift." /> -
    +

    Calculate predicted environmental concentrations in surface water due to drift

    + Source: R/PEC_sw_drift.R +
    +

    This is a basic, vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing with input via spray drift.

    + 
    PEC_sw_drift(rate, applications = 1, water_depth = 30,
   drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
   distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
    -

    Arguments

    +

    Arguments

    @@ -176,5 +196,8 @@ Johannes Ranke + + + diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index a99821d..37ba843 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -21,17 +21,23 @@ + + + - - - + + + +in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not implemented." /> + + + @@ -54,8 +60,12 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp - pfm + + pfm + 0.4.5 + + @@ -79,22 +95,26 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp -
    +

    Calculate PEC surface water due to runoff and erosion as in Exposit 3

    + Source: R/PEC_sw_exposit_runoff.R +
    +

    This is a reimplementation of the calculation described in the Exposit 3.01 spreadsheet file, in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not implemented.

    + 
    PEC_sw_exposit_runoff(rate, Koc, DT50 = Inf, t_runoff = 3,
   exposit_reduction_version = c("3.01", "2.0"), V_ditch = 30,
   V_event = 100)
    -

    Arguments

    +

    Arguments

    @@ -144,7 +164,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp

    See also

    -

    perc_runoff_exposit for runoff loss percentages and perc_runoff_reduction_exposit for runoff reduction percentages used

    +

    perc_runoff_exposit for runoff loss percentages and perc_runoff_reduction_exposit for runoff reduction percentages used

    Examples

    @@ -196,5 +216,8 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp + + + diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 0c9516d..5e66d25 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -59,8 +65,12 @@ to be used with the FOCUS calculator." /> - pfm + + pfm + 0.4.5 + + @@ -84,12 +100,15 @@ to be used with the FOCUS calculator." /> -
    +

    Calculate PEC surface water at FOCUS Step 1

    + Source: R/PEC_sw_focus.R +
    +

    This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, authored by Michael Klein, in R. Note that results for multiple @@ -99,6 +118,7 @@ this implementation. Only Step 1 PECs are calculated. However, input files are generated that are suitable as input also for Step 2 to be used with the FOCUS calculator.

    + 
    PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL,
   f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
@@ -107,7 +127,7 @@ to be used with the FOCUS calculator.
    
   "average crop cover", "full canopy"), met_form_water = TRUE,
   txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)
    -

    Arguments

    +

    Arguments

    @@ -339,5 +359,8 @@ should be written

    + + + diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index ee1e275..5dc6cea 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -22,18 +22,24 @@ water concentrations — PEC_sw_sed • pfm + + + - - - + + + + + + @@ -56,8 +62,12 @@ PEC calculator" /> - pfm + + pfm + 0.4.5 + + @@ -81,23 +97,27 @@ PEC calculator" /> -
    +

    Calculate predicted environmental concentrations in sediment from surface water concentrations

    + Source: R/PEC_sw_sed.R +
    +

    The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator

    + 
    PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
   sediment_depth = 5, water_depth = 30, sediment_density = 1.3,
   PEC_sed_units = c("µg/kg", "mg/kg"))
    -

    Arguments

    +

    Arguments

    @@ -170,5 +190,8 @@ Johannes Ranke + + + diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html index fbe643d..12c9a0d 100644 --- a/docs/reference/PELMO_path.html +++ b/docs/reference/PELMO_path.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,19 +94,23 @@ -
    +

    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

    +

    Arguments

    @@ -130,5 +150,8 @@ + + + diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 1c2aabe..dc068c3 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -59,8 +65,12 @@ and run using wine." /> - pfm + + pfm + 0.4.5 + + @@ -84,12 +100,15 @@ and run using wine." /> -
    +

    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 @@ -99,6 +118,7 @@ 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,
@@ -109,7 +129,7 @@ and run using wine.
    
 
 evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")
    -

    Arguments

    +

    Arguments

    @@ -209,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

    #> #>
    # We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)
    #> User System verstrichen -#> 220.760 1.509 30.234
    if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.388 0.088 30.344
    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. @@ -255,5 +275,8 @@ the period.plm file generated by the FOCUS PELMO GUI.

    + + + diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index 2c7c5bf..e6fc526 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,20 +94,24 @@ -
    +

    Actual and maximum moving window time average concentrations for SFO kinetics

    + Source: R/SFO_actual_twa.R +
    +

    Actual and maximum moving window time average concentrations for SFO kinetics

    + 
    SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50,
   100))
    -

    Arguments

    +

    Arguments

    @@ -154,5 +174,8 @@ Johannes Ranke + + + diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 5310a3f..4e673bf 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ checked against the spreadsheet published on the CRC website" /> - pfm + + pfm + 0.4.5 + + @@ -79,20 +95,24 @@ checked against the spreadsheet published on the CRC website" /> -
    +

    Determine the SSLRC mobility classification for a chemical substance from its Koc

    + Source: R/SSLRC_mobility_classification.R +
    +

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

    + 
    SSLRC_mobility_classification(Koc)
    -

    Arguments

    +

    Arguments

    @@ -144,5 +164,8 @@ Johannes Ranke + + + diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 3bd0533..a078e31 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> - pfm + + pfm + 0.4.5 + + @@ -79,16 +95,20 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> -
    +

    R6 class for holding TOXSWA cwa concentration data and associated statistics

    + Source: R/TOXSWA_cwa.R +
    +

    An R6 class for holding TOXSWA cwa concentration data and some associated statistics. Usually, an instance of this class will be generated by read.TOXSWA_cwa.

    + 
    TOXSWA_cwa
    @@ -186,5 +206,8 @@ for the requested moving window sizes in days.

    + + + diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 0c03fff..501f002 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 +
    +
    @@ -78,20 +94,24 @@ -
    +

    Create a chemical compound object for FOCUS Step 1 calculations

    + Source: R/PEC_sw_focus.R +
    +

    Create a chemical compound object for FOCUS Step 1 calculations

    + 
    chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA,
   DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1)
    -

    Arguments

    +

    Arguments

    @@ -167,5 +187,8 @@ systems

    + + + diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html index 8cefafb..02d2d0c 100644 --- a/docs/reference/create_run_list.html +++ b/docs/reference/create_run_list.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,19 +94,23 @@ -
    +

    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

    +

    Arguments

    @@ -134,5 +154,8 @@ as used in FOCUS_GW_scenarios_2012< + + + diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 159f662..9cee8fe 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -22,18 +22,24 @@ published by the JKI — drift_data_JKI • pfm + + + - - - + + + + + + @@ -56,8 +62,12 @@ published by the German Julius-Kühn Institute (JKI)." /> - pfm + + pfm + 0.4.5 + + @@ -81,17 +97,21 @@ published by the German Julius-Kühn Institute (JKI)." /> -
    +

    Deposition from spray drift expressed as percent of the applied dose as published by the JKI

    + Source: R/drift_data_JKI.R +
    +

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

    +

    Format

    @@ -125,7 +145,7 @@ as its licence is not clear.

    drift_data_JKI <- list() for (n in 1:8) { - drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) + drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), crop = JKI_crops) @@ -267,5 +287,8 @@ as its licence is not clear.

    + + + diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 2b6e77d..2a36788 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ this function." /> - pfm + + pfm + 0.4.5 +
    +
    @@ -81,18 +97,22 @@ this function." /> -
    +

    Retrieve endpoint information from the chyaml field of a chent object

    + Source: R/endpoint.R +
    +

    R6 class objects of class chent represent chemical entities and can hold a list of information loaded from a chemical yaml file in their chyaml field. Such information is extracted and optionally aggregated by this function.

    + 
    endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
   lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
@@ -112,7 +132,7 @@ this function.
    
   geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3),
   raw = FALSE)
    -

    Arguments

    +

    Arguments

    @@ -207,5 +227,8 @@ exponent is often called 1/n.

    + + + diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html index e743986..c15c73a 100644 --- a/docs/reference/focus_80th.html +++ b/docs/reference/focus_80th.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ values obtained by PELMO." /> - pfm + + pfm + 0.4.5 + + @@ -81,22 +97,26 @@ values obtained by PELMO." /> -
    +

    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

    +

    Arguments

    @@ -132,5 +152,8 @@ values obtained by PELMO.

    + + + diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index b1c283d..b8c2415 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ returns 0 if at least one element of the vector is 0." /> - pfm + + pfm + 0.4.5 + + @@ -81,22 +97,26 @@ returns 0 if at least one element of the vector is 0." /> -
    +

    Calculate the geometric mean

    + Source: R/geomean.R +
    +

    Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function checks for negative values, removes NA values per default and returns 0 if at least one element of the vector is 0.

    + 
    geomean(x, na.rm = TRUE)
    -

    Arguments

    +

    Arguments

    @@ -148,5 +168,8 @@ Johannes Ranke + + + diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html index 9c3a659..7e331ec 100644 --- a/docs/reference/get_flux.html +++ b/docs/reference/get_flux.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,19 +94,23 @@ -
    +

    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

    +

    Arguments

    @@ -122,5 +142,8 @@ + + + diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html index a55306d..2d1dc02 100644 --- a/docs/reference/get_interval.html +++ b/docs/reference/get_interval.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,19 +94,23 @@ -
    +

    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

    +

    Arguments

    @@ -126,5 +146,8 @@ + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 8aaa938..395b446 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -21,13 +21,19 @@ + + + - - - + + + + + + @@ -50,8 +56,12 @@ - pfm + + pfm + 0.4.5 + + @@ -75,181 +91,262 @@ -
    -
    +
    +
    -

    - Reference - version 0.4-5 -

    +

    Reference

    -
    -
    +
    - - - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -

    General utility functions

    -

    Functions that are independent of specific fate modelling areas

    -
    -

    geomean

    -

    Calculate the geometric mean

    -

    one_box

    -

    Create a time series of decline data

    -

    plot

    -

    Plot time series of decline data

    -

    sawtooth

    -

    Create decline time series for multiple applications

    -

    twa

    -

    Calculate a time weighted average concentration

    -

    max_twa

    -

    The maximum time weighted average concentration for a moving window

    -

    Predicted environmental concentrations in soil

    -

    -
    -

    PEC_soil

    -

    Calculate predicted environmental concentrations in soil

    -

    soil_scenario_data_EFSA_2015

    -

    Properties of the predefined scenarios from the EFSA guidance from 2015

    -

    Predicted environmental concentrations in groundwater

    -

    -
    -

    PELMO_runs run_PELMO evaluate_PELMO

    -

    Set up runs for FOCUS PELMO

    -

    Predicted environmental concentrations in surface water

    -

    -
    -

    PEC_sw_drift

    -

    Calculate predicted environmental concentrations in surface water due to drift

    -

    drift_data_JKI

    -

    Deposition from spray drift expressed as percent of the applied dose as +

    +

    General utility functions

    +

    Functions that are independent of specific fate modelling areas

    +
    +

    geomean()

    +

    Calculate the geometric mean

    +

    one_box()

    +

    Create a time series of decline data

    +

    plot(<one_box>)

    +

    Plot time series of decline data

    +

    sawtooth()

    +

    Create decline time series for multiple applications

    +

    twa()

    +

    Calculate a time weighted average concentration

    +

    max_twa()

    +

    The maximum time weighted average concentration for a moving window

    +

    pfm_degradation()

    +

    Calculate a time course of relative concentrations based on an mkinmod model

    +

    SFO_actual_twa()

    +

    Actual and maximum moving window time average concentrations for SFO kinetics

    +

    Predicted environmental concentrations in soil

    +

    +
    +

    PEC_soil()

    +

    Calculate predicted environmental concentrations in soil

    +

    soil_scenario_data_EFSA_2015

    +

    Properties of the predefined scenarios from the EFSA guidance from 2015

    +

    Predicted environmental concentrations in groundwater

    +

    +
    +

    FOCUS_GW_scenarios_2012

    +

    A very small subset of the FOCUS Groundwater scenario definitions

    +

    create_run_list()

