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class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Subset of EFSA crop interception default values for groundwater modelling</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/EFSA_GW_interception_2014.R" class="external-link"><code>R/EFSA_GW_interception_2014.R</code></a></small> + <div class="d-none name"><code>EFSA_GW_interception_2014.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Subset of EFSA crop interception default values for groundwater modelling</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A matrix containing interception values, currently only for some selected crops</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>European Food Safety Authority (2014) EFSA Guidance Document for evaluating laboratory and field dissipation studies to obtain DegT50 values of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>12</b>(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) - <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( - <span class='st'>"Beans (field + vegetable)"</span>, - <span class='st'>"Peas"</span>, - <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, - <span class='st'>"Tomatoes"</span>, - <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) - <span class='no'>EFSA_GW_interception_2014</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), - <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.25</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.8</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.35</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.85</span>, <span class='fl'>5</span>), <span class='fl'>0.85</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_GW_interception_2014</span>, - <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_GW_interception_2014.RData"</span>) -} -<span class='no'>EFSA_GW_interception_2014</span></div><div class='output co'>#> BBCH -#> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x -#> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 -#> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 -#> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 -#> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 -#> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 -#> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 -#> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to define the data</span></span></span> +<span class="r-in"><span> <span class="va">bbch</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fl">0</span><span class="op">:</span><span class="fl">9</span>, <span class="st">"x"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">crops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="st">"Beans (field + vegetable)"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Peas"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Summer oilseed rape"</span>, <span class="st">"Winter oilseed rape"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Tomatoes"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Spring cereals"</span>, <span class="st">"Winter cereals"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">crops</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">bbch</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> dimnames <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Crop <span class="op">=</span> <span class="va">crops</span>, BBCH <span class="op">=</span> <span class="va">bbch</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Beans (field + vegetable)"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.25</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.4</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.8</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Peas"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.35</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.55</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.85</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.85</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Summer oilseed rape"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.4</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.9</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Winter oilseed rape"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.4</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.9</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Tomatoes"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.5</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Spring cereals"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0.2</span>, <span class="fl">0.8</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.9</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0.8</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_GW_interception_2014</span><span class="op">[</span><span class="st">"Winter cereals"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0.2</span>, <span class="fl">0.8</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.9</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0.8</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">EFSA_GW_interception_2014</span>,</span></span> +<span class="r-in"><span> file <span class="op">=</span> <span class="st">"../data/EFSA_GW_interception_2014.RData"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="va">EFSA_GW_interception_2014</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> BBCH</span> +<span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> +<span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85</span> +<span class="r-out co"><span class="r-pr">#></span> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90</span> +<span class="r-out co"><span class="r-pr">#></span> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90</span> +<span class="r-out co"><span class="r-pr">#></span> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div 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class="logo" alt=""><h1>Subset of EFSA crop washoff default values</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/EFSA_washoff_2017.R" class="external-link"><code>R/EFSA_washoff_2017.R</code></a></small> + <div class="d-none name"><code>EFSA_washoff_2017.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Subset of EFSA crop washoff default values</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A matrix containing wash-off factors, currently only for some selected crops</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>European Food Safety Authority (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 doi:10.2903/j.efsa.2017.4982</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) - <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( - <span class='st'>"Beans (field + vegetable)"</span>, - <span class='st'>"Peas"</span>, - <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, - <span class='st'>"Tomatoes"</span>, - <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) - <span class='no'>EFSA_washoff_2017</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), - <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.5</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.1</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>5</span>), <span class='fl'>0.3</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.55</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fl'>0.5</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>2</span>), <span class='fl'>0.55</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.1</span>, <span class='fl'>0.4</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fl'>0.4</span>) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_washoff_2017</span>, - <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_washoff_2017.RData"</span>) -} -<span class='no'>EFSA_washoff_2017</span></div><div class='output co'>#> BBCH -#> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x -#> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 -#> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 -#> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 -#> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 -#> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 -#> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 -#> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to define the data</span></span></span> +<span class="r-in"><span> <span class="va">bbch</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fl">0</span><span class="op">:</span><span class="fl">9</span>, <span class="st">"x"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">crops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="st">"Beans (field + vegetable)"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Peas"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Summer oilseed rape"</span>, <span class="st">"Winter oilseed rape"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Tomatoes"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Spring cereals"</span>, <span class="st">"Winter cereals"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">crops</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">bbch</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> dimnames <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Crop <span class="op">=</span> <span class="va">crops</span>, BBCH <span class="op">=</span> <span class="va">bbch</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Beans (field + vegetable)"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.6</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.75</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.35</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Peas"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.4</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.6</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.65</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.35</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Summer oilseed rape"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.4</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.6</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Winter oilseed rape"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.1</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.4</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.55</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Tomatoes"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.55</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.75</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">5</span><span class="op">)</span>, <span class="fl">0.35</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Spring cereals"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.4</span>, <span class="fl">0.5</span>, <span class="fl">0.5</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.65</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.65</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0.55</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">EFSA_washoff_2017</span><span class="op">[</span><span class="st">"Winter cereals"</span>, <span class="op">]</span> <span class="op"><-</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>, <span class="fl">0.6</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.55</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0.6</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0.4</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">EFSA_washoff_2017</span>,</span></span> +<span class="r-in"><span> file <span class="op">=</span> <span class="st">"../data/EFSA_washoff_2017.RData"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="va">EFSA_washoff_2017</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> BBCH</span> +<span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> +<span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30</span> +<span class="r-out co"><span class="r-pr">#></span> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55</span> +<span class="r-out co"><span class="r-pr">#></span> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html 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The soil definitions are from page 46ff. from FOCUS (2012).</p> </div> - <pre class="usage"><span class='no'>FOCUS_GW_scenarios_2012</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_GW_scenarios_2012</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An object of class <code>list</code> of length 2.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. FOrum for the Co-ordination of pesticde fate models and their USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>FOCUS_GW_scenarios_2012</span></div><div class='output co'>#> $names -#> Cha Ham Jok Kre Oke -#> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" -#> Pia Por Sev Thi -#> "Piacenza" "Porto" "Sevilla" "Thiva" -#> -#> $soils -#> location horizon number pH_H2O perc_clay perc_oc rel_deg -#> 1 Cha Ap 1 8.0 30.0 1.39 1.0 -#> 2 Cha B1 2 8.1 31.0 0.93 0.5 -#> 3 Cha B2 3 8.2 25.0 0.70 0.5 -#> 4 Cha II C1 4 8.5 26.0 0.30 0.3 -#> 5 Cha II C1 5 8.5 26.0 0.30 0.0 -#> 6 Cha II C2 6 8.5 24.0 0.27 0.0 -#> 7 Cha M 7 8.3 31.0 0.21 0.0 -#> 8 Ham Ap 1 6.4 7.2 1.50 1.0 -#> 9 Ham BvI 2 5.6 6.7 1.00 0.5 -#> 10 Ham BvII 3 5.6 0.9 0.20 0.3 -#> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 -#> 12 Ham Cv 5 5.5 0.0 0.00 0.3 -#> 13 Ham Cv 6 5.5 0.0 0.00 0.0 -#> 14 Jok Ap 1 6.2 3.6 4.06 1.0 -#> 15 Jok Bs 2 5.6 1.8 0.84 0.5 -#> 16 Jok BC1 3 5.4 1.2 0.36 0.3 -#> 17 Jok BC2 4 5.4 1.7 0.29 0.3 -#> 18 Jok BC2 5 5.4 1.7 0.29 0.0 -#> 19 Jok Cg 6 5.3 1.9 0.21 0.0 -#> 20 Kre <NA> 1 7.7 14.0 3.60 1.0 -#> 21 Kre <NA> 2 7.0 25.0 1.00 0.5 -#> 22 Kre <NA> 3 7.1 27.0 0.50 0.5 -#> 23 Kre <NA> 4 7.1 27.0 0.50 0.3 -#> 24 Kre <NA> 5 7.1 27.0 0.50 0.0 -#> 25 Oke A 1 5.8 18.0 2.20 1.0 -#> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 -#> 27 Oke BC 3 6.5 14.0 0.40 0.3 -#> 28 Oke C 4 6.6 9.0 0.10 0.3 -#> 29 Oke C 5 6.6 9.0 0.10 0.0 -#> 30 Pia Ap 1 7.0 15.0 1.26 1.0 -#> 31 Pia Ap 2 7.0 15.0 1.26 0.5 -#> 32 Pia Bw 3 6.3 7.0 0.47 0.5 -#> 33 Pia Bw 4 6.3 7.0 0.47 0.3 -#> 34 Pia 2C 5 6.4 0.0 0.00 0.3 -#> 35 Pia 2C 6 6.4 0.0 0.00 0.0 -#> 36 Por <NA> 1 4.9 10.0 1.42 1.0 -#> 37 Por <NA> 2 4.8 8.0 0.78 0.5 -#> 38 Por <NA> 3 4.8 8.0 0.78 0.3 -#> 39 Por <NA> 4 4.8 8.0 0.78 0.0 -#> 40 Sev <NA> 1 7.3 14.0 0.93 1.0 -#> 41 Sev <NA> 2 7.3 13.0 0.93 1.0 -#> 42 Sev <NA> 3 7.8 15.0 0.70 0.5 -#> 43 Sev <NA> 4 8.1 16.0 0.58 0.3 -#> 44 Sev <NA> 5 8.1 16.0 0.58 0.0 -#> 45 Sev <NA> 6 8.2 22.0 0.49 0.0 -#> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 -#> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 -#> 48 Thi Bw 3 7.8 29.6 0.57 0.5 -#> 49 Thi Bw 4 7.8 31.9 0.31 0.3 -#> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 -#> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_GW_scenarios_2012</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $names</span> +<span class="r-out co"><span class="r-pr">#></span> Cha Ham Jok Kre Oke </span> +<span class="r-out co"><span class="r-pr">#></span> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" </span> +<span class="r-out co"><span class="r-pr">#></span> Pia Por Sev Thi </span> +<span class="r-out co"><span class="r-pr">#></span> "Piacenza" "Porto" "Sevilla" "Thiva" </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $soils</span> +<span class="r-out co"><span class="r-pr">#></span> location horizon number pH_H2O perc_clay perc_oc rel_deg</span> +<span class="r-out co"><span class="r-pr">#></span> 1 Cha Ap 1 8.0 30.0 1.39 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 Cha B1 2 8.1 31.0 0.93 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 3 Cha B2 3 8.2 25.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 4 Cha II C1 4 8.5 26.0 0.30 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 5 Cha II C1 5 8.5 26.0 0.30 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 6 Cha II C2 6 8.5 24.0 0.27 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 7 Cha M 7 8.3 31.0 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 8 Ham Ap 1 6.4 7.2 1.50 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 9 Ham BvI 2 5.6 6.7 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 Ham BvII 3 5.6 0.9 0.20 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 12 Ham Cv 5 5.5 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 13 Ham Cv 6 5.5 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 14 Jok Ap 1 6.2 3.6 4.06 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 15 Jok Bs 2 5.6 1.8 0.84 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 16 Jok BC1 3 5.4 1.2 0.36 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 17 Jok BC2 4 5.4 1.7 0.29 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 18 Jok BC2 5 5.4 1.7 0.29 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 19 Jok Cg 6 5.3 1.9 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 Kre <NA> 1 7.7 14.0 3.60 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 21 Kre <NA> 2 7.0 25.0 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 22 Kre <NA> 3 7.1 27.0 0.50 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 23 Kre <NA> 4 7.1 27.0 0.50 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 24 Kre <NA> 5 7.1 27.0 0.50 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 25 Oke A 1 5.8 18.0 2.20 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 26 Oke Bw1 2 6.3 17.