diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-06-06 02:48:44 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-06-06 02:48:44 +0200 |
| commit | 197606de234a936751ac3c1db2e4feb3fa117a92 (patch) | |
| tree | 89b32979142a37737ba73e8a012b809abba8e92d | |
| parent | 282820693c62b958e12104f4bb6229c04803f098 (diff) | |
Rebuild docs with pkgdown 1.1.0
58 files changed, 1616 insertions, 537 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index fb977ce..5695281 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-5 -Date: 2018-03-01 +Date: 2018-03-05 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) @@ -26,4 +26,5 @@ License: GPL LazyLoad: yes LazyData: yes Encoding: UTF-8 +URL: https://github.com/jranke/pfm RoxygenNote: 6.0.1 diff --git a/_pkgdown.yml b/_pkgdown.yml index 87afa93..4f16d24 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -13,19 +13,33 @@ reference: - sawtooth - twa - max_twa + - pfm_degradation + - SFO_actual_twa - title: Predicted environmental concentrations in soil contents: - PEC_soil - soil_scenario_data_EFSA_2015 - title: Predicted environmental concentrations in groundwater contents: + - FOCUS_GW_scenarios_2012 + - create_run_list - PELMO_runs + - PELMO_path + - FOCUS_PELMO_crop_sze_names + - FOCUS_PELMO_crops + - FOCUS_PELMO_location_codes + - focus_80th - title: Predicted environmental concentrations in surface water contents: - PEC_sw_drift - drift_data_JKI - PEC_sw_drainage_UK + - PEC_sw_sed + - chent_focus_sw - PEC_sw_focus + - FOCUS_Step_12_scenarios + - perc_runoff_exposit + - perc_runoff_reduction_exposit - PEC_sw_exposit_runoff - TOXSWA_cwa - read.TOXSWA_cwa @@ -35,3 +49,4 @@ reference: contents: - SSLRC_mobility_classification - GUS + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script> <script src="pkgdown.js"></script> - - + + + <meta property="og:title" content="Authors" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -66,8 +76,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -75,15 +91,15 @@ </header> - <div class="row"> - <div class="contents col-md-12"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> <h1>Authors</h1> </div> <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid'></a> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a> </p> </li> </ul> @@ -105,5 +121,8 @@ </footer> </div> + + </body> </html> + 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 @@ <title>Utilities for Pesticide Fate Modelling • pfm</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Utilities for Pesticide Fate Modelling"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> +<script src="pkgdown.js"></script><meta property="og:title" content="Utilities for Pesticide Fate Modelling"> <meta property="og:description" content="Utilities for simple calculations of predicted environmental concentrations ('PEC' values) and for dealing with data from some FOCUS pesticide fate modelling software packages."> @@ -29,8 +29,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -43,7 +47,14 @@ <a href="reference/index.html">Reference</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"></ul> +<ul class="nav navbar-nav navbar-right"> +<li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> </div> <!--/.nav-collapse --> </div> @@ -58,18 +69,18 @@ <div class="page-header"><h1 class="hasAnchor"> <a href="#pfm" class="anchor"></a>pfm</h1></div> <p>The R package <strong>pfm</strong> 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:</p> -<div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software:<span class="st"> </span>you can redistribute it and/or modify it under +<div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software<span class="op">:</span><span class="st"> </span>you can redistribute it and<span class="op">/</span>or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later version. -This program is distributed in the hope that it will be useful, but WITHOUT +This program is distributed <span class="cf">in</span> 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 <span class="cf">for</span> more details. You should have received a copy of the GNU General Public License along with -this program. If not, see <http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">></span></code></pre></div> +this program. If not, see <span class="op"><</span>http<span class="op">:</span><span class="er">//</span>www.gnu.org<span class="op">/</span>licenses<span class="op">/</span><span class="er">></span></code></pre></div> <div id="installation" class="section level2"> <h2 class="hasAnchor"> <a href="#installation" class="anchor"></a>Installation</h2> @@ -92,13 +103,29 @@ this program. If not, see <http:<span class="er">//</span>www.gnu.org/license </div> <div class="col-md-3" id="sidebar"> - <h2>License</h2> -<p>GPL</p> + <div class="links"> +<h2>Links</h2> +<ul class="list-unstyled"> +<li>Browse source code at <br><a href="https://github.com/jranke/pfm">https://github.com/jranke/pfm</a> +</li> +<li>Report a bug at <br><a href="NA">NA</a> +</li> +</ul> +</div> +<div class="license"> +<h2>License</h2> +<ul class="list-unstyled"> +<li>GPL</li> +</ul> +</div> +<div class="developers"> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li> </ul> </div> + + </div> </div> @@ -113,5 +140,7 @@ this program. If not, see <http:<span class="er">//</span>www.gnu.org/license </footer> </div> + + </body> </html> 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 <li>, and enclosing <li> if in dropdown - var menu_anchor = $(value); + // Add class to parent <li>, and enclosing <li> 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 = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>"; + if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>"; - $(".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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012" /> <meta property="og:description" content="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)." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +95,20 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>A very small subset of the FOCUS Groundwater scenario definitions</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_GW_scenarios_2012.R'><code>R/FOCUS_GW_scenarios_2012.R</code></a></small> + <div class="hidden name"><code>FOCUS_GW_scenarios_2012.Rd</code></div> </div> + <div class="ref-description"> <p>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).</p> + </div> <pre class="usage"><span class='no'>FOCUS_GW_scenarios_2012</span></pre> @@ -191,5 +211,8 @@ soil definitions are from page 46ff. from FOCUS (2012).</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names" /> <meta property="og:description" content="A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 @@ -34,6 +37,9 @@ 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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ files used for Beans (field) and Beans (vegetable) are the same." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ files used for Beans (field) and Beans (vegetable) are the same." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,18 +97,22 @@ files used for Beans (field) and Beans (vegetable) are the same." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>FOCUS PELMO crop acronyms used for naming sceneario files</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_PELMO_data.R'><code>R/FOCUS_PELMO_data.R</code></a></small> + <div class="hidden name"><code>FOCUS_PELMO_crop_sze_names.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='no'>FOCUS_PELMO_crop_sze_names</span></pre> @@ -135,5 +155,8 @@ files used for Beans (field) and Beans (vegetable) are the same.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="FOCUS PELMO crop names — FOCUS_PELMO_crops" /> <meta property="og:description" content="A named character vector with the crop names used in the PELMO 5.5.3 GUI. @@ -35,6 +38,9 @@ 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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -73,8 +83,14 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -82,12 +98,15 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>FOCUS PELMO crop names</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_PELMO_data.R'><code>R/FOCUS_PELMO_data.R</code></a></small> + <div class="hidden name"><code>FOCUS_PELMO_crops.Rd</code></div> </div> + <div class="ref-description"> <p>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 <code>ape</code>.</p> + </div> <pre class="usage"><span class='no'>FOCUS_PELMO_crops</span></pre> @@ -147,5 +167,8 @@ in the three letter code, i.e. 'Peas (animals)' has the code <code>ape</code>.</ </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes" /> <meta property="og:description" content="A named character vector of one letter location codes used in FOCUS PELMO, indexed by three letter acronyms." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ indexed by three letter acronyms." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ indexed by three letter acronyms." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +95,20 @@ indexed by three letter acronyms." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Location codes in FOCUS PELMO</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_PELMO_data.R'><code>R/FOCUS_PELMO_data.R</code></a></small> + <div class="hidden name"><code>FOCUS_PELMO_location_codes.Rd</code></div> </div> + <div class="ref-description"> <p>A named character vector of one letter location codes used in FOCUS PELMO, indexed by three letter acronyms.</p> + </div> <pre class="usage"><span class='no'>FOCUS_PELMO_location_codes</span></pre> @@ -125,5 +145,8 @@ indexed by three letter acronyms.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios" /> <meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ The text file is not included in the package as its licence is not clear." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ The text file is not included in the package as its licence is not clear." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +95,20 @@ The text file is not included in the package as its licence is not clear." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_Step_12_scenarios.R'><code>R/FOCUS_Step_12_scenarios.R</code></a></small> + <div class="hidden name"><code>FOCUS_Step_12_scenarios.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -294,5 +314,8 @@ The text file is not included in the package as its licence is not clear.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS" /> <meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,8 +81,14 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -80,17 +96,21 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/GUS.R'><code>R/GUS.R</code></a></small> + <div class="hidden name"><code>GUS.Rd</code></div> </div> + <div class="ref-description"> <p>The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> + </div> <pre class="usage"><span class='fu'>GUS</span>(<span class='no'>...</span>) @@ -105,7 +125,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> <span class='co'># S3 method for GUS_result</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -219,5 +239,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil" /> <meta property="og:description" content="This is a basic calculation of a contaminant concentration in bulk soil @@ -34,6 +37,9 @@ 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)." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,18 +97,22 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in soil</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_soil.R'><code>R/PEC_soil.R</code></a></small> + <div class="hidden name"><code>PEC_soil.Rd</code></div> </div> + <div class="ref-description"> <p>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).</p> + </div> <pre class="usage"><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, @@ -100,7 +120,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p> <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2015"</span>), <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -276,5 +296,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK" /> <meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ published on the CRC website" /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ published on the CRC website" /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,21 +95,25 @@ published on the CRC website" /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_drainage_UK.R'><code>R/PEC_sw_drainage_UK.R</code></a></small> + <div class="hidden name"><code>PEC_sw_drainage_UK.Rd</code></div> </div> + <div class="ref-description"> <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> + </div> <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -164,5 +184,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift" /> <meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ with input via spray drift." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,8 +81,14 @@ with input via spray drift." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -80,23 +96,27 @@ with input via spray drift." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in surface water due to drift</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_drift.R'><code>R/PEC_sw_drift.R</code></a></small> + <div class="hidden name"><code>PEC_sw_drift.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='fu'>PEC_sw_drift</span>(<span class='no'>rate</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"JKI"</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -176,5 +196,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff" /> <meta property="og:description" content="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." /> +in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not implemented." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,22 +95,26 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate PEC surface water due to runoff and erosion as in Exposit 3</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_exposit_runoff.R'><code>R/PEC_sw_exposit_runoff.R</code></a></small> + <div class="hidden name"><code>PEC_sw_exposit_runoff.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>(<span class='no'>rate</span>, <span class='no'>Koc</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"3.01"</span>, <span class='st'>"2.0"</span>), <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -144,7 +164,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p> + <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -196,5 +216,8 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" /> <meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, @@ -37,6 +40,9 @@ 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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -59,8 +65,12 @@ to be used with the FOCUS calculator." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,8 +85,14 @@ to be used with the FOCUS calculator." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -84,12 +100,15 @@ to be used with the FOCUS calculator." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate PEC surface water at FOCUS Step 1</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_focus.R'><code>R/PEC_sw_focus.R</code></a></small> + <div class="hidden name"><code>PEC_sw_focus.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>, @@ -107,7 +127,7 @@ to be used with the FOCUS calculator.</p> <span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -339,5 +359,8 @@ should be written</p></td> </footer> </div> + + </body> </html> + 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</title> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed" /> <meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ PEC calculator" /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ PEC calculator" /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,23 +97,27 @@ PEC calculator" /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in sediment from surface water concentrations</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_sed.R'><code>R/PEC_sw_sed.R</code></a></small> + <div class="hidden name"><code>PEC_sw_sed.Rd</code></div> </div> + <div class="ref-description"> <p>The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator</p> + </div> <pre class="usage"><span class='fu'>PEC_sw_sed</span>(<span class='no'>PEC_sw</span>, <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>, <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>, <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -170,5 +190,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Create a path of run directories as the PELMO GUI does — PELMO_path" /> <meta property="og:description" content="Create a path of run directories as the PELMO GUI does" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,19 +94,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create a path of run directories as the PELMO GUI does</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>PELMO_path.Rd</code></div> </div> + <div class="ref-description"> <p>Create a path of run directories as the PELMO GUI does</p> + </div> <pre class="usage"><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -130,5 +150,8 @@ </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Set up runs for FOCUS PELMO — PELMO_runs" /> <meta property="og:description" content="Per default, the runs are not only set up but also executed with FOCUS @@ -37,6 +40,9 @@ maintained on github is supported. In such installations, FOCUS PELMO is installed into the package installation directory of PELMO.installeR and run using wine." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -59,8 +65,12 @@ and run using wine." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,8 +85,14 @@ and run using wine." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -84,12 +100,15 @@ and run using wine." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Set up runs for FOCUS PELMO</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>PELMO_runs.Rd</code></div> </div> + <div class="ref-description"> <p>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 <code>PELMO.installeR</code> and run using <code>wine</code>.</p> + </div> <pre class="usage"><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>execute</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>), <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, @@ -109,7 +129,7 @@ and run using <code>wine</code>.</p> <span class='fu'>evaluate_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -209,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> #> #> </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span> <span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#> User System verstrichen -#> 220.760 1.509 30.234 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'><-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) { +#> 0.388 0.088 30.344 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'><-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) { <span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]])) }</div><div class='output co'>#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'> <span class='co'># Demonstrate some results with metabolites.</span> @@ -255,5 +275,8 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa" /> <meta property="og:description" content="Actual and maximum moving window time average concentrations for SFO kinetics" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,20 +94,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Actual and maximum moving window time average concentrations for SFO kinetics</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/SFO_actual_twa.R'><code>R/SFO_actual_twa.R</code></a></small> + <div class="hidden name"><code>SFO_actual_twa.Rd</code></div> </div> + <div class="ref-description"> <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> + </div> <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</span>))</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -154,5 +174,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification" /> <meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ checked against the spreadsheet published on the CRC website" /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ checked against the spreadsheet published on the CRC website" /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,20 +95,24 @@ checked against the spreadsheet published on the CRC website" /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/SSLRC_mobility_classification.R'><code>R/SSLRC_mobility_classification.R</code></a></small> + <div class="hidden name"><code>SSLRC_mobility_classification.Rd</code></div> </div> + <div class="ref-description"> <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> + </div> <pre class="usage"><span class='fu'>SSLRC_mobility_classification</span>(<span class='no'>Koc</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -144,5 +164,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa" /> <meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +95,20 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>R6 class for holding TOXSWA cwa concentration data and associated statistics</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/TOXSWA_cwa.R'><code>R/TOXSWA_cwa.R</code></a></small> + <div class="hidden name"><code>TOXSWA_cwa.Rd</code></div> </div> + <div class="ref-description"> <p>An R6 class for holding TOXSWA cwa concentration data and some associated statistics. Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> + </div> <pre class="usage"><span class='no'>TOXSWA_cwa</span></pre> @@ -186,5 +206,8 @@ for the requested moving window sizes in days.</p></dd> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw" /> <meta property="og:description" content="Create a chemical compound object for FOCUS Step 1 calculations" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,20 +94,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create a chemical compound object for FOCUS Step 1 calculations</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_focus.R'><code>R/PEC_sw_focus.R</code></a></small> + <div class="hidden name"><code>chent_focus_sw.Rd</code></div> </div> + <div class="ref-description"> <p>Create a chemical compound object for FOCUS Step 1 calculations</p> + </div> <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>name</span>, <span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -167,5 +187,8 @@ systems</p></td> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Create a list of runs that we can traverse — create_run_list" /> <meta property="og:description" content="Create a list of runs that we can traverse" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,19 +94,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create a list of runs that we can traverse</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>create_run_list.Rd</code></div> </div> + <div class="ref-description"> <p>Create a list of runs that we can traverse</p> + </div> <pre class="usage"><span class='fu'>create_run_list</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>check_psm_files</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -134,5 +154,8 @@ as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012< </footer> </div> + + </body> </html> + 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</title> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI" /> <meta property="og:description" content="Deposition from spray drift expressed as percent of the applied dose as published by the German Julius-Kühn Institute (JKI)." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ published by the German Julius-Kühn Institute (JKI)." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ published by the German Julius-Kühn Institute (JKI)." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,17 +97,21 @@ published by the German Julius-Kühn Institute (JKI)." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/drift_data_JKI.R'><code>R/drift_data_JKI.R</code></a></small> + <div class="hidden name"><code>drift_data_JKI.Rd</code></div> </div> + <div class="ref-description"> <p>Deposition from spray drift expressed as percent of the applied dose as published by the German Julius-Kühn Institute (JKI).</p> + </div> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -125,7 +145,7 @@ as its licence is not clear.</p> <span class='no'>drift_data_JKI</span> <span class='kw'><-</span> <span class='fu'>list</span>() <span class='kw'>for</span> (<span class='no'>n</span> <span class='kw'>in</span> <span class='fl'>1</span>:<span class='fl'>8</span>) { - <span class='no'>drift_data_raw</span> <span class='kw'><-</span> <span class='fu'>read_excel</span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>) + <span class='no'>drift_data_raw</span> <span class='kw'><-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/readxl/topics/read_excel'>read_excel</a></span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>) <span class='no'>drift_data</span> <span class='kw'><-</span> <span class='fu'>as.matrix</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>2</span>:<span class='fl'>4</span>]) <span class='fu'>dimnames</span>(<span class='no'>drift_data</span>) <span class='kw'><-</span> <span class='fu'>list</span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='fu'>as.integer</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>1</span>]), <span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>) @@ -267,5 +287,8 @@ as its licence is not clear.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint" /> <meta property="og:description" content="R6 class objects of class chent represent chemical entities @@ -34,6 +37,9 @@ 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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ this function." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ this function." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,18 +97,22 @@ this function." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/endpoint.R'><code>R/endpoint.R</code></a></small> + <div class="hidden name"><code>endpoint.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>), <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>, @@ -112,7 +132,7 @@ this function.</p> <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>), <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -207,5 +227,8 @@ exponent is often called 1/n.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate the 80th percentile according to FOCUS guidance — focus_80th" /> <meta property="og:description" content="This is nowadays defined as the mean of the 16th and the 17th @@ -34,6 +37,9 @@ 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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ values obtained by PELMO." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ values obtained by PELMO." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,22 +97,26 @@ values obtained by PELMO." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the 80th percentile according to FOCUS guidance</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>focus_80th.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='fu'>focus_80th</span>(<span class='no'>c_period</span>, <span class='kw'>old</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -132,5 +152,8 @@ values obtained by PELMO.</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate the geometric mean — geomean" /> <meta property="og:description" content="Based on some posts in a thread on Stackoverflow @@ -34,6 +37,9 @@ 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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ returns 0 if at least one element of the vector is 0." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,8 +82,14 @@ returns 0 if at least one element of the vector is 0." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,22 +97,26 @@ returns 0 if at least one element of the vector is 0." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the geometric mean</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/geomean.R'><code>R/geomean.R</code></a></small> + <div class="hidden name"><code>geomean.Rd</code></div> </div> + <div class="ref-description"> <p>Based on some posts in a thread on Stackoverflow <a href='http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> This function checks for negative values, removes NA values per default and returns 0 if at least one element of the vector is 0.</p> + </div> <pre class="usage"><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -148,5 +168,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux" /> <meta property="og:description" content="Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,19 +94,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>get_flux.Rd</code></div> </div> + <div class="ref-description"> <p>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file</p> + </div> <pre class="usage"><span class='fu'>get_flux</span>(<span class='no'>chem_file</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -122,5 +142,8 @@ </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Get the application interval in years from a psm file — get_interval" /> <meta property="og:description" content="Get the application interval in years from a psm file" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,19 +94,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Get the application interval in years from a psm file</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>get_interval.Rd</code></div> </div> + <div class="ref-description"> <p>Get the application interval in years from a psm file</p> + </div> <pre class="usage"><span class='fu'>get_interval</span>(<span class='no'>psm_file</span>, <span class='no'>location_code</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -126,5 +146,8 @@ </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Function reference" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -66,8 +76,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -75,181 +91,262 @@ </header> - <div class="row"> - <div class="col-md-9"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> - <h1> - Reference - <small>version 0.4-5</small> - </h1> + <h1>Reference</h1> </div> - <div class="contents"> - <table class="ref-index"> + <table class="ref-index"> - <colgroup> - <col class="alias" /> - <col class="title" /> - </colgroup> + <colgroup> + + <col class="alias" /> + <col class="title" /> + </colgroup> - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2> - <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="geomean.html">geomean</a></code> </p> - </td> - <td><p>Calculate the geometric mean</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="one_box.html">one_box</a></code> </p> - </td> - <td><p>Create a time series of decline data</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="plot.one_box.html">plot</a></code> </p> - </td> - <td><p>Plot time series of decline data</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="sawtooth.html">sawtooth</a></code> </p> - </td> - <td><p>Create decline time series for multiple applications</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="twa.html">twa</a></code> </p> - </td> - <td><p>Calculate a time weighted average concentration</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="max_twa.html">max_twa</a></code> </p> - </td> - <td><p>The maximum time weighted average concentration for a moving window</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="PEC_soil.html">PEC_soil</a></code> </p> - </td> - <td><p>Calculate predicted environmental concentrations in soil</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p> - </td> - <td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="PELMO_runs.html">PELMO_runs</a></code> <code><a href="PELMO_runs.html">run_PELMO</a></code> <code><a href="PELMO_runs.html">evaluate_PELMO</a></code> </p> - </td> - <td><p>Set up runs for FOCUS PELMO</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="PEC_sw_drift.html">PEC_sw_drift</a></code> </p> - </td> - <td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p> - </td> - <td><p>Deposition from spray drift expressed as percent of the applied dose as + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2> + <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="geomean.html">geomean()</a></code> </p> + </td> + <td><p>Calculate the geometric mean</p></td> + </tr><tr> + + <td> + <p><code><a href="one_box.html">one_box()</a></code> </p> + </td> + <td><p>Create a time series of decline data</p></td> + </tr><tr> + + <td> + <p><code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </p> + </td> + <td><p>Plot time series of decline data</p></td> + </tr><tr> + + <td> + <p><code><a href="sawtooth.html">sawtooth()</a></code> </p> + </td> + <td><p>Create decline time series for multiple applications</p></td> + </tr><tr> + + <td> + <p><code><a href="twa.html">twa()</a></code> </p> + </td> + <td><p>Calculate a time weighted average concentration</p></td> + </tr><tr> + + <td> + <p><code><a href="max_twa.html">max_twa()</a></code> </p> + </td> + <td><p>The maximum time weighted average concentration for a moving window</p></td> + </tr><tr> + + <td> + <p><code><a href="pfm_degradation.html">pfm_degradation()</a></code> </p> + </td> + <td><p>Calculate a time course of relative concentrations based on an mkinmod model</p></td> + </tr><tr> + + <td> + <p><code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </p> + </td> + <td><p>Actual and maximum moving window time average concentrations for SFO kinetics</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="PEC_soil.html">PEC_soil()</a></code> </p> + </td> + <td><p>Calculate predicted environmental concentrations in soil</p></td> + </tr><tr> + + <td> + <p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p> + </td> + <td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p> + </td> + <td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td> + </tr><tr> + + <td> + <p><code><a href="create_run_list.html">create_run_list()</a></code> </p> + </td> + <td><p>Create a list of runs that we can traverse</p></td> + </tr><tr> + + <td> + <p><code><a href="PELMO_runs.html">PELMO_runs()</a></code> <code><a href="PELMO_runs.html">run_PELMO()</a></code> <code><a href="PELMO_runs.html">evaluate_PELMO()</a></code> </p> + </td> + <td><p>Set up runs for FOCUS PELMO</p></td> + </tr><tr> + + <td> + <p><code><a href="PELMO_path.html">PELMO_path()</a></code> </p> + </td> + <td><p>Create a path