    +

    Create a list of runs that we can traverse

    +

    PELMO_runs() run_PELMO() evaluate_PELMO()

    +

    Set up runs for FOCUS PELMO

    +

    PELMO_path()

    +

    Create a path of run directories as the PELMO GUI does

    +

    FOCUS_PELMO_crop_sze_names

    +

    FOCUS PELMO crop acronyms used for naming sceneario files

    +

    FOCUS_PELMO_crops

    +

    FOCUS PELMO crop names

    +

    FOCUS_PELMO_location_codes

    +

    Location codes in FOCUS PELMO

    +

    focus_80th()

    +

    Calculate the 80th percentile according to FOCUS guidance

    +

    Predicted environmental concentrations in surface water

    +

    +
    +

    PEC_sw_drift()

    +

    Calculate predicted environmental concentrations in surface water due to drift

    +

    drift_data_JKI

    +

    Deposition from spray drift expressed as percent of the applied dose as published by the JKI

    -

    PEC_sw_drainage_UK

    -

    Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

    -

    PEC_sw_focus

    -

    Calculate PEC surface water at FOCUS Step 1

    -

    PEC_sw_exposit_runoff

    -

    Calculate PEC surface water due to runoff and erosion as in Exposit 3

    -

    TOXSWA_cwa

    -

    R6 class for holding TOXSWA cwa concentration data and associated statistics

    -

    read.TOXSWA_cwa

    -

    Read TOXSWA surface water concentrations

    -

    plot

    -

    Plot TOXSWA surface water concentrations

    -

    Classifications and indicators

    -

    Evaluating environmental fate properties

    -
    -

    SSLRC_mobility_classification

    -

    Determine the SSLRC mobility classification for a chemical substance from its Koc

    -

    GUS print

    -

    Groundwater ubiquity score based on Gustafson (1989)

    -
    + + + +

    PEC_sw_drainage_UK()

    + +

    Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

    + + + +

    PEC_sw_sed()

    + +

    Calculate predicted environmental concentrations in sediment from surface +water concentrations

    + + + +

    chent_focus_sw()

    + +

    Create a chemical compound object for FOCUS Step 1 calculations

    + + + +

    PEC_sw_focus()

    + +

    Calculate PEC surface water at FOCUS Step 1

    + + + +

    FOCUS_Step_12_scenarios

    + +

    Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

    + + + +

    perc_runoff_exposit

    + +

    Runoff loss percentages as used in Exposit 3

    + + + +

    perc_runoff_reduction_exposit

    + +

    Runoff reduction percentages as used in Exposit

    + + + +

    PEC_sw_exposit_runoff()

    + +

    Calculate PEC surface water due to runoff and erosion as in Exposit 3

    + + + +

    TOXSWA_cwa

    + +

    R6 class for holding TOXSWA cwa concentration data and associated statistics

    + + + +

    read.TOXSWA_cwa()

    + +

    Read TOXSWA surface water concentrations

    + + + +

    plot(<TOXSWA_cwa>)

    + +

    Plot TOXSWA surface water concentrations

    + + + + +

    Classifications and indicators

    +

    Evaluating environmental fate properties

    + + + + + +

    SSLRC_mobility_classification()

    + +

    Determine the SSLRC mobility classification for a chemical substance from its Koc

    + + + +

    GUS() print(<GUS_result>)

    + +

    Groundwater ubiquity score based on Gustafson (1989)

    + + +
    + + + diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index a596d60..0875c46 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -57,8 +63,12 @@ max_twa." /> - pfm + + pfm + 0.4.5 +
    + @@ -82,12 +98,15 @@ max_twa." /> -
    +

    The maximum time weighted average concentration for a moving window

    + Source: R/twa.R +
    +

    If you generate your time series using sawtooth, you need to make sure that the length of the time series allows @@ -95,10 +114,11 @@ for finding the maximum. It is therefore recommended to check this using plot.one_box using the window size for the argument max_twa.