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 27 Oke BC 3 6.5 14.0 0.40 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 28 Oke C 4 6.6 9.0 0.10 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 29 Oke C 5 6.6 9.0 0.10 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 30 Pia Ap 1 7.0 15.0 1.26 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 31 Pia Ap 2 7.0 15.0 1.26 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 32 Pia Bw 3 6.3 7.0 0.47 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 33 Pia Bw 4 6.3 7.0 0.47 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 34 Pia 2C 5 6.4 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 35 Pia 2C 6 6.4 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 36 Por <NA> 1 4.9 10.0 1.42 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 37 Por <NA> 2 4.8 8.0 0.78 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 38 Por <NA> 3 4.8 8.0 0.78 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 39 Por <NA> 4 4.8 8.0 0.78 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 Sev <NA> 1 7.3 14.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 41 Sev <NA> 2 7.3 13.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 42 Sev <NA> 3 7.8 15.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 43 Sev <NA> 4 8.1 16.0 0.58 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 44 Sev <NA> 5 8.1 16.0 0.58 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 45 Sev <NA> 6 8.2 22.0 0.49 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 46 Thi Ap1 1 7.7 25.3 0.74 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 47 Thi Ap2 2 7.7 25.3 0.74 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 48 Thi Bw 3 7.8 29.6 0.57 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 49 Thi Bw 4 7.8 31.9 0.31 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 50 Thi Ck1 5 7.8 32.9 0.18 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 51 Thi Ck1 6 7.8 32.9 0.18 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index bbfb592..dc1e4c3 100644 --- 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src="" class="logo" alt=""><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/HEAD/R/FOCUS_Step_12_scenarios.R" class="external-link"><code>R/FOCUS_Step_12_scenarios.R</code></a></small> + <div class="d-none name"><code>FOCUS_Step_12_scenarios.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list containing the scenario names in a character vector called 'names', the drift percentiles in a matrix called 'drift', interception percentages in a matrix called 'interception' and the runoff/drainage percentages for Step 2 calculations in a matrix called 'rd'.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to extract the data</span> - <span class='no'>scenario_path</span> <span class='kw'><-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span> - <span class='no'>scenarios</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>] - <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>() - <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span> - <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>sce</span>) <span class='kw'><-</span> <span class='no'>sce</span>$<span class='no'>Crop</span> - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>] - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>] - <span class='no'>sce_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>] - <span class='no'>rd</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>] - <span class='no'>rd_mat</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>), - <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>)) - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span> - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>) -} - -<span class='co'># And this is the resulting data</span> -<span class='no'>FOCUS_Step_12_scenarios</span></div><div class='output co'>#> $names -#> [1] "cereals, spring" "cereals, winter" -#> [3] "citrus" "cotton" -#> [5] "field beans" "grass / alfalfa" -#> [7] "hops" "legumes" -#> [9] "maize" "oil seed rape, spring" -#> [11] "oil seed rape, winter" "olives" -#> [13] "pome / stone fruit, early applns" "pome / stone fruit, late applns" -#> [15] "potatoes" "soybeans" -#> [17] "sugar beets" "sunflowers" -#> [19] "tobacco" "vegetables, bulb" -#> [21] "vegetables, fruiting" "vegetables, leafy" -#> [23] "vegetables, root" "vines, early applns" -#> [25] "vines, late applns" "appln, aerial" -#> [27] "appln, hand (crop < 50 cm)" "appln, hand (crop > 50 cm)" -#> [29] "no drift (incorp or seed trtmt)" -#> -#> $drift -#> 1 2 3 4 5 6 -#> cereals, spring 2.759 2.438 2.024 1.862 1.794 1.631 -#> cereals, winter 2.759 2.438 2.024 1.862 1.794 1.631 -#> citrus 15.725 12.129 11.011 10.124 9.743 9.204 -#> cotton 2.759 2.438 2.024 1.862 1.794 1.631 -#> field beans 2.759 2.438 2.024 1.862 1.794 1.631 -#> grass / alfalfa 2.759 2.438 2.024 1.862 1.794 1.631 -#> hops 19.326 17.723 15.928 15.378 15.114 14.902 -#> legumes 2.759 2.438 2.024 1.862 1.794 1.631 -#> maize 2.759 2.438 2.024 1.862 1.794 1.631 -#> oil seed rape, spring 2.759 2.438 2.024 1.862 1.794 1.631 -#> oil seed rape, winter 2.759 2.438 2.024 1.862 1.794 1.631 -#> olives 15.725 12.129 11.011 10.124 9.743 9.204 -#> pome / stone fruit, early applns 29.197 25.531 23.960 23.603 23.116 22.760 -#> pome / stone fruit, late applns 15.725 12.129 11.011 10.124 9.743 9.204 -#> potatoes 2.759 2.438 2.024 1.862 1.794 1.631 -#> soybeans 2.759 2.438 2.024 1.862 1.794 1.631 -#> sugar beets 2.759 2.438 2.024 1.862 1.794 1.631 -#> sunflowers 2.759 2.438 2.024 1.862 1.794 1.631 -#> tobacco 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, bulb 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, fruiting 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, leafy 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, root 2.759 2.438 2.024 1.862 1.794 1.631 -#> vines, early applns 2.699 2.496 2.546 2.499 2.398 2.336 -#> vines, late applns 8.028 7.119 6.898 6.631 6.636 6.431 -#> appln, aerial 33.200 33.200 33.200 33.200 33.200 33.200 -#> appln, hand (crop < 50 cm) 2.759 2.438 2.024 1.862 1.794 1.631 -#> appln, hand (crop > 50 cm) 8.028 7.119 6.898 6.631 6.636 6.431 -#> no drift (incorp or seed trtmt) 0.000 0.000 0.000 0.000 0.000 0.000 -#> 7 8 >8 -#> cereals, spring 1.578 1.512 1.512 -#> cereals, winter 1.578 1.512 1.512 -#> citrus 9.102 8.656 8.656 -#> cotton 1.578 1.512 1.512 -#> field beans 1.578 1.512 1.512 -#> grass / alfalfa 1.578 1.512 1.512 -#> hops 14.628 13.520 13.520 -#> legumes 1.578 1.512 1.512 -#> maize 1.578 1.512 1.512 -#> oil seed rape, spring 1.578 1.512 1.512 -#> oil seed rape, winter 1.578 1.512 1.512 -#> olives 9.102 8.656 8.656 -#> pome / stone fruit, early applns 22.690 22.241 22.241 -#> pome / stone fruit, late applns 9.102 8.656 8.656 -#> potatoes 1.578 1.512 1.512 -#> soybeans 1.578 1.512 1.512 -#> sugar beets 1.578 1.512 1.512 -#> sunflowers 1.578 1.512 1.512 -#> tobacco 1.578 1.512 1.512 -#> vegetables, bulb 1.578 1.512 1.512 -#> vegetables, fruiting 1.578 1.512 1.512 -#> vegetables, leafy 1.578 1.512 1.512 -#> vegetables, root 1.578 1.512 1.512 -#> vines, early applns 2.283 2.265 2.265 -#> vines, late applns 6.227 6.173 6.173 -#> appln, aerial 33.200 33.200 33.200 -#> appln, hand (crop < 50 cm) 1.578 1.512 1.512 -#> appln, hand (crop > 50 cm) 6.227 6.173 6.173 -#> no drift (incorp or seed trtmt) 0.000 0.000 0.000 -#> -#> $interception -#> no interception minimal crop cover -#> cereals, spring 0 0.00 -#> cereals, winter 0 0.00 -#> citrus 0 0.80 -#> cotton 0 0.30 -#> field beans 0 0.25 -#> grass / alfalfa 0 0.40 -#> hops 0 0.20 -#> legumes 0 0.25 -#> maize 0 0.25 -#> oil seed rape, spring 0 0.40 -#> oil seed rape, winter 0 0.40 -#> olives 0 0.70 -#> pome / stone fruit, early applns 0 0.20 -#> pome / stone fruit, late applns 0 0.20 -#> potatoes 0 0.15 -#> soybeans 0 0.20 -#> sugar beets 0 0.20 -#> sunflowers 0 0.20 -#> tobacco 0 0.20 -#> vegetables, bulb 0 0.10 -#> vegetables, fruiting 0 0.25 -#> vegetables, leafy 0 0.25 -#> vegetables, root 0 0.25 -#> vines, early applns 0 0.40 -#> vines, late applns 0 0.40 -#> appln, aerial 0 0.20 -#> appln, hand (crop < 50 cm) 0 0.20 -#> appln, hand (crop > 50 cm) 0 0.20 -#> no drift (incorp or seed trtmt) 0 0.00 -#> average crop cover full canopy -#> cereals, spring 0.20 0.70 -#> cereals, winter 0.20 0.70 -#> citrus 0.80 0.80 -#> cotton 0.60 0.75 -#> field beans 0.40 0.70 -#> grass / alfalfa 0.60 0.75 -#> hops 0.50 0.70 -#> legumes 0.50 0.70 -#> maize 0.50 0.75 -#> oil seed rape, spring 0.70 0.75 -#> oil seed rape, winter 0.70 0.75 -#> olives 0.70 0.70 -#> pome / stone fruit, early applns 0.40 0.65 -#> pome / stone fruit, late applns 0.40 0.65 -#> potatoes 0.50 0.70 -#> soybeans 0.50 0.75 -#> sugar beets 0.70 0.75 -#> sunflowers 0.50 0.75 -#> tobacco 0.70 0.75 -#> vegetables, bulb 0.25 0.40 -#> vegetables, fruiting 0.50 0.70 -#> vegetables, leafy 0.40 0.70 -#> vegetables, root 0.50 0.70 -#> vines, early applns 0.50 0.60 -#> vines, late applns 0.50 0.60 -#> appln, aerial 0.50 0.70 -#> appln, hand (crop < 50 cm) 0.50 0.70 -#> appln, hand (crop > 50 cm) 0.50 0.70 -#> no drift (incorp or seed trtmt) 0.00 0.00 -#> -#> $rd -#> Region -#> Time North South -#> Oct-Feb 5 4 -#> Mar-May 2 4 -#> Jun-Sep 2 3 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to extract the data</span></span></span> +<span class="r-in"><span> <span class="va">scenario_path</span> <span class="op"><-</span> <span class="st">"inst/extdata/FOCUS_Step_12_scenarios.txt"</span></span></span> +<span class="r-in"><span> <span class="va">scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">9</span><span class="op">:</span><span class="fl">38</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">sce</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">scenarios</span>, sep <span class="op">=</span> <span class="st">"\t"</span>, header <span class="op">=</span> <span class="cn">TRUE</span>, check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span> <span class="op">=</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op"><-</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">drift</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">11</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">interception</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">12</span><span class="op">:</span><span class="fl">15</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">sce_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">41</span><span class="op">:</span><span class="fl">46</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">rd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">sce_2</span>, sep <span class="op">=</span> <span class="st">"\t"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="va">rd_mat</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="va">rd</span><span class="op">$</span><span class="va">V2</span>, nrow <span class="op">=</span> <span class="fl">3</span>, byrow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">rd_mat</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Oct-Feb"</span>, <span class="st">"Mar-May"</span>, <span class="st">"Jun-Sep"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"South"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">rd</span> <span class="op">=</span> <span class="va">rd_mat</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">FOCUS_Step_12_scenarios</span>, file <span class="op">=</span> <span class="st">"data/FOCUS_Step_12_scenarios.RData"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And this is the resulting data</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_Step_12_scenarios</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $names</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "cereals, spring" "cereals, winter" </span> +<span class="r-out co"><span class="r-pr">#></span> [3] "citrus" "cotton" </span> +<span class="r-out co"><span class="r-pr">#></span> [5] "field beans" "grass / alfalfa" </span> +<span class="r-out co"><span class="r-pr">#></span> [7] "hops" "legumes" </span> +<span class="r-out co"><span class="r-pr">#></span> [9] "maize" "oil seed rape, spring" </span> +<span class="r-out co"><span class="r-pr">#></span> [11] "oil seed rape, winter" "olives" </span> +<span class="r-out co"><span class="r-pr">#></span> [13] "pome / stone fruit, early applns" "pome / stone fruit, late applns" </span> +<span class="r-out co"><span class="r-pr">#></span> [15] "potatoes" "soybeans" </span> +<span class="r-out co"><span class="r-pr">#></span> [17] "sugar beets" "sunflowers" </span> +<span class="r-out co"><span class="r-pr">#></span> [19] "tobacco" "vegetables, bulb" </span> +<span class="r-out co"><span class="r-pr">#></span> [21] "vegetables, fruiting" "vegetables, leafy" </span> +<span class="r-out co"><span class="r-pr">#></span> [23] "vegetables, root" "vines, early applns" </span> +<span class="r-out co"><span class="r-pr">#></span> [25] "vines, late applns" "appln, aerial" </span> +<span class="r-out co"><span class="r-pr">#></span> [27] "appln, hand (crop < 50 cm)" "appln, hand (crop > 50 cm)" </span> +<span class="r-out co"><span class="r-pr">#></span> [29] "no drift (incorp or seed trtmt)" </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $drift</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2 3 4 5 6</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, spring 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, winter 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> citrus 15.725 12.129 11.011 10.124 9.743 9.204</span> +<span class="r-out co"><span class="r-pr">#></span> cotton 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> field beans 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> grass / alfalfa 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> hops 19.326 17.723 15.928 15.378 15.114 14.902</span> +<span class="r-out co"><span class="r-pr">#></span> legumes 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> maize 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, spring 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, winter 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> olives 15.725 12.129 11.011 10.124 9.743 9.204</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, early applns 29.197 25.531 23.960 23.603 23.116 22.760</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, late applns 15.725 12.129 11.011 10.124 9.743 9.204</span> +<span class="r-out co"><span class="r-pr">#></span> potatoes 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> soybeans 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> sugar beets 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> sunflowers 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> tobacco 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, bulb 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, fruiting 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, leafy 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, root 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> vines, early applns 2.699 2.496 2.546 2.499 2.398 2.336</span> +<span class="r-out co"><span class="r-pr">#></span> vines, late applns 8.028 7.119 6.898 6.631 6.636 6.431</span> +<span class="r-out co"><span class="r-pr">#></span> appln, aerial 33.200 33.200 33.200 33.200 33.200 33.200</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop < 50 cm) 2.759 2.438 2.024 1.862 1.794 1.631</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop > 50 cm) 8.028 7.119 6.898 6.631 6.636 6.431</span> +<span class="r-out co"><span class="r-pr">#></span> no drift (incorp or seed trtmt) 0.000 0.000 0.000 0.000 0.000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> 7 8 >8</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, spring 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, winter 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> citrus 9.102 8.656 8.656</span> +<span class="r-out co"><span class="r-pr">#></span> cotton 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> field beans 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> grass / alfalfa 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> hops 14.628 13.520 13.520</span> +<span class="r-out co"><span class="r-pr">#></span> legumes 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> maize 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, spring 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, winter 