of run directories as the PELMO GUI does</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_PELMO_crop_sze_names.html">FOCUS_PELMO_crop_sze_names</a></code> </p> + </td> + <td><p>FOCUS PELMO crop acronyms used for naming sceneario files</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_PELMO_crops.html">FOCUS_PELMO_crops</a></code> </p> + </td> + <td><p>FOCUS PELMO crop names</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_PELMO_location_codes.html">FOCUS_PELMO_location_codes</a></code> </p> + </td> + <td><p>Location codes in FOCUS PELMO</p></td> + </tr><tr> + + <td> + <p><code><a href="focus_80th.html">focus_80th()</a></code> </p> + </td> + <td><p>Calculate the 80th percentile according to FOCUS guidance</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> </p> + </td> + <td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td> + </tr><tr> + + <td> + <p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p> + </td> + <td><p>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK</a></code> </p> - </td> - <td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="PEC_sw_focus.html">PEC_sw_focus</a></code> </p> - </td> - <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff</a></code> </p> - </td> - <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> - </td> - <td><p>R6 class for holding TOXSWA cwa concentration data and associated statistics</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code> </p> - </td> - <td><p>Read TOXSWA surface water concentrations</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="plot.TOXSWA_cwa.html">plot</a></code> </p> - </td> - <td><p>Plot TOXSWA surface water concentrations</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2> - <p class="section-desc"><p>Evaluating environmental fate properties</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification</a></code> </p> - </td> - <td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="GUS.html">GUS</a></code> <code><a href="GUS.html">print</a></code> </p> - </td> - <td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td> - </tr> - </tbody> - </table> - </div> + </tr><tr> + + <td> + <p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> </p> + </td> + <td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td> + </tr><tr> + + <td> + <p><code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </p> + </td> + <td><p>Calculate predicted environmental concentrations in sediment from surface +water concentrations</p></td> + </tr><tr> + + <td> + <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p> + </td> + <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td> + </tr><tr> + + <td> + <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p> + </td> + <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </p> + </td> + <td><p>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</p></td> + </tr><tr> + + <td> + <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p> + </td> + <td><p>Runoff loss percentages as used in Exposit 3</p></td> + </tr><tr> + + <td> + <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p> + </td> + <td><p>Runoff reduction percentages as used in Exposit</p></td> + </tr><tr> + + <td> + <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p> + </td> + <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td> + </tr><tr> + + <td> + <p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> + </td> + <td><p>R6 class for holding TOXSWA cwa concentration data and associated statistics</p></td> + </tr><tr> + + <td> + <p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </p> + </td> + <td><p>Read TOXSWA surface water concentrations</p></td> + </tr><tr> + + <td> + <p><code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> </p> + </td> + <td><p>Plot TOXSWA surface water concentrations</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2> + <p class="section-desc"><p>Evaluating environmental fate properties</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> </p> + </td> + <td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td> + </tr><tr> + + <td> + <p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> </p> + </td> + <td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td> + </tr> + </tbody> + </table> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -276,5 +373,8 @@ published by the JKI</p></td> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="The maximum time weighted average concentration for a moving window — max_twa" /> <meta property="og:description" content="If you generate your time series using sawtooth, @@ -35,6 +38,9 @@ for finding the maximum. It is therefore recommended to check this using plot.one_box using the window size for the argument max_twa." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ max_twa." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -73,8 +83,14 @@ max_twa." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -82,12 +98,15 @@ max_twa." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>The maximum time weighted average concentration for a moving window</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/twa.R'><code>R/twa.R</code></a></small> + <div class="hidden name"><code>max_twa.Rd</code></div> </div> + <div class="ref-description"> <p>If you generate your time series using <code><a href='sawtooth.html'>sawtooth</a></code>, 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 <code><a href='plot.one_box.html'>plot.one_box</a></code> using the window size for the argument <code>max_twa</code>.</p> + </div> <pre class="usage"><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -127,7 +147,7 @@ SFO, FOMC and DFOP models and to the parent compound</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='twa.html'>twa</a></code></p> + <div class='dont-index'><p><code><a href='twa.html'>twa</a></code></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -177,5 +197,8 @@ SFO, FOMC and DFOP models and to the parent compound</p> </footer> </div> + + </body> </html> + diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png Binary files differindex eeccb4c..5015348 100644 --- a/docs/reference/one_box-1.png +++ b/docs/reference/one_box-1.png diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png Binary files differindex 89fa0b9..eb60bd6 100644 --- a/docs/reference/one_box-2.png +++ b/docs/reference/one_box-2.png diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png Binary files differindex 0af2c7b..fcb308b 100644 --- a/docs/reference/one_box-3.png +++ b/docs/reference/one_box-3.png 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Create a time series of decline data — one_box" /> <meta property="og:description" content="Create a time series of decline data" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,15 +94,19 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create a time series of decline data</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/twa.R'><code>R/twa.R</code></a></small> + <div class="hidden name"><code>one_box.Rd</code></div> </div> + <div class="ref-description"> <p>Create a time series of decline data</p> + </div> <pre class="usage"><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) @@ -100,7 +120,7 @@ <span class='co'># S3 method for mkinfit</span> <span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -145,16 +165,16 @@ all observed variables.