    + 
    max_twa(x, window = 21)
    -

    Arguments

    +

    Arguments

    @@ -127,7 +147,7 @@ SFO, FOMC and DFOP models and to the parent compound

    See also

    -

    twa

    +

    twa

    Examples

    @@ -177,5 +197,8 @@ SFO, FOMC and DFOP models and to the parent compound

    + + + diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png index eeccb4c..5015348 100644 Binary files a/docs/reference/one_box-1.png and b/docs/reference/one_box-1.png differ diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png index 89fa0b9..eb60bd6 100644 Binary files a/docs/reference/one_box-2.png and b/docs/reference/one_box-2.png differ diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png index 0af2c7b..fcb308b 100644 Binary files a/docs/reference/one_box-3.png and b/docs/reference/one_box-3.png differ diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index bfed3a1..1e793d0 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,15 +94,19 @@ -
    +

    Create a time series of decline data

    + Source: R/twa.R +
    +

    Create a time series of decline data

    + 
    one_box(x, ini, ..., t_end = 100, res = 0.01)
 
@@ -100,7 +120,7 @@
 # S3 method for mkinfit
 one_box(x, ini = "model", ..., t_end = 100, res = 0.01)
    -

    Arguments

    +

    Arguments

    @@ -145,16 +165,16 @@ all observed variables.

    Examples

    # Only use a half-life
 pred_0 <- one_box(10)
-plot(pred_0)
    
+plot(pred_0)
    
 # Use a fitted mkinfit model
 require(mkin)
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 pred_1 <- one_box(fit)
-plot(pred_1)
    
+plot(pred_1)
    
 # Use a model with more than one observed variable
 m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
 pred_2 <- one_box(fit_2, ini = "model")
-plot(pred_2)
    +plot(pred_2)
    + + + diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index 1098378..e24e0ad 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,15 +94,19 @@ -
    +

    Runoff loss percentages as used in Exposit 3

    + Source: R/PEC_sw_exposit_runoff.R +
    +

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

    +

    Format

    @@ -146,5 +166,8 @@
    + + + diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 10d7f24..69acbac 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 +
    +
    @@ -78,15 +94,19 @@ -
    +

    Runoff reduction percentages as used in Exposit

    + Source: R/PEC_sw_exposit_runoff.R +
    +

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

    + 
    perc_runoff_reduction_exposit
    @@ -146,5 +166,8 @@ from which the values were taken.

    + + + diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index da01e3f..42be741 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -21,3 +21,13 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 828c500..899a0a4 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 +
    +
    @@ -78,21 +94,25 @@ -
    +

    Calculate a time course of relative concentrations based on an mkinmod model

    + Source: R/pfm_degradation.R +
    +

    Calculate a time course of relative concentrations based on an mkinmod model

    + 
    pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
   log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by =
   step_days))
    -

    Arguments

    +

    Arguments

    @@ -160,5 +180,8 @@ Johannes Ranke + + + diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png index 9fabca9..79f5bfd 100644 Binary files a/docs/reference/plot.TOXSWA_cwa-1.png and b/docs/reference/plot.TOXSWA_cwa-1.png differ diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png index 57a655f..d306e0f 100644 Binary files a/docs/reference/plot.TOXSWA_cwa-2.png and b/docs/reference/plot.TOXSWA_cwa-2.png differ diff --git a/docs/reference/plot.TOXSWA_cwa-3.png b/docs/reference/plot.TOXSWA_cwa-3.png index 5dc1f37..e347b3f 100644 Binary files a/docs/reference/plot.TOXSWA_cwa-3.png and b/docs/reference/plot.TOXSWA_cwa-3.png differ diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png index 55f08fe..0cb99f8 100644 Binary files a/docs/reference/plot.TOXSWA_cwa-4.png and b/docs/reference/plot.TOXSWA_cwa-4.png differ diff --git a/docs/reference/plot.TOXSWA_cwa-5.png b/docs/reference/plot.TOXSWA_cwa-5.png index a46c66c..44eb28f 100644 Binary files a/docs/reference/plot.TOXSWA_cwa-5.png and b/docs/reference/plot.TOXSWA_cwa-5.png differ diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 1ff489a..cf5bdf9 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ segment of a TOXSWA surface water body." /> - pfm + + pfm + 0.4.5 + + @@ -79,16 +95,20 @@ segment of a TOXSWA surface water body." /> -
    +

    Plot TOXSWA surface water concentrations

    + Source: R/TOXSWA_cwa.R +
    +

    Plot TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body.