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> olives 9.102 8.656 8.656</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, early applns 22.690 22.241 22.241</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, late applns 9.102 8.656 8.656</span> +<span class="r-out co"><span class="r-pr">#></span> potatoes 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> soybeans 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> sugar beets 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> sunflowers 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> tobacco 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, bulb 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, fruiting 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, leafy 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, root 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> vines, early applns 2.283 2.265 2.265</span> +<span class="r-out co"><span class="r-pr">#></span> vines, late applns 6.227 6.173 6.173</span> +<span class="r-out co"><span class="r-pr">#></span> appln, aerial 33.200 33.200 33.200</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop < 50 cm) 1.578 1.512 1.512</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop > 50 cm) 6.227 6.173 6.173</span> +<span class="r-out co"><span class="r-pr">#></span> no drift (incorp or seed trtmt) 0.000 0.000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $interception</span> +<span class="r-out co"><span class="r-pr">#></span> no interception minimal crop cover</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, spring 0 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, winter 0 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> citrus 0 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> cotton 0 0.30</span> +<span class="r-out co"><span class="r-pr">#></span> field beans 0 0.25</span> +<span class="r-out co"><span class="r-pr">#></span> grass / alfalfa 0 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> hops 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> legumes 0 0.25</span> +<span class="r-out co"><span class="r-pr">#></span> maize 0 0.25</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, spring 0 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, winter 0 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> olives 0 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, early applns 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, late applns 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> potatoes 0 0.15</span> +<span class="r-out co"><span class="r-pr">#></span> soybeans 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> sugar beets 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> sunflowers 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> tobacco 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, bulb 0 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, fruiting 0 0.25</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, leafy 0 0.25</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, root 0 0.25</span> +<span class="r-out co"><span class="r-pr">#></span> vines, early applns 0 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> vines, late applns 0 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> appln, aerial 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop < 50 cm) 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop > 50 cm) 0 0.20</span> +<span class="r-out co"><span class="r-pr">#></span> no drift (incorp or seed trtmt) 0 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> average crop cover full canopy</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, spring 0.20 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> cereals, winter 0.20 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> citrus 0.80 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> cotton 0.60 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> field beans 0.40 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> grass / alfalfa 0.60 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> hops 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> legumes 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> maize 0.50 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, spring 0.70 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> oil seed rape, winter 0.70 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> olives 0.70 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, early applns 0.40 0.65</span> +<span class="r-out co"><span class="r-pr">#></span> pome / stone fruit, late applns 0.40 0.65</span> +<span class="r-out co"><span class="r-pr">#></span> potatoes 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> soybeans 0.50 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> sugar beets 0.70 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> sunflowers 0.50 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> tobacco 0.70 0.75</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, bulb 0.25 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, fruiting 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, leafy 0.40 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> vegetables, root 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> vines, early applns 0.50 0.60</span> +<span class="r-out co"><span class="r-pr">#></span> vines, late applns 0.50 0.60</span> +<span class="r-out co"><span class="r-pr">#></span> appln, aerial 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop < 50 cm) 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> appln, hand (crop > 50 cm) 0.50 0.70</span> +<span class="r-out co"><span class="r-pr">#></span> no drift (incorp or seed trtmt) 0.00 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $rd</span> +<span class="r-out co"><span class="r-pr">#></span> Region</span> +<span class="r-out co"><span class="r-pr">#></span> Time North South</span> +<span class="r-out co"><span class="r-pr">#></span> Oct-Feb 5 4</span> +<span class="r-out co"><span class="r-pr">#></span> Mar-May 2 4</span> +<span class="r-out co"><span class="r-pr">#></span> Jun-Sep 2 3</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a 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template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Actual and maximum moving window time average concentrations for FOMC kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/FOMC_actual_twa.R" class="external-link"><code>R/FOMC_actual_twa.R</code></a></small> + <div class="d-none name"><code>FOMC_actual_twa.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Actual and maximum moving window time average concentrations for FOMC kinetics</p> </div> - <pre class="usage"><span class='fu'>FOMC_actual_twa</span>( - <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, - <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, - <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>alpha</th> - <td><p>Parameter of the FOMC model</p></td> - </tr> - <tr> - <th>beta</th> - <td><p>Parameter of the FOMC model</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times, and window sizes for time weighted average concentrations</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span></span> +<span> alpha <span class="op">=</span> <span class="fl">1.0001</span>,</span> +<span> beta <span class="op">=</span> <span class="fl">10</span>,</span> +<span> times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</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><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>alpha</dt> +<dd><p>Parameter of the FOMC model</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> actual twa -#> 0 1.00000000 NaN -#> 1 0.90908224 0.9530973 -#> 2 0.83331814 0.9115995 -#> 4 0.71426168 0.8411664 -#> 7 0.58820408 0.7580202 -#> 14 0.41663019 0.6253074 -#> 21 0.32254415 0.5387324 -#> 28 0.26312277 0.4767543 -#> 42 0.19227599 0.3925054 -#> 50 0.16663681 0.3583198 -#> 100 0.09088729 0.2397608</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> + +<dt>beta</dt> +<dd><p>Parameter of the FOMC model</p></dd> + + +<dt>times</dt> +<dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span>alpha <span class="op">=</span> <span class="fl">1.0001</span>, beta <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> actual twa</span> +<span class="r-out co"><span class="r-pr">#></span> 0 1.00000000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.90908224 0.9530973</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.83331814 0.9115995</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.71426168 0.8411664</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.58820408 0.7580202</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.41663019 0.6253074</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.32254415 0.5387324</span> +<span class="r-out co"><span class="r-pr">#></span> 28 0.26312277 0.4767543</span> +<span class="r-out co"><span class="r-pr">#></span> 42 0.19227599 0.3925054</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.16663681 0.3583198</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0.09088729 0.2397608</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index e371c1a..d2aa03b 100644 --- a/docs/reference/GUS.html +++ 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name"><code>GUS.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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>) - -<span class='co'># S3 method for numeric</span> -<span class='fu'>GUS</span>(<span class='no'>DT50</span>, <span class='no'>Koc</span>, <span class='no'>...</span>) - -<span class='co'># S3 method for chent</span> -<span class='fu'>GUS</span>( - <span class='no'>chent</span>, - <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, - <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, - <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, - <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='no'>...</span> -) - -<span class='co'># S3 method for GUS_result</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>...</th> - <td><p>Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>Half-life of the chemical in soil. Should be a field + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">GUS</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">GUS</span><span class="op">(</span><span class="va">DT50</span>, <span class="va">Koc</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for chent</span></span> +<span><span class="fu">GUS</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> degradation_value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span> +<span> lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span> +<span> redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span> +<span> sorption_value <span class="op">=</span> <span class="st">"Kfoc"</span>,</span> +<span> degradation_aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> sorption_aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for GUS_result</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>...</dt> +<dd><p>Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.</p></dd> + + +<dt>DT50</dt> +<dd><p>Half-life of the chemical in soil. Should be a field half-life according to Gustafson (1989). However, leaching to the sub-soil can not completely be excluded in field dissipation experiments and Gustafson did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption constant normalised to organic carbon. Gustafson +be conducted under use conditions.</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption constant normalised to organic carbon. Gustafson does not mention the nonlinearity of the sorption constant commonly found and usually described by Freundlich sorption, therefore it is unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).</p></td> - </tr> - <tr> - <th>chent</th> - <td><p>If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.</p></td> - </tr> - <tr> - <th>degradation_value</th> - <td><p>Which of the available degradation values should -be used?</p></td> - </tr> - <tr> - <th>lab_field</th> - <td><p>Should laboratory or field half-lives be used? This +(and if the reference concentration would be in soil or in porewater).</p></dd> + + +<dt>chent</dt> +<dd><p>If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.</p></dd> + + +<dt>degradation_value</dt> +<dd><p>Which of the available degradation values should +be used?</p></dd> + + +<dt>lab_field</dt> +<dd><p>Should laboratory or field half-lives be used? This defaults to lab in this implementation, in order to avoid double-accounting for mobility. If comparability with the original GUS values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.</p></td> - </tr> - <tr> - <th>redox</th> - <td><p>Aerobic or anaerobic degradation data</p></td> - </tr> - <tr> - <th>sorption_value</th> - <td><p>Which of the available sorption values should be used? +field half-lives obtained under actual use conditions should be used.</p></dd> + + +<dt>redox</dt> +<dd><p>Aerobic or anaerobic degradation data</p></dd> + + +<dt>sorption_value</dt> +<dd><p>Which of the available sorption values should be used? Defaults to Kfoc as this is what is generally available from the European pesticide peer review process. These values generally use a reference concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.</p></td> - </tr> - <tr> - <th>degradation_aggregator</th> - <td><p>Function for aggregating half-lives</p></td> - </tr> - <tr> - <th>sorption_aggregator</th> - <td><p>Function for aggregation Koc values</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An object of class GUS_result to be printed</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>The number of digits used in the print method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list with the DT50 and Koc used as well as the resulting score - of class GUS_result</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +be Koc values at a concentration of 1 mg/L in the water phase.</p></dd> + + +<dt>degradation_aggregator</dt> +<dd><p>Function for aggregating half-lives</p></dd> + + +<dt>sorption_aggregator</dt> +<dd><p>Function for aggregation Koc values</p></dd> + +<dt>x</dt> +<dd><p>An object of class GUS_result to be printed</p></dd> + + +<dt>digits</dt> +<dd><p>The number of digits used in the print method</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + + +<p>A list with the DT50 and Koc used as well as the resulting score + of class GUS_result</p> + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple method for assessing pesticide leachability. <em>Environmental toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - </ul> - - <h2>Author</h2> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div 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template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Get the relative accumulation of an FOMC model over multiples of an interval</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_soil.R" class="external-link"><code>R/PEC_soil.R</code></a></small> + <div class="d-none name"><code>PEC_FOMC_accu_rel.Rd</code></div> </div> - <div class="ref-description"> - + <div class="ref-description section level2"> <p>Get the relative accumulation of an FOMC model over multiples of an interval</p> - </div> - <pre class="usage"><span class='fu'>PEC_FOMC_accu_rel</span>(<span class='no'>n</span>, <span class='no'>interval</span>, <span class='no'>FOMC</span>)</pre> - - <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> - <th>n</th> - <td><p>number of applications</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>Time between applications</p></td> - </tr> - <tr> - <th>FOMC</th> - <td><p>Named numeric vector containing the FOMC parameters alpha and beta</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_FOMC_accu_rel</span><span class="op">(</span><span class="va">n</span>, <span class="va">interval</span>, <span class="va">FOMC</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>n</dt> +<dd><p>number of applications</p></dd> - <p>A numeric vector containing all n accumulation factors for the n applications</p> + +<dt>interval</dt> +<dd><p>Time between applications</p></dd> + + +<dt>FOMC</dt> +<dd><p>Named numeric vector containing the FOMC parameters alpha and beta</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - </ul> +<p>A numeric vector containing all n accumulation factors for the n applications</p> + </div> - </div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a 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If an interval is given, an attempt is made at calculating a long term maximum concentration using the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> - </span> - </div> + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> -</li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> - + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Calculate predicted environmental concentrations in soil</h1> - <div class="hidden name"><code>PEC_soil.