</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span> <span class='no'>pred_0</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='fl'>10</span>) -<span class='fu'>plot</span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Use a fitted mkinfit model</span> <span class='fu'>require</span>(<span class='no'>mkin</span>) <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>pred_1</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>) -<span class='fu'>plot</span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Use a model with more than one observed variable</span> <span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinmod'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>) -<span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='432.632880098887' /></div></pre> +<span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -181,5 +201,8 @@ all observed variables.</p></td> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit" /> <meta property="og:description" content="A table of the loss percentages used in Exposit 3 for the twelve different Koc classes" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,15 +94,19 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Runoff loss percentages as used in Exposit 3</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_exposit_runoff.R'><code>R/PEC_sw_exposit_runoff.R</code></a></small> + <div class="hidden name"><code>perc_runoff_exposit.Rd</code></div> </div> + <div class="ref-description"> <p>A table of the loss percentages used in Exposit 3 for the twelve different Koc classes</p> + </div> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -146,5 +166,8 @@ </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit" /> <meta property="og:description" content="A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,15 +94,19 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Runoff reduction percentages as used in Exposit</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_exposit_runoff.R'><code>R/PEC_sw_exposit_runoff.R</code></a></small> + <div class="hidden name"><code>perc_runoff_reduction_exposit.Rd</code></div> </div> + <div class="ref-description"> <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> + </div> <pre class="usage"><span class='no'>perc_runoff_reduction_exposit</span></pre> @@ -146,5 +166,8 @@ from which the values were taken.</p><dl class='dl-horizontal'> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" /> <meta property="og:description" content="Calculate a time course of relative concentrations based on an mkinmod model" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,21 +94,25 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate a time course of relative concentrations based on an mkinmod model</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/pfm_degradation.R'><code>R/pfm_degradation.R</code></a></small> + <div class="hidden name"><code>pfm_degradation.Rd</code></div> </div> + <div class="ref-description"> <p>Calculate a time course of relative concentrations based on an mkinmod model</p> + </div> <pre class="usage"><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>))</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -160,5 +180,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png Binary files differindex 9fabca9..79f5bfd 100644 --- a/docs/reference/plot.TOXSWA_cwa-1.png +++ b/docs/reference/plot.TOXSWA_cwa-1.png diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png Binary files differindex 57a655f..d306e0f 100644 --- a/docs/reference/plot.TOXSWA_cwa-2.png +++ b/docs/reference/plot.TOXSWA_cwa-2.png diff --git a/docs/reference/plot.TOXSWA_cwa-3.png b/docs/reference/plot.TOXSWA_cwa-3.png Binary files differindex 5dc1f37..e347b3f 100644 --- a/docs/reference/plot.TOXSWA_cwa-3.png +++ b/docs/reference/plot.TOXSWA_cwa-3.png diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png Binary files differindex 55f08fe..0cb99f8 100644 --- a/docs/reference/plot.TOXSWA_cwa-4.png +++ b/docs/reference/plot.TOXSWA_cwa-4.png diff --git a/docs/reference/plot.TOXSWA_cwa-5.png b/docs/reference/plot.TOXSWA_cwa-5.png Binary files differindex a46c66c..44eb28f 100644 --- a/docs/reference/plot.TOXSWA_cwa-5.png +++ b/docs/reference/plot.TOXSWA_cwa-5.png 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa" /> <meta property="og:description" content="Plot TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ segment of a TOXSWA surface water body." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -70,8 +80,14 @@ segment of a TOXSWA surface water body." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +95,20 @@ segment of a TOXSWA surface water body." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot TOXSWA surface water concentrations</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/TOXSWA_cwa.R'><code>R/TOXSWA_cwa.R</code></a></small> + <div class="hidden name"><code>plot.TOXSWA_cwa.Rd</code></div> </div> + <div class="ref-description"> <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body.</p> + </div> <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span> <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>, @@ -96,7 +116,7 @@ segment of a TOXSWA surface water body.</p> <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -147,11 +167,11 @@ to suspended matter?</p></td> <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='fu'>plot</span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='432.632880098887' /></div></pre> +<span class='fu'>plot</span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -180,5 +200,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + diff --git a/docs/reference/plot.one_box-1.png b/docs/reference/plot.one_box-1.png Binary files differindex 7bd9555..6179195 100644 --- a/docs/reference/plot.one_box-1.png +++ b/docs/reference/plot.one_box-1.png diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png Binary files differindex 1a489d6..56f1454 100644 --- a/docs/reference/plot.one_box-2.png +++ b/docs/reference/plot.one_box-2.png diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png Binary files differindex ef78a0e..183035a 100644 --- a/docs/reference/plot.one_box-3.png +++ b/docs/reference/plot.one_box-3.png 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Plot time series of decline data — plot.one_box" /> <meta property="og:description" content="Plot time series of decline data" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,22 +94,26 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot time series of decline data</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/twa.R'><code>R/twa.R</code></a></small> + <div class="hidden name"><code>plot.one_box.Rd</code></div> </div> + <div class="ref-description"> <p>Plot time series of decline data</p> + </div> <pre class="usage"><span class='co'># S3 method for one_box</span> <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>range</span>(<span class='fu'>time</span>(<span class='no'>x</span>)), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fu'>max</span>(<span class='no'>x</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'>dimnames</span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -134,17 +154,17 @@ be shown if max_twa is not NULL.