    + 
    # S3 method for TOXSWA_cwa
 plot(x, time_column = c("datetime", "t", "t_firstjan",
@@ -96,7 +116,7 @@ segment of a TOXSWA surface water body.
    
   threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = "C",
   ...)
    -

    Arguments

    +

    Arguments

    @@ -147,11 +167,11 @@ to suspended matter?

    H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
   basedir = "SwashProjects/project_H_sw/TOXSWA",
   zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
-plot(H_sw_D4_pond)
    plot(H_sw_D4_pond, time_column = "t")
    plot(H_sw_D4_pond, time_column = "t_firstjan")
    plot(H_sw_D4_pond, time_column = "t_rel_to_max")
    
+plot(H_sw_D4_pond)
    plot(H_sw_D4_pond, time_column = "t")
    plot(H_sw_D4_pond, time_column = "t_firstjan")
    plot(H_sw_D4_pond, time_column = "t_rel_to_max")
    
 H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
   basedir = "SwashProjects/project_H_sw/TOXSWA",
   zipfile = system.file("testdata/SwashProjects.zip", package = "pfm"))
-plot(H_sw_R1_stream, time_column = "t_rel_to_max")
    +plot(H_sw_R1_stream, time_column="t_rel_to_max")
    + + + diff --git a/docs/reference/plot.one_box-1.png b/docs/reference/plot.one_box-1.png index 7bd9555..6179195 100644 Binary files a/docs/reference/plot.one_box-1.png and b/docs/reference/plot.one_box-1.png differ diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png index 1a489d6..56f1454 100644 Binary files a/docs/reference/plot.one_box-2.png and b/docs/reference/plot.one_box-2.png differ diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png index ef78a0e..183035a 100644 Binary files a/docs/reference/plot.one_box-3.png and b/docs/reference/plot.one_box-3.png differ diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 63e351a..e4ffef4 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - pfm + + pfm + 0.4.5 + + @@ -78,22 +94,26 @@ -
    +

    Plot time series of decline data

    + Source: R/twa.R +
    +

    Plot time series of decline data

    + 
    # S3 method for one_box
 plot(x, xlim = range(time(x)), ylim = c(0, max(x)),
   xlab = "Time", ylab = "Residue", max_twa = NULL,
   max_twa_var = dimnames(x)[[2]][1], ...)
    -

    Arguments

    +

    Arguments

    @@ -134,17 +154,17 @@ be shown if max_twa is not NULL.

    See also

    -

    sawtooth

    +

    sawtooth

    Examples

    dfop_pred <- one_box("DFOP", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7))
-plot(dfop_pred)
    plot(sawtooth(dfop_pred, 3, 7), max_twa = 21)
    
+plot(dfop_pred)
    plot(sawtooth(dfop_pred, 3, 7), max_twa = 21)
    
 # Use a fitted mkinfit model
 m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
 pred_2 <- one_box(fit_2, ini = 1)
 pred_2_saw <- sawtooth(pred_2, 2, 7)
-plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
    +plot(pred_2_saw, max_twa=21, max_twa_var="m1")
    + + + diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 6afdaa7..d838794 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -57,8 +63,12 @@ of the hourly averages (ConLiqWatLay)." /> - pfm + + pfm + 0.4.5 + + @@ -82,12 +98,15 @@ of the hourly averages (ConLiqWatLay)." /> -
    +

    Read TOXSWA surface water concentrations

    + Source: R/TOXSWA_cwa.R +
    +

    Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last @@ -95,12 +114,13 @@ segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay).