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculate predicted environmental concentrations in soil</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_soil.R" class="external-link"><code>R/PEC_soil.R</code></a></small> + <div class="d-none name"><code>PEC_soil.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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 @@ -51,7 +58,8 @@ the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil</span><span class="op">(</span></span> <span> <span class="va">rate</span>,</span> <span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> @@ -78,8 +86,8 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>rate</dt> <dd><p>Application rate in units specified below</p></dd> @@ -195,14 +203,14 @@ soil concentrations? Based on equation (7) given in the PPR panel opinion p. 13).</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The predicted concentration in soil</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>This assumes that the complete load to soil during the time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion cited below (EFSA PPR panel 2012), only temperature correction using the @@ -210,8 +218,8 @@ Arrhenius equation is performed.</p> <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2017, p. 14/15) can easily be calculated.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>While time weighted average (TWA) concentrations given in the examples from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance @@ -227,8 +235,8 @@ from 2017 (p. 92).</p> (destination 'PECgw') is taken from the chent object, otherwise the DT50 with destination 'PECsoil'.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>EFSA Panel on Plant Protection Products and their Residues (2012) Scientific Opinion on the science behind the guidance for scenario selection and scenario parameterisation for predicting environmental @@ -245,13 +253,13 @@ from 2017 (p. 92).</p> in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 doi:10.2903/j.efsa.2015.4093</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span>, interception <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> scenario</span> <span class="r-out co"><span class="r-pr">#></span> t_avg default</span> @@ -297,26 +305,22 @@ from 2017 (p. 92).</p> <span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">100</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index c3b09f4..ddaa9d1 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -1,171 +1,98 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm</title> - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" 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href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculate initial and accumulation PEC soil for a set of metabolites</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_soil.R" class="external-link"><code>R/PEC_soil.R</code></a></small> + <div class="d-none name"><code>PEC_soil_mets.Rd</code></div> + </div> -<meta property="og:title" content="Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets" /> + <div class="ref-description section level2"> + <p>Calculate initial and accumulation PEC soil for a set of metabolites</p> + </div> -<meta property="og:description" content="Calculate initial and accumulation PEC soil for a set of metabolites" /> -<meta name="twitter:card" content="summary" /> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil_mets</span><span class="op">(</span><span class="va">rate</span>, <span class="va">mw_parent</span>, <span class="va">mets</span>, interval <span class="op">=</span> <span class="fl">365</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>mw_parent</dt> +<dd><p>The molecular weight of the parent compound</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>mets</dt> +<dd><p>A dataframe with metabolite identifiers as rownames +and columns "mw", "occ" and "DT50" holding their molecular weight, +maximum occurrence in soil and their soil DT50</p></dd> - - </header> +<dt>interval</dt> +<dd><p>The interval for accumulation calculations</p></dd> -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Calculate initial and accumulation PEC soil for a set of metabolites</h1> - - <div class="hidden name"><code>PEC_soil_mets.Rd</code></div> - </div> - <div class="ref-description"> - - <p>Calculate initial and accumulation PEC soil for a set of metabolites</p> - - </div> - - <pre class="usage"><span class='fu'>PEC_soil_mets</span>(<span class='no'>rate</span>, <span class='no'>mw_parent</span>, <span class='no'>mets</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='no'>...</span>)</pre> - - <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> - <th>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>mw_parent</th> - <td><p>The molecular weight of the parent compound</p></td> - </tr> - <tr> - <th>mets</th> - <td><p>A dataframe with metabolite identifiers as rownames -and columns "mw", "occ" and "DT50" holding their molecular weight, -maximum occurrence in soil and their soil DT50</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>The interval for accumulation calculations</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments are passed to PEC_soil</p></td> - </tr> - </table> - +<dt>...</dt> +<dd><p>Further arguments are passed to PEC_soil</p></dd> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> 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class="external-link"><code>R/PEC_sw_drainage_UK.R</code></a></small> + <div class="d-none name"><code>PEC_sw_drainage_UK.Rd</code></div> + </div> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <div class="ref-description section level2"> + <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> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> latest_application <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> soil_DT50 <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> model <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> model_parms <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>rate</dt> +<dd><p>Application rate in g/ha</p></dd> +<dt>interception</dt> +<dd><p>The fraction of the application rate that does not reach the soil</p></dd> -<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" /> +<dt>Koc</dt> +<dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> +<dt>latest_application</dt> +<dd><p>Latest application date, formatted as e.g. "01 July"</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>soil_DT50</dt> +<dd><p>Soil degradation half-life, if SFO kinetics are to be used</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>model</dt> +<dd><p>The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object</p></dd> - - </header> +<dt>model_parms</dt> +<dd><p>A named numeric vector containing the model parameters</p></dd> -<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> +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - <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> +<p>The predicted concentration in surface water in µg/L</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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction of the application rate that does not reach the soil</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient normalised to organic carbon in L/kg</p></td> - </tr> - <tr> - <th>latest_application</th> - <td><p>Latest application date, formatted as e.g. "01 July"</p></td> - </tr> - <tr> - <th>soil_DT50</th> - <td><p>Soil degradation half-life, if SFO kinetics are to be used</p></td> - </tr> - <tr> - <th>model</th> - <td><p>The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object</p></td> - </tr> - <tr> - <th>model_parms</th> - <td><p>A named numeric vector containing the model parameters</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in surface water in µg/L</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (for UK specific authorisation requests) - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> accessed 2019-09-27</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drainage_UK</span>(<span class='fl'>150</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)</div><div class='output co'>#> [1] 8.076923</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span><span class="fl">150</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 8.076923</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index e2c325b..3e1d4c8 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,221 +1,166 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + <div class="ref-description section level2"> + <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> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drift</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> applications <span class="op">=</span> <span class="fl">1</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> drift_percentages <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> drift_data <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"JKI"</span>, <span class="st">"RF"</span><span class="op">)</span>,</span> +<span> crop <span class="op">=</span> <span class="st">"Ackerbau"</span>,</span> +<span> distances <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">5</span>, <span class="fl">10</span>, <span class="fl">20</span><span class="op">)</span>,</span> +<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> +<span> PEC_units <span class="op">=</span> <span class="st">"µg/L"</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> +<dt>applications</dt> +<dd><p>Number of applications for selection of drift percentile</p></dd> +<dt>water_depth</dt> +<dd><p>Depth of the water body in cm</p></dd> -<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." /> +<dt>drift_percentages</dt> +<dd><p>Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.</p></dd> +<dt>drift_data</dt> +<dd><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] +included in the package is used. If 'RF', the Rautmann formula is used, if +implemented for the crop type and number of applications</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> - </span> - </div> +<dt>crop</dt> +<dd><p>Crop name (use German names for JKI data), defaults to "Ackerbau"</p></dd> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - +<dt>distances</dt> +<dd><p>The distances in m for which to get PEC values</p></dd> - </header> -<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> +<dt>rate_units</dt> +<dd><p>Defaults to g/ha</p></dd> + + +<dt>PEC_units</dt> +<dd><p>Requested units for the calculated PEC. Only µg/L currently supported</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - <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> +<p>The predicted concentration in surface water</p> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> + <p>Johannes Ranke</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"JKI"</span>, <span class='st'>"RF"</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'><a href='https://rdrr.io/r/base/c.html'>c</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>applications</th> - <td><p>Number of applications for selection of drift percentile</p></td> - </tr> - <tr> - <th>water_depth</th> - <td><p>Depth of the water body in cm</p></td> - </tr> - <tr> - <th>drift_percentages</th> - <td><p>Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.</p></td> - </tr> - <tr> - <th>drift_data</th> - <td><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] -included in the package is used. If 'RF', the Rautmann formula is used, if -implemented for the crop type and number of applications</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>Crop name (use German names for JKI data), defaults to "Ackerbau"</p></td> - </tr> - <tr> - <th>distances</th> - <td><p>The distances in m for which to get PEC values</p></td> - </tr> - <tr> - <th>rate_units</th> - <td><p>Defaults to g/ha</p></td> - </tr> - <tr> - <th>PEC_units</th> - <td><p>Requested units for the calculated PEC. Only µg/L currently supported</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in surface water</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m -#> 0.92333333 0.19000000 0.09666667 0.05000000 </div><div class='input'><span class='co'># Alternatively, we can use the formula for a single application to "Ackerbau" from the paper</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"RF"</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m -#> 0.92350000 0.19114149 0.09699222 0.04921742 </div><div class='input'> -<span class='co'># This makes it possible to also use different substances</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>5</span>, <span class='fl'>6</span>, <span class='fl'>10</span>, <span class='fl'>20</span>, <span class='fl'>50</span>, <span class='fl'>100</span>), <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"RF"</span>)</div><div class='output co'>#> 1 m 3 m 5 m 6 m 10 m 20 m 50 m -#> 0.92350000 0.31512171 0.19114149 0.15990435 0.09699222 0.04921742 0.02007497 -#> 100 m -#> 0.01018678 </div><div class='input'> -<span class='co'># Using custom drift percentages is also supported</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2.77</span>, <span class='fl'>0.95</span>, <span class='fl'>0.57</span>, <span class='fl'>0.48</span>, <span class='fl'>0.29</span>, <span class='fl'>0.15</span>, <span class='fl'>0.06</span>, <span class='fl'>0.03</span>))</div><div class='output co'>#> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % -#> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 -#> 0.03 % -#> 0.01000000 </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.19000000 0.09666667 0.05000000 </span> +<span class="r-in"><span><span class="co"># Alternatively, we can use the formula for a single application to "Ackerbau" from the paper</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92350000 0.19114149 0.09699222 0.04921742 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This makes it possible to also use different substances</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 3 m 5 m 6 m 10 m 20 m 50 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92350000 0.31512171 0.19114149 0.15990435 0.09699222 0.04921742 0.02007497 </span> +<span class="r-out co"><span class="r-pr">#></span> 100 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01018678 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Using custom drift percentages is also supported</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_percentages <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2.77</span>, <span class="fl">0.95</span>, <span class="fl">0.57</span>, <span class="fl">0.48</span>, <span class="fl">0.29</span>, <span class="fl">0.15</span>, <span class="fl">0.06</span>, <span class="fl">0.03</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.03 % </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01000000 </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - 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Although there are four groups of +compounds ("Gefährdungsgruppen"), only one distinction is made in the +calculations, between compounds with low mobility (group 1) and compounds +with modest to high mobility (groups 2, 3 and 4). In this implementation, +the group is derived only from the Koc, if not given explicitly. 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Although there are four groups of compounds ("Gefährdungsgruppen"), only one distinction is made in the @@ -121,123 +64,123 @@ the group is derived only from the Koc, if not given explicitly. For details, see the discussion of the function arguments below.</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_drainage</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>mobility</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"low"</span>, <span class='st'>"high"</span>), - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>t_drainage</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>V_drainage</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>spring</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>autumn</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span> -)</pre> - - <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> - <th>rate</th> - <td><p>The application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction intercepted by the crop</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger -value of 550 L/kg is used in order to decide if Koc >> 500.</p></td> - </tr> - <tr> - <th>mobility</th> - <td><p>Overrides what is determined from the Koc.</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The soil half-life in days</p></td> - </tr> - <tr> - <th>t_drainage</th> - <td><p>The time between application and the drainage event, where degradation occurs, in days</p></td> - </tr> - <tr> - <th>V_ditch</th> - <td><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></td> - </tr> - <tr> - <th>V_drainage</th> - <td><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for -autumn/winter/early spring.</p></td> - </tr> - <tr> - <th>dilution</th> - <td><p>The dilution factor</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> mobility <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"low"</span>, <span class="st">"high"</span><span class="op">)</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> t_drainage <span class="op">=</span> <span class="fl">3</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> +<span> V_drainage <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> +<span> dilution <span class="op">=</span> <span class="fl">2</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <a href="https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3" class="external-link">https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>rate</dt> +<dd><p>The application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction intercepted by the crop</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger +value of 550 L/kg is used in order to decide if Koc >> 500.</p></dd> + + +<dt>mobility</dt> +<dd><p>Overrides what is determined from the Koc.</p></dd> + + +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> + + +<dt>t_drainage</dt> +<dd><p>The time between application and the drainage event, where degradation occurs, in days</p></dd> + + +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> - <p>A list containing the following components</p><dl class='dl-horizontal'> - <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd> - <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> - <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance + +<dt>V_drainage</dt> +<dd><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for +autumn/winter/early spring.</p></dd> + + +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + -</dl> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <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> - <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_drainage</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_drainage_total -#> spring autumn -#> 0.2 1.0 -#> -#> $perc_peak -#> spring autumn -#> 12.5 25.0 -#> -#> $PEC_sw_drainage -#> spring autumn -#> 1.562500 4.807692 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> + <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> + </div> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_drainage_total</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2 1.0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $perc_peak</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 12.5 25.0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_drainage</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 1.562500 4.807692 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 81549e0..a3845ee 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -1,262 +1,202 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> 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name"><code>PEC_sw_exposit_runoff.Rd</code></div> + </div> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <div class="ref-description section level2"> + <p>This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, +in the worksheet "Konzept Runoff".</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> t_runoff <span class="op">=</span> <span class="fl">3</span>,</span> +<span> exposit_reduction_version <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"3.02"</span>, <span class="st">"3.01a"</span>, <span class="st">"3.01a2"</span>, <span class="st">"2.0"</span><span class="op">)</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> +<span> V_event <span class="op">=</span> <span class="fl">100</span>,</span> +<span> dilution <span class="op">=</span> <span class="fl">2</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3" class="external-link">https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>rate</dt> +<dd><p>The application rate in g/ha</p></dd> +<dt>interception</dt> +<dd><p>The fraction intercepted by the crop</p></dd> -<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 3.02 spreadsheet file, -in the worksheet "Konzept Runoff"." /> -<meta name="twitter:card" content="summary" /> +<dt>Koc</dt> +<dd><p>The sorption coefficient to soil organic carbon</p></dd> +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>t_runoff</dt> +<dd><p>The time between application and the runoff event, where degradation occurs, in days</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>exposit_reduction_version</dt> +<dd><p>The version of the reduction factors to be used. "3.02" is the current +version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer +zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations +performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved +and the bound fraction.</p></dd> - - </header> +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> -<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> - - <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 3.02 spreadsheet file, -in the worksheet "Konzept Runoff".</p> - </div> +<dt>V_event</dt> +<dd><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></dd> - <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</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'>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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"3.01a"</span>, <span class='st'>"3.01a2"</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>, - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span> -)</pre> - - <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> - <th>rate</th> - <td><p>The application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction intercepted by the crop</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient to soil organic carbon</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The soil half-life in days</p></td> - </tr> - <tr> - <th>t_runoff</th> - <td><p>The time between application and the runoff event, where degradation occurs, in days</p></td> - </tr> - <tr> - <th>exposit_reduction_version</th> - <td><p>The version of the reduction factors to be used. "3.02" is the current -version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer -zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations -performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved -and the bound fraction.</p></td> - </tr> - <tr> - <th>V_ditch</th> - <td><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></td> - </tr> - <tr> - <th>V_event</th> - <td><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></td> - </tr> - <tr> - <th>dilution</th> - <td><p>The dilution factor</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> - <p>A list containing the following components</p><dl class='dl-horizontal'> - <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd> - <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> - <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + -</dl> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <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> - <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_runoff -#> dissolved bound -#> 0.248 0.001 -#> -#> $runoff -#> dissolved bound total -#> No buffer 1.240 0.00500 1.24500 -#> 5 m 0.744 0.00300 0.74700 -#> 10 m 0.496 0.00075 0.49675 -#> 20 m 0.248 0.00025 0.24825 -#> -#> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 4.769231 0.019230769 4.788462 -#> 5 m 4.133333 0.016666667 4.150000 -#> 10 m 3.542857 0.005357143 3.548214 -#> 20 m 2.480000 0.002500000 2.482500 -#> </div><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>600</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>195</span>, <span class='kw'>exposit</span> <span class='kw'>=</span> <span class='st'>"3.01a"</span>)</div><div class='output co'>#> $perc_runoff -#> dissolved bound -#> 0.037 0.159 -#> -#> $runoff -#> dissolved bound total -#> No buffer 0.21964521 0.94388078 1.16352600 -#> 3 m 0.16473391 0.66071655 0.82545046 -#> 5 m 0.13178713 0.56632847 0.69811560 -#> 6 m 0.12080487 0.42474635 0.54555122 -#> 10 m 0.08785809 0.14158212 0.22944020 -#> 20 m 0.04392904 0.04719404 0.09112308 -#> -#> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 0.8447893 3.6303107 4.4751000 -#> 3 m 0.7844472 3.1462693 3.9307165 -#> 5 m 0.7321507 3.1462693 3.8784200 -#> 6 m 0.7106169 2.4985080 3.2091248 -#> 10 m 0.6275578 1.0113008 1.6388586 -#> 20 m 0.4392904 0.4719404 0.9112308 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> + <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> + </div> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> +<span class="r-out co"><span class="r-pr">#></span> 0.248 0.001 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 1.240 0.00500 1.24500</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.744 0.00300 0.74700</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.496 0.00075 0.49675</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.248 0.00025 0.24825</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 4.769231 0.019230769 4.788462</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 4.133333 0.016666667 4.150000</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 3.542857 0.005357143 3.548214</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 2.480000 0.002500000 2.482500</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">600</span>, Koc <span class="op">=</span> <span class="fl">10000</span>, DT50 <span class="op">=</span> <span class="fl">195</span>, exposit <span class="op">=</span> <span class="st">"3.01a"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> +<span class="r-out co"><span class="r-pr">#></span> 0.037 0.159 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.21964521 0.94388078 1.16352600</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.16473391 0.66071655 0.82545046</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.13178713 0.56632847 0.69811560</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.12080487 0.42474635 0.54555122</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.08785809 0.14158212 0.22944020</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.04392904 0.04719404 0.09112308</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.8447893 3.6303107 4.4751000</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.7844472 3.1462693 3.9307165</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.7321507 3.1462693 3.8784200</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.7106169 2.4985080 3.2091248</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.6275578 1.0113008 1.6388586</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.4392904 0.4719404 0.9112308</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 55a7400..78f6453 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><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, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="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 +applications should be compared to the corresponding results for a +single application. At current, this is not done automatically in +this implementation. Only Step 1 PECs are calculated. 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Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in @@ -8,44 +14,47 @@ input files are generated that are suitable as input also for Step 2 to be used with the FOCUS calculator."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> - </span> - </div> + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> -</li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small> - + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Calculate PEC surface water at FOCUS Step 1</h1> - <div class="hidden name"><code>PEC_sw_focus.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculate PEC surface water at FOCUS Step 1</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_focus.R" class="external-link"><code>R/PEC_sw_focus.R</code></a></small> + <div class="d-none name"><code>PEC_sw_focus.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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 applications should be compared to the corresponding results for a @@ -55,7 +64,8 @@ input files are generated that are suitable as input also for Step 2 to be used with the FOCUS calculator.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_focus</span><span class="op">(</span></span> <span> <span class="va">parent</span>,</span> <span> <span class="va">rate</span>,</span> @@ -77,8 +87,8 @@ to be used with the FOCUS calculator.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>parent</dt> <dd><p>A list containing substance specific parameters, e.g. conveniently generated by [chent_focus_sw].</p></dd> @@ -161,8 +171,8 @@ should be written</p></dd> <dd><p>Should the input text file be appended?</p></dd> </dl></div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The formulas for input to the waterbody via runoff/drainage of the parent and subsequent formation of the metabolite in water is not documented in the model description coming with the calculator. As one would @@ -171,8 +181,8 @@ should be written</p></dd> correction and the formation fraction in water/sediment systems.</p> <p>Step 2 is not implemented.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). FOrum for the Co-ordination of pesticde fate models and their USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p> @@ -181,8 +191,8 @@ should be written</p></dd> http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Parent only</span></span></span> <span class="r-in"><span><span class="va">dummy_1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"Dummy 1"</span>, cwsat <span class="op">=</span> <span class="fl">6000</span>, DT50_ws <span class="op">=</span> <span class="fl">6</span>, Koc <span class="op">=</span> <span class="fl">344.8</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">dummy_1</span>, <span class="fl">3000</span>, f_drift <span class="op">=</span> <span class="fl">0</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, append <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> @@ -284,26 +294,22 @@ should be written</p></dd> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div 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template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><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/HEAD/R/PEC_sw_sed.R" class="external-link"><code>R/PEC_sw_sed.R</code></a></small> + <div class="d-none name"><code>PEC_sw_sed.Rd</code></div> + </div> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <div class="ref-description section level2"> + <p>The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_sed</span><span class="op">(</span></span> +<span> <span class="va">PEC_sw</span>,</span> +<span> percentage <span class="op">=</span> <span class="fl">100</span>,</span> +<span> method <span class="op">=</span> <span class="st">"percentage"</span>,</span> +<span> sediment_depth <span class="op">=</span> <span class="fl">5</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> sediment_density <span class="op">=</span> <span class="fl">1.3</span>,</span> +<span> PEC_sed_units <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"µg/kg"</span>, <span class="st">"mg/kg"</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>PEC_sw</dt> +<dd><p>Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated</p></dd> +<dt>percentage</dt> +<dd><p>The percentage in sediment, used for the percentage method</p></dd> -<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" /> +<dt>method</dt> +<dd><p>The method used for the calculation</p></dd> +<dt>sediment_depth</dt> +<dd><p>Depth of the sediment layer</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>water_depth</dt> +<dd><p>Depth of the water body in cm</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>sediment_density</dt> +<dd><p>The density of the sediment in L/kg (equivalent to +g/cm3)</p></dd> - - </header> +<dt>PEC_sed_units</dt> +<dd><p>The units of the estimated sediment PEC value</p></dd> -<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> +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - <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> +<p>The predicted concentration in sediment</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'><a href='https://rdrr.io/r/base/c.html'>c</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>PEC_sw</th> - <td><p>Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated</p></td> - </tr> - <tr> - <th>percentage</th> - <td><p>The percentage in sediment, used for the percentage method</p></td> - </tr> - <tr> - <th>method</th> - <td><p>The method used for the calculation</p></td> - </tr> - <tr> - <th>sediment_depth</th> - <td><p>Depth of the sediment layer</p></td> - </tr> - <tr> - <th>water_depth</th> - <td><p>Depth of the water body in cm</p></td> - </tr> - <tr> - <th>sediment_density</th> - <td><p>The density of the sediment in L/kg (equivalent to -g/cm3)</p></td> - </tr> - <tr> - <th>PEC_sed_units</th> - <td><p>The units of the estimated sediment PEC value</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in sediment</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#> 1 m -#> 2.130769 </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_sed</span><span class="op">(</span><span class="fu"><a href="PEC_sw_drift.html">PEC_sw_drift</a></span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>, percentage <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m </span> +<span class="r-out co"><span class="r-pr">#></span> 2.130769 </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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href="https://github.com/jranke/pfm/blob/HEAD/R/SFO_actual_twa.R" class="external-link"><code>R/SFO_actual_twa.R</code></a></small> + <div class="d-none name"><code>SFO_actual_twa.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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'><a href='https://rdrr.io/r/base/c.html'>c</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>DT50</th> - <td><p>The half-life.</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times, and window sizes for time weighted average concentrations</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO_actual_twa</span><span class="op">(</span>DT50 <span class="op">=</span> <span class="fl">1000</span>, times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</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><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>DT50</dt> +<dd><p>The half-life.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>SFO_actual_twa</span>(<span class='fl'>10</span>)</div><div class='output co'>#> actual twa -#> 0 1.0000000000 NaN -#> 1 0.9330329915 0.9661297 -#> 2 0.8705505633 0.9337803 -#> 4 0.7578582833 0.8733416 -#> 7 0.6155722067 0.7923030 -#> 14 0.3789291416 0.6400113 -#> 21 0.2332582479 0.5267498 -#> 28 0.1435872944 0.4412651 -#> 42 0.0544094102 0.3248093 -#> 50 0.0312500000 0.2795222 -#> 100 0.0009765625 0.1441286</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> + +<dt>times</dt> +<dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SFO_actual_twa</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> actual twa</span> +<span class="r-out co"><span class="r-pr">#></span> 0 1.0000000000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.9330329915 0.9661297</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.8705505633 0.9337803</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.7578582833 0.8733416</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.6155722067 0.7923030</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.3789291416 0.6400113</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.2332582479 0.5267498</span> +<span class="r-out co"><span class="r-pr">#></span> 28 0.1435872944 0.4412651</span> +<span class="r-out co"><span class="r-pr">#></span> 42 0.0544094102 0.3248093</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.0312500000 0.2795222</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0.0009765625 0.1441286</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git 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class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><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/HEAD/R/SSLRC_mobility_classification.R" class="external-link"><code>R/SSLRC_mobility_classification.R</code></a></small> + <div class="d-none name"><code>SSLRC_mobility_classification.Rd</code></div> </div> - <div class="ref-description"> - + <div class="ref-description section level2"> <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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient normalised to organic carbon in L/kg</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="va">Koc</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A list containing the classification and the percentage of the - compound transported per 10 mm drain water</p> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>Koc</dt> +<dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<p>A list containing the classification and the percentage of the + compound transported per 10 mm drain water</p> + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (for UK specific authorisation requests) - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> accessed 2019-09-27</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>100</span>)</div><div class='output co'>#> $`Mobility classification` -#> [1] "Moderately mobile" -#> -#> $`Percentage drained per mm of drain water` -#> [1] 0.7 -#> </div><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>10000</span>)</div><div class='output co'>#> $`Mobility classification` -#> [1] "Non mobile" -#> -#> $`Percentage drained per mm of drain water` -#> [1] 0.008 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "Moderately mobile"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`Percentage drained per mm of drain water`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.7</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "Non mobile"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`Percentage drained per mm of drain water`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - 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+ <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> - <div class="hidden name"><code>TOXSWA_cwa.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/TOXSWA_cwa.R" class="external-link"><code>R/TOXSWA_cwa.R</code></a></small> + <div class="d-none name"><code>TOXSWA_cwa.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified @@ -52,12 +59,12 @@ by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An <code>R6Class</code> generator object.</p> </div> - <div id="public-fields"> - <h2>Public fields</h2> + <div class="section level2"> + <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> <p></p><div class="r6-fields"><dl><dt><code>filename</code></dt> <dd><p>Length one character vector holding the filename.</p></dd> @@ -94,8 +101,8 @@ for the requested moving window sizes in days.</p></dd> </dl><p></p></div> </div> - <div id="methods"> - <h2>Methods</h2> + <div class="section level2"> + <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> @@ -220,8 +227,8 @@ suspended matter will be used.</p></dd> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> <span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> <span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> @@ -230,53 +237,25 @@ suspended matter will be used.</p></dd> <span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 </span> -<span class="r-out co"><span class="r-pr">#></span> datetime t t_firstjan t_rel_to_max cwa_mug_per_L</span> -<span class="r-out co"><span class="r-pr">#></span> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0</span> -<span class="r-out co"><span class="r-pr">#></span> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0</span> -<span class="r-out co"><span class="r-pr">#></span> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0</span> -<span class="r-out co"><span class="r-pr">#></span> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0</span> -<span class="r-out co"><span class="r-pr">#></span> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0</span> -<span class="r-out co"><span class="r-pr">#></span> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0</span> -<span class="r-out co"><span class="r-pr">#></span> cwa_tot_mug_per_L</span> -<span class="r-out co"><span class="r-pr">#></span> 20 0</span> -<span class="r-out co"><span class="r-pr">#></span> 40 0</span> -<span class="r-out co"><span class="r-pr">#></span> 60 0</span> -<span class="r-out co"><span class="r-pr">#></span> 80 0</span> -<span class="r-out co"><span class="r-pr">#></span> 100 0</span> -<span class="r-out co"><span class="r-pr">#></span> 120 0</span> -<span class="r-out co"><span class="r-pr">#></span> Moving window analysis</span> -<span class="r-out co"><span class="r-pr">#></span> window max_TWAC max_AUC_h max_AUC_d</span> -<span class="r-out co"><span class="r-pr">#></span> 1 7 days 2.3926551 401.9660 16.74859</span> -<span class="r-out co"><span class="r-pr">#></span> 2 21 days 0.8369248 421.8101 17.57542</span> -<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 2 </span> -<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> -<span class="r-out co"><span class="r-pr">#></span> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501</span> -<span class="r-out co"><span class="r-pr">#></span> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162</span> -<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 10 </span> -<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> -<span class="r-out co"><span class="r-pr">#></span> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in head(self$cwas):</span> could not find function "head"</span> </code></pre></div> </div> - 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It is not clarified when it can be regarded reliable, but the @@ -122,60 +61,62 @@ the compound should not be ionogenic (weak acid/base) or ionic.</p> </div> - <pre class="usage"><span class='fu'>TSCF</span>(<span class='no'>log_Kow</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"briggs82"</span>, <span class='st'>"dettenmaier09"</span>))</pre> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">TSCF</span><span class="op">(</span><span class="va">log_Kow</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"briggs82"</span>, <span class="st">"dettenmaier09"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> - <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> - <th>log_Kow</th> - <td><p>The decadic logarithm of the octanol-water partition constant</p></td> - </tr> - <tr> - <th>method</th> - <td><p>Short name of the estimation method.</p></td> - </tr> - </table> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>log_Kow</dt> +<dd><p>The decadic logarithm of the octanol-water partition constant</p></dd> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<dt>method</dt> +<dd><p>Short name of the estimation method.</p></dd> +</dl></div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> + <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake by plant roots. Environ. Sci. Technol 43, 324 - 329</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>TSCF</span>, -<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"log Kow"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"TSCF"</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span>))</div><div class='input'><span class='no'>TSCF_2</span> <span class='kw'><-</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>TSCF</span>(<span class='no'>x</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"dettenmaier09"</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/curve.html'>curve</a></span>(<span class='no'>TSCF_2</span>, -<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>2</span>, <span class='kw'>bty</span> <span class='kw'>=</span> <span class='st'>"n"</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Briggs et al. (1982)"</span>, <span class='st'>"Dettenmaier et al. (2009)"</span>))</div><div class='img'><img src='TSCF-1.png' alt='' width='700' height='433' /></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">TSCF</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, xlab <span class="op">=</span> <span class="st">"log Kow"</span>, ylab <span class="op">=</span> <span class="st">"TSCF"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="TSCF-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="va">TSCF_2</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">TSCF</span><span class="op">(</span><span class="va">x</span>, method <span class="op">=</span> <span class="st">"dettenmaier09"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/curve.html" class="external-link">curve</a></span><span class="op">(</span><span class="va">TSCF_2</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in curve(TSCF_2, -1, 5, add = TRUE, lty = 2):</span> could not find function "curve"</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></span><span class="op">(</span><span class="st">"topright"</span>, lty <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, bty <span class="op">=</span> <span class="st">"n"</span>,</span></span> +<span class="r-in"><span> legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Briggs et al. (1982)"</span>, <span class="st">"Dettenmaier et al. (2009)"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in legend("topright", lty = 1:2, bty = "n", legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)")):</span> could not find function "legend"</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 70fd16d..5ffa6b4 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -1,206 +1,135 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - 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1 calculations</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">chent_focus_sw</span><span class="op">(</span></span> +<span> <span class="va">name</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> DT50_ws <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_soil <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_water <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_sediment <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> cwsat <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> mw <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> max_soil <span class="op">=</span> <span class="fl">1</span>,</span> +<span> max_ws <span class="op">=</span> <span class="fl">1</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>name</dt> +<dd><p>Length one character vector containing the name</p></dd> +<dt>Koc</dt> +<dd><p>Partition coefficient between organic carbon and water +in L/kg.</p></dd> -<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" /> +<dt>DT50_ws</dt> +<dd><p>Half-life in water/sediment systems in days</p></dd> +<dt>DT50_soil</dt> +<dd><p>Half-life in soil in days</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>DT50_water</dt> +<dd><p>Half-life in water in days (Step 2)</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>DT50_sediment</dt> +<dd><p>Half-life in sediment in days (Step 2)</p></dd> - - </header> +<dt>cwsat</dt> +<dd><p>Water solubility in mg/L</p></dd> -<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> - - <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> +<dt>mw</dt> +<dd><p>Molar weight in g/mol.</p></dd> - <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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>name</th> - <td><p>Length one character vector containing the name</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>Partition coefficient between organic carbon and water -in L/kg.</p></td> - </tr> - <tr> - <th>DT50_ws</th> - <td><p>Half-life in water/sediment systems in days</p></td> - </tr> - <tr> - <th>DT50_soil</th> - <td><p>Half-life in soil in days</p></td> - </tr> - <tr> - <th>DT50_water</th> - <td><p>Half-life in water in days (Step 2)</p></td> - </tr> - <tr> - <th>DT50_sediment</th> - <td><p>Half-life in sediment in days (Step 2)</p></td> - </tr> - <tr> - <th>cwsat</th> - <td><p>Water solubility in mg/L</p></td> - </tr> - <tr> - <th>mw</th> - <td><p>Molar weight in g/mol.</p></td> - </tr> - <tr> - <th>max_soil</th> - <td><p>Maximum observed fraction (dimensionless) in soil</p></td> - </tr> - <tr> - <th>max_ws</th> - <td><p>Maximum observed fraction (dimensionless) in water/sediment -systems</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list with the substance specific properties</p> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - </ul> +<dt>max_soil</dt> +<dd><p>Maximum observed fraction (dimensionless) in soil</p></dd> - </div> -</div> +<dt>max_ws</dt> +<dd><p>Maximum observed fraction (dimensionless) in water/sediment +systems</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + + +<p>A list with the substance specific properties</p> + </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + 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from spray drift expressed as percent of the applied dose as + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</h1> - - <div class="hidden name"><code>drift_data_JKI.Rd</code></div> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/drift_data_JKI.R" class="external-link"><code>R/drift_data_JKI.R</code></a></small> + <div class="d-none name"><code>drift_data_JKI.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late (Obstbau frueh, spaet).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html @@ -133,8 +68,9 @@ on 2015-06-11</p> <p>Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The data were extracted from the spreadsheet cited below using the R code given in the example section. The spreadsheet is not included in the package as its licence is not clear.</p> @@ -148,272 +84,269 @@ these values are used for spray applications with handheld/knapsack equipment (tragbare Spritz- und Sprühgerate).</p> <p>Values for non-professional use listed in the JKI spreadsheet were not included.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to extract the data</span> - <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>readxl</span>) - <span class='no'>abdrift_path</span> <span class='kw'><-</span> <span class='st'>"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span> - <span class='no'>JKI_crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>, <span class='st'>"Weinbau frueh"</span>, <span class='st'>"Weinbau spaet"</span>, - <span class='st'>"Hopfenbau"</span>, <span class='st'>"Flaechenkulturen > 900 l/ha"</span>, <span class='st'>"Gleisanlagen"</span>) - <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>JKI_crops</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>, - <span class='st'>"Vines early"</span>, <span class='st'>"Vines late"</span>, <span class='st'>"Hops"</span>, <span class='st'>"Areic cultures > 900 L/ha"</span>, <span class='st'>"Railroad tracks"</span>) - <span class='no'>drift_data_JKI</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></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'><a href='https://rdrr.io/pkg/readxl/man/read_excel.html'>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'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>9</span>, <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>JKI_crops</span>)) - <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>drift_data</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='no'>drift_data_raw</span><span class='kw'>[[</span><span class='fl'>1</span>]][<span class='fl'>1</span>:<span class='fl'>9</span>], - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>) - <span class='kw'>if</span> (<span class='no'>n</span> <span class='kw'>==</span> <span class='fl'>1</span>) { <span class='co'># Values for railroad tracks only present for one application</span> - <span class='no'>drift_data</span>[, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>3</span>, <span class='fl'>5</span>:<span class='fl'>8</span>)] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>:<span class='fl'>7</span>, <span class='fl'>11</span>)][<span class='fl'>1</span>:<span class='fl'>9</span>, ]) - } <span class='kw'>else</span> { - <span class='no'>drift_data</span>[, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>3</span>, <span class='fl'>5</span>:<span class='fl'>7</span>)] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>:<span class='fl'>7</span>)][<span class='fl'>1</span>:<span class='fl'>9</span>, ]) - } - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='no'>n</span>]] <span class='kw'><-</span> <span class='no'>drift_data</span> - } - - <span class='co'># Manual data entry from the Rautmann paper</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>1</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.95</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>1</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.7</span>, <span class='fl'>1.18</span>, <span class='fl'>0.39</span>, <span class='fl'>0.2</span>, <span class='fl'>0.13</span>, <span class='fl'>0.07</span>, <span class='fl'>0.04</span>, <span class='fl'>0.03</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>2</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.79</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>2</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.53</span>, <span class='fl'>1.09</span>, <span class='fl'>0.35</span>, <span class='fl'>0.18</span>, <span class='fl'>0.11</span>, <span class='fl'>0.06</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>3</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.68</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>3</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.49</span>, <span class='fl'>1.04</span>, <span class='fl'>0.32</span>, <span class='fl'>0.16</span>, <span class='fl'>0.10</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>4</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.62</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>4</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.44</span>, <span class='fl'>1.02</span>, <span class='fl'>0.31</span>, <span class='fl'>0.16</span>, <span class='fl'>0.10</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>5</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.59</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>5</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.37</span>, <span class='fl'>1.00</span>, <span class='fl'>0.31</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>6</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.56</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>6</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.29</span>, <span class='fl'>0.97</span>, <span class='fl'>0.30</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>7</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.55</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>7</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.24</span>, <span class='fl'>0.94</span>, <span class='fl'>0.29</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>8</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.52</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>8</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.16</span>, <span class='fl'>0.91</span>, <span class='fl'>0.28</span>, <span class='fl'>0.14</span>, <span class='fl'>0.09</span>, <span class='fl'>0.04</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - - <span class='co'># Save the data</span> - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>) -} - -<span class='co'># And these are the resulting data</span> -<span class='no'>drift_data_JKI</span></div><div class='output co'>#> [[1]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.77 NA NA NA NA -#> 3 0.95 29.20 15.73 2.70 8.02 -#> 5 0.57 19.89 8.41 1.18 3.62 -#> 10 0.29 11.81 3.60 0.39 1.23 -#> 15 0.20 5.55 1.81 0.20 0.65 -#> 20 0.15 2.77 1.09 0.13 0.42 -#> 30 0.10 1.04 0.54 0.07 0.22 -#> 40 0.07 0.52 0.32 0.04 0.14 -#> 50 0.06 0.30 0.22 0.03 0.10 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 4.440 NA -#> 3 19.33 NA 0.018721696 -#> 5 11.57 0.180 0.014363896 -#> 10 5.77 0.050 0.010026007 -#> 15 3.84 0.020 0.008124366 -#> 20 1.79 0.012 0.006998158 -#> 30 0.56 0.005 0.005670811 -#> 40 0.25 0.003 NA -#> 50 0.13 0.002 0.004350831 -#> -#> [[2]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.38 NA NA NA NA -#> 3 0.79 25.53 12.13 2.53 7.23 -#> 5 0.47 16.87 6.81 1.09 3.22 -#> 10 0.24 9.61 3.11 0.35 1.07 -#> 15 0.16 5.61 1.58 0.18 0.56 -#> 20 0.12 2.59 0.90 0.11 0.36 -#> 30 0.08 0.87 0.40 0.06 0.19 -#> 40 0.06 0.40 0.23 0.03 0.12 -#> 50 0.05 0.22 0.15 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 3.780 NA -#> 3 17.73 NA NA -#> 5 9.60 0.160 NA -#> 10 4.18 0.040 NA -#> 15 2.57 0.020 NA -#> 20 1.21 0.011 NA -#> 30 0.38 0.005 NA -#> 40 0.17 0.003 NA -#> 50 0.09 0.002 NA -#> -#> [[3]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.01 NA NA NA NA -#> 3 0.68 23.96 11.01 2.49 6.90 -#> 5 0.41 15.79 6.04 1.04 3.07 -#> 10 0.20 8.96 2.67 0.32 1.02 -#> 15 0.14 4.24 1.39 0.16 0.54 -#> 20 0.10 2.01 0.80 0.10 0.34 -#> 30 0.07 0.70 0.36 0.05 0.18 -#> 40 0.05 0.33 0.21 0.03 0.11 -#> 50 0.04 0.19 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 3.420 NA -#> 3 15.93 NA NA -#> 5 8.57 0.150 NA -#> 10 3.70 0.040 NA -#> 15 2.26 0.020 NA -#> 20 1.05 0.010 NA -#> 30 0.34 0.004 NA -#> 40 0.15 0.003 NA -#> 50 0.08 0.002 NA -#> -#> [[4]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.85 NA NA NA NA -#> 3 0.62 23.61 10.12 2.44 6.71 -#> 5 0.38 15.42 5.60 1.02 2.99 -#> 10 0.19 8.66 2.50 0.31 0.99 -#> 15 0.13 4.01 1.28 0.16 0.52 -#> 20 0.10 1.89 0.75 0.10 0.33 -#> 30 0.06 0.66 0.35 0.05 0.17 -#> 40 0.05 0.31 0.20 0.03 0.11 -#> 50 0.04 0.17 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 2.290 NA -#> 3 15.38 NA NA -#> 5 8.26 0.120 NA -#> 10 3.55 0.030 NA -#> 15 2.17 0.020 NA -#> 20 0.93 0.009 NA -#> 30 0.31 0.004 NA -#> 40 0.14 0.002 NA -#> 50 0.08 0.002 NA -#> -#> [[5]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.75 NA NA NA NA -#> 3 0.59 23.12 9.74 2.37 6.59 -#> 5 0.36 15.06 5.41 1.00 2.93 -#> 10 0.18 8.42 2.43 0.31 0.98 -#> 15 0.12 3.83 1.24 0.15 0.51 -#> 20 0.09 1.81 0.72 0.09 0.33 -#> 30 0.06 0.63 0.34 0.05 0.17 -#> 40 0.05 0.30 0.20 0.03 0.11 -#> 50 0.04 0.17 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 2.120 NA -#> 3 15.12 NA NA -#> 5 7.99 0.110 NA -#> 10 3.36 0.030 NA -#> 15 2.03 0.010 NA -#> 20 0.88 0.008 NA -#> 30 0.29 0.004 NA -#> 40 0.14 0.002 NA -#> 50 0.07 0.002 NA -#> -#> [[6]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.64 NA NA NA NA -#> 3 0.56 22.76 9.21 2.29 6.41 -#> 5 0.34 14.64 5.18 0.97 2.85 -#> 10 0.17 8.04 2.38 0.30 0.95 -#> 15 0.11 3.71 1.20 0.15 0.50 -#> 20 0.09 1.75 0.68 0.09 0.32 -#> 30 0.06 0.61 0.31 0.05 0.17 -#> 40 0.04 0.29 0.17 0.03 0.11 -#> 50 0.03 0.16 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.980 NA -#> 3 14.90 NA NA -#> 5 7.79 0.100 NA -#> 10 3.23 0.030 NA -#> 15 1.93 0.010 NA -#> 20 0.83 0.008 NA -#> 30 0.28 0.004 NA -#> 40 0.13 0.002 NA -#> 50 0.07 0.001 NA -#> -#> [[7]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.61 NA NA NA NA -#> 3 0.55 22.69 9.10 2.24 6.33 -#> 5 0.33 14.45 5.11 0.94 2.81 -#> 10 0.17 7.83 2.33 0.29 0.94 -#> 15 0.11 3.62 1.20 0.15 0.49 -#> 20 0.08 1.71 0.67 0.09 0.31 -#> 30 0.06 0.60 0.30 0.05 0.16 -#> 40 0.04 0.28 0.17 0.03 0.10 -#> 50 0.03 0.16 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.930 NA -#> 3 14.63 NA NA -#> 5 7.60 0.100 NA -#> 10 3.13 0.030 NA -#> 15 1.86 0.010 NA -#> 20 0.81 0.008 NA -#> 30 0.26 0.004 NA -#> 40 0.12 0.002 NA -#> 50 0.06 0.001 NA -#> -#> [[8]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.52 NA NA NA NA -#> 3 0.52 22.24 8.66 2.16 6.26 -#> 5 0.31 14.09 4.92 0.91 2.78 -#> 10 0.16 7.58 2.29 0.28 0.93 -#> 15 0.11 3.48 1.14 0.14 0.49 -#> 20 0.08 1.65 0.65 0.09 0.31 -#> 30 0.05 0.57 0.29 0.04 0.16 -#> 40 0.04 0.27 0.16 0.03 0.10 -#> 50 0.03 0.15 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.640 NA -#> 3 13.53 NA NA -#> 5 7.15 0.090 NA -#> 10 3.01 0.020 NA -#> 15 1.82 0.010 NA -#> 20 0.78 0.007 NA -#> 30 0.25 0.003 NA -#> 40 0.12 0.002 NA -#> 50 0.06 0.001 NA -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to extract the data</span></span></span> +<span class="r-in"><span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://readxl.tidyverse.org" class="external-link">readxl</a></span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">abdrift_path</span> <span class="op"><-</span> <span class="st">"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span></span></span> +<span class="r-in"><span> <span class="va">JKI_crops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Ackerbau"</span>, <span class="st">"Obstbau frueh"</span>, <span class="st">"Obstbau spaet"</span>, <span class="st">"Weinbau frueh"</span>, <span class="st">"Weinbau spaet"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Hopfenbau"</span>, <span class="st">"Flaechenkulturen > 900 l/ha"</span>, <span class="st">"Gleisanlagen"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">JKI_crops</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Field crops"</span>, <span class="st">"Pome/stone fruit, early"</span>, <span class="st">"Pome/stone fruit, late"</span>,</span></span> +<span class="r-in"><span> <span class="st">"Vines early"</span>, <span class="st">"Vines late"</span>, <span class="st">"Hops"</span>, <span class="st">"Areic cultures > 900 L/ha"</span>, <span class="st">"Railroad tracks"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="kw">for</span> <span class="op">(</span><span class="va">n</span> <span class="kw">in</span> <span class="fl">1</span><span class="op">:</span><span class="fl">8</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_raw</span> <span class="op"><-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html" class="external-link">read_excel</a></span><span class="op">(</span><span class="va">abdrift_path</span>, sheet <span class="op">=</span> <span class="va">n</span> <span class="op">+</span> <span class="fl">1</span>, skip <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="cn">NA</span>, nrow <span class="op">=</span> <span class="fl">9</span>, ncol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">JKI_crops</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">drift_data</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>distance <span class="op">=</span> <span class="va">drift_data_raw</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">9</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> crop <span class="op">=</span> <span class="va">JKI_crops</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="va">n</span> <span class="op">==</span> <span class="fl">1</span><span class="op">)</span> <span class="op">{</span> <span class="co"># Values for railroad tracks only present for one application</span></span></span> +<span class="r-in"><span> <span class="va">drift_data</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">5</span><span class="op">:</span><span class="fl">8</span><span class="op">)</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">drift_data_raw</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span><span class="op">:</span><span class="fl">7</span>, <span class="fl">11</span><span class="op">)</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">9</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">drift_data</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">5</span><span class="op">:</span><span class="fl">7</span><span class="op">)</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">drift_data_raw</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span><span class="op">:</span><span class="fl">7</span><span class="op">)</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">9</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="va">n</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="va">drift_data</span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Manual data entry from the Rautmann paper</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.95</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.7</span>, <span class="fl">1.18</span>, <span class="fl">0.39</span>, <span class="fl">0.2</span>, <span class="fl">0.13</span>, <span class="fl">0.07</span>, <span class="fl">0.04</span>, <span class="fl">0.03</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.79</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.53</span>, <span class="fl">1.09</span>, <span class="fl">0.35</span>, <span class="fl">0.18</span>, <span class="fl">0.11</span>, <span class="fl">0.06</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.68</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.49</span>, <span class="fl">1.04</span>, <span class="fl">0.32</span>, <span class="fl">0.16</span>, <span class="fl">0.10</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">4</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.62</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">4</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.44</span>, <span class="fl">1.02</span>, <span class="fl">0.31</span>, <span class="fl">0.16</span>, <span class="fl">0.10</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">5</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.59</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">5</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.37</span>, <span class="fl">1.00</span>, <span class="fl">0.31</span>, <span class="fl">0.15</span>, <span class="fl">0.09</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">6</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.56</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">6</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.29</span>, <span class="fl">0.97</span>, <span class="fl">0.30</span>, <span class="fl">0.15</span>, <span class="fl">0.09</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">7</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.55</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">7</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.24</span>, <span class="fl">0.94</span>, <span class="fl">0.29</span>, <span class="fl">0.15</span>, <span class="fl">0.09</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">8</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="st">"3"</span>, <span class="st">"Ackerbau"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">0.52</span></span></span> +<span class="r-in"><span> <span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">8</span><span class="op">]</span><span class="op">]</span><span class="op">[</span>, <span class="st">"Weinbau frueh"</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">2.16</span>, <span class="fl">0.91</span>, <span class="fl">0.28</span>, <span class="fl">0.14</span>, <span class="fl">0.09</span>, <span class="fl">0.04</span>, <span class="fl">0.03</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Save the data</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">drift_data_JKI</span>, file <span class="op">=</span> <span class="st">"data/drift_data_JKI.RData"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And these are the resulting data</span></span></span> +<span class="r-in"><span><span class="va">drift_data_JKI</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.77 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.95 29.20 15.73 2.70 8.02</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.57 19.89 8.41 1.18 3.62</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.29 11.81 3.60 0.39 1.23</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.20 5.55 1.81 0.20 0.65</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.15 2.77 1.09 0.13 0.42</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.10 1.04 0.54 0.07 0.22</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.07 0.52 0.32 0.04 0.14</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.30 0.22 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 4.440 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 19.33 NA 0.018721696</span> +<span class="r-out co"><span class="r-pr">#></span> 5 11.57 0.180 0.014363896</span> +<span class="r-out co"><span class="r-pr">#></span> 10 5.77 0.050 0.010026007</span> +<span class="r-out co"><span class="r-pr">#></span> 15 3.84 0.020 0.008124366</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.79 0.012 0.006998158</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.56 0.005 0.005670811</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.25 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.13 0.002 0.004350831</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[2]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.38 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.79 25.53 12.13 2.53 7.23</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.47 16.87 6.81 1.09 3.22</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.24 9.61 3.11 0.35 1.07</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.16 5.61 1.58 0.18 0.56</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.12 2.59 0.90 0.11 0.36</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.08 0.87 0.40 0.06 0.19</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.06 0.40 0.23 0.03 0.12</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.05 0.22 0.15 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 3.780 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 17.73 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 9.60 0.160 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 4.18 0.040 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.57 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.21 0.011 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.38 0.005 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.17 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.09 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[3]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.01 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.68 23.96 11.01 2.49 6.90</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.41 15.79 6.04 1.04 3.07</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.20 8.96 2.67 0.32 1.02</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.14 4.24 1.39 0.16 0.54</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.10 2.01 0.80 0.10 0.34</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.07 0.70 0.36 0.05 0.18</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.33 0.21 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.19 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 3.420 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.93 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 8.57 0.150 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.70 0.040 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.26 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.05 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.34 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.15 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.08 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[4]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.85 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.62 23.61 10.12 2.44 6.71</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.38 15.42 5.60 1.02 2.99</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.19 8.66 2.50 0.31 0.99</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.13 4.01 1.28 0.16 0.52</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.10 1.89 0.75 0.10 0.33</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.66 0.35 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.31 0.20 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.17 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 2.290 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.38 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 8.26 0.120 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.55 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.17 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.93 0.009 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.31 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.14 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.08 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[5]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.75 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.59 23.12 9.74 2.37 6.59</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.36 15.06 5.41 1.00 2.93</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.18 8.42 2.43 0.31 0.98</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.12 3.83 1.24 0.15 0.51</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.09 1.81 0.72 0.09 0.33</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.63 0.34 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.30 0.20 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.17 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 2.120 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.12 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.99 0.110 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.36 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.03 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.88 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.29 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.14 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.07 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[6]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.64 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.56 22.76 9.21 2.29 6.41</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.34 14.64 5.18 0.97 2.85</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.17 8.04 2.38 0.30 0.95</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.71 1.20 0.15 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.09 1.75 0.68 0.09 0.32</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.61 0.31 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.29 0.17 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.16 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.980 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 14.90 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.79 0.100 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.23 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.93 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.83 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.28 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.13 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.07 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[7]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.61 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.55 22.69 9.10 2.24 6.33</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.33 14.45 5.11 0.94 2.81</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.17 7.83 2.33 0.29 0.94</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.62 1.20 0.15 0.49</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.08 1.71 0.67 0.09 0.31</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.60 0.30 0.05 0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.28 0.17 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.16 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.930 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 14.63 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.60 0.100 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.13 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.86 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.81 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.26 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.12 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[8]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.52 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.52 22.24 8.66 2.16 6.26</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.31 14.09 4.92 0.91 2.78</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.16 7.58 2.29 0.28 0.93</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.48 1.14 0.14 0.49</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.08 1.65 0.65 0.09 0.31</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.05 0.57 0.29 0.04 0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.27 0.16 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.15 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.640 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 13.53 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.15 0.090 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.01 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.82 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.78 0.007 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.25 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.12 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 39071ee..5e038b1 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,250 +1,182 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta 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Such information is extracted and optionally aggregated by +this function.</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoint</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> medium <span class="op">=</span> <span class="st">"soil"</span>,</span> +<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"degradation"</span>, <span class="st">"sorption"</span><span class="op">)</span>,</span> +<span> lab_field <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"laboratory"</span>, <span class="st">"field"</span><span class="op">)</span>,</span> +<span> redox <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"aerobic"</span>, <span class="st">"anaerobic"</span><span class="op">)</span>,</span> +<span> value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"DT50ref"</span>, <span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span> +<span> aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> raw <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> signif <span class="op">=</span> <span class="fl">3</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_DT50</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> signif <span class="op">=</span> <span class="fl">3</span>,</span> +<span> lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span> +<span> value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span> +<span> redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span> +<span> raw <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_Kfoc</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">geomean</span>, signif <span class="op">=</span> <span class="fl">3</span>, value <span class="op">=</span> <span class="st">"Kfoc"</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_N</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">mean</span>, signif <span class="op">=</span> <span class="fl">3</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_sorption</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> values <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span> +<span> aggregators <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="va">geomean</span>, Koc <span class="op">=</span> <span class="va">geomean</span>, N <span class="op">=</span> <span class="va">mean</span><span class="op">)</span>,</span> +<span> signif <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="fl">3</span>, N <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>,</span> +<span> raw <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>chent</dt> +<dd><p>The chent object to get the information from</p></dd> +<dt>medium</dt> +<dd><p>The medium for which information is sought</p></dd> -<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 -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" /> +<dt>type</dt> +<dd><p>The information type</p></dd> +<dt>lab_field</dt> +<dd><p>If not NA, do we want laboratory or field endpoints</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>redox</dt> +<dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>value</dt> +<dd><p>The name of the value we want. The list given in the +usage section is not exclusive</p></dd> - - </header> +<dt>aggregator</dt> +<dd><p>The aggregator function. Can be mean, +<code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd> -<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> - - <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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>), - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>, <span class='st'>"anaerobic"</span>), - <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), - <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span> -) - -<span class='fu'>soil_DT50</span>( - <span class='no'>chent</span>, - <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, - <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, - <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -) - -<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>soil_sorption</span>( - <span class='no'>chent</span>, - <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), - <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <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'><a href='https://rdrr.io/r/base/c.html'>c</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>chent</th> - <td><p>The chent object to get the information from</p></td> - </tr> - <tr> - <th>medium</th> - <td><p>The medium for which information is sought</p></td> - </tr> - <tr> - <th>type</th> - <td><p>The information type</p></td> - </tr> - <tr> - <th>lab_field</th> - <td><p>If not NA, do we want laboratory or field endpoints</p></td> - </tr> - <tr> - <th>redox</th> - <td><p>If not NA, are we looking for aerobic or anaerobic data</p></td> - </tr> - <tr> - <th>value</th> - <td><p>The name of the value we want. The list given in the -usage section is not exclusive</p></td> - </tr> - <tr> - <th>aggregator</th> - <td><p>The aggregator function. Can be mean, -<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</p></td> - </tr> - <tr> - <th>raw</th> - <td><p>Should the number(s) be returned as stored in the chent +<dt>raw</dt> +<dd><p>Should the number(s) be returned as stored in the chent object (could be a character value) to retain original information -about precision?</p></td> - </tr> - <tr> - <th>signif</th> - <td><p>How many significant digits do we want</p></td> - </tr> - <tr> - <th>values</th> - <td><p>The values to be returned</p></td> - </tr> - <tr> - <th>aggregators</th> - <td><p>A named vector of aggregator functions to be used</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The result from applying the aggregator function to +about precision?</p></dd> + + +<dt>signif</dt> +<dd><p>How many significant digits do we want</p></dd> + + +<dt>values</dt> +<dd><p>The values to be returned</p></dd> + + +<dt>aggregators</dt> +<dd><p>A named vector of aggregator functions to be used</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + + +<p>The result from applying the aggregator function to the values converted to a numeric vector, rounded to the given number of significant digits, or, if raw = TRUE, the values as