</p></td> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='sawtooth.html'>sawtooth</a></code></p> + <div class='dont-index'><p><code><a href='sawtooth.html'>sawtooth</a></code></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>)) -<span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Use a fitted mkinfit model</span> <span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='432.632880098887' /></div></pre> +<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -171,5 +191,8 @@ be shown if max_twa is not NULL.</p></td> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" /> <meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific @@ -35,6 +38,9 @@ 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)." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ of the hourly averages (ConLiqWatLay)." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -73,8 +83,14 @@ of the hourly averages (ConLiqWatLay)." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -82,12 +98,15 @@ of the hourly averages (ConLiqWatLay)." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Read TOXSWA surface water concentrations</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/TOXSWA_cwa.R'><code>R/TOXSWA_cwa.R</code></a></small> + <div class="hidden name"><code>read.TOXSWA_cwa.Rd</code></div> </div> + <div class="ref-description"> <p>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).</p> + </div> <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -186,5 +206,8 @@ Johannes Ranke </footer> </div> + + </body> </html> + diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 448d0c4..02a6b7c 100644 --- a/docs/reference/sawtooth-1.png +++ b/docs/reference/sawtooth-1.png diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex ef78a0e..183035a 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Create decline time series for multiple applications — sawtooth" /> <meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ times, with an interval i." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,8 +81,14 @@ times, with an interval i." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -80,22 +96,26 @@ times, with an interval i." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create decline time series for multiple applications</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/twa.R'><code>R/twa.R</code></a></small> + <div class="hidden name"><code>sawtooth.Rd</code></div> </div> + <div class="ref-description"> <p>If the number of application cycles <code>n</code> is greater than 1, the application pattern specified in <code>applications</code> is repeated <code>n</code> times, with an interval <code>i</code>.</p> + </div> <pre class="usage"><span class='fu'>sawtooth</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, (<span class='no'>n</span> - <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>))</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -122,11 +142,11 @@ the corresponding amounts applied in the second column.</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>)) <span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>) -<span class='fu'>plot</span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#> $max #> parent m1 #> 0.7834480 0.8617048 @@ -163,5 +183,8 @@ the corresponding amounts applied in the second column.</p></td> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015" /> <meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,8 +81,14 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -80,17 +96,21 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/soil_scenario_data_EFSA_2015.R'><code>R/soil_scenario_data_EFSA_2015.R</code></a></small> + <div class="hidden name"><code>soil_scenario_data_EFSA_2015.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -169,5 +189,8 @@ doi:10.2903/j.efsa.2015.4093</p> </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Sum up values according to FOCUS periods — sum_periods" /> <meta property="og:description" content="Sum up values according to FOCUS periods" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -69,8 +79,14 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,19 +94,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Sum up values according to FOCUS periods</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> + <div class="hidden name"><code>sum_periods.Rd</code></div> </div> + <div class="ref-description"> <p>Sum up values according to FOCUS periods</p> + </div> <pre class="usage"><span class='fu'>sum_periods</span>(<span class='no'>annual</span>, <span class='no'>interval</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -126,5 +146,8 @@ </footer> </div> + + </body> </html> + 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 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Calculate a time weighted average concentration — twa" /> <meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ is after one window has passed." /> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">pfm</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,8 +81,14 @@ is after one window has passed." /> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="https://github.com/jranke/pfm"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -80,24 +96,28 @@ is after one window has passed." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate a time weighted average concentration</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/twa.R'><code>R/twa.R</code></a></small> + <div class="hidden name"><code>twa.Rd</code></div> </div> + <div class="ref-description"> <p>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.</p> + </div> <pre class="usage"><span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>) <span class='co'># S3 method for one_box</span> <span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -112,7 +132,7 @@ is after one window has passed.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='max_twa.html'>max_twa</a></code></p> + <div class='dont-index'><p><code><a href='max_twa.html'>max_twa</a></code></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -156,5 +176,8 @@ is after one window has passed.</p> </footer> </div> + + </body> </html> + |