    + 
    read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
   substance = "parent", total = FALSE, windows = NULL,
   thresholds = NULL)
    -

    Arguments

    +

    Arguments

    @@ -186,5 +206,8 @@ Johannes Ranke + + + diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png index 448d0c4..02a6b7c 100644 Binary files a/docs/reference/sawtooth-1.png and b/docs/reference/sawtooth-1.png differ diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png index ef78a0e..183035a 100644 Binary files a/docs/reference/sawtooth-2.png and b/docs/reference/sawtooth-2.png differ diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index cfd62f5..6b2ce13 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -21,18 +21,24 @@ + + + - - - + + + + + + @@ -55,8 +61,12 @@ times, with an interval i." /> - pfm + + pfm + 0.4.5 + + @@ -80,22 +96,26 @@ times, with an interval i." /> -
    +

    Create decline time series for multiple applications

    + Source: R/twa.R +
    +

    If the number of application cycles n is greater than 1, the application pattern specified in applications is repeated n times, with an interval i.

    + 
    sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0, (n -
   1) * i, length.out = n), amount = 1))
    -

    Arguments

    +

    Arguments

    @@ -122,11 +142,11 @@ the corresponding amounts applied in the second column.

    Examples

    applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3))
 pred <- one_box(10)
-plot(sawtooth(pred, applications = applications))
    
+plot(sawtooth(pred, applications = applications))
    
 m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
 pred_2 <- one_box(fit_2, ini = 1)
 pred_2_saw <- sawtooth(pred_2, 2, 7)
-plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
    
+plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
    
 max_twa(pred_2_saw)
    #> $max
 #>    parent        m1 
 #> 0.7834480 0.8617048 
@@ -163,5 +183,8 @@ the corresponding amounts applied in the second column.
    
       
    
    
 
+  
+
   
 
+
diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
index e7f209a..77759b5 100644
--- a/docs/reference/soil_scenario_data_EFSA_2015.html
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -21,18 +21,24 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -55,8 +61,12 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
         
         
       
-      pfm
+      
+        pfm
+        0.4.5
+      
     
+
     
   
 
@@ -80,17 +96,21 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Properties of the predefined scenarios from the EFSA guidance from 2015
    
+    Source: R/soil_scenario_data_EFSA_2015.R
+    
     
    
 
+    
    
     
     
    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
    
@@ -169,5 +189,8 @@ doi:10.2903/j.efsa.2015.4093
    
       
    
    
 
+  
+
   
 
+
diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html
index 51ed429..96cbaf2 100644
--- a/docs/reference/sum_periods.html
+++ b/docs/reference/sum_periods.html
@@ -21,16 +21,22 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -53,8 +59,12 @@
         
         
       
-      pfm
+      
+        pfm
+        0.4.5
+      
     
    
+
     
   
    
 
@@ -78,19 +94,23 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Sum up values according to FOCUS periods
    
+    Source: R/PELMO_runs.R
+    
     
    
 
+    
    
     
     
    Sum up values according to FOCUS periods
    
     
+    
    
 
     
    sum_periods(annual, interval)
    
     
-    
     Arguments
    
+    
    Arguments
    @@ -126,5 +146,8 @@ + + + diff --git a/docs/reference/twa.html b/docs/reference/twa.html index fad5fd9..8f8e98f 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -21,18 +21,24 @@ + + + - - - + + + + + + @@ -55,8 +61,12 @@ is after one window has passed." /> - pfm + + pfm + 0.4.5 + + @@ -80,24 +96,28 @@ is after one window has passed." /> -
    +

    Calculate a time weighted average concentration

    + Source: R/twa.R +
    +

    The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned is after one window has passed.

    + 
    twa(x, window = 21)
 
 # S3 method for one_box
 twa(x, window = 21)
    -

    Arguments

    +

    Arguments

    @@ -112,7 +132,7 @@ is after one window has passed.

    See also

    -

    max_twa

    +

    max_twa

    Examples

    @@ -156,5 +176,8 @@ is after one window has passed.

    + + + -- cgit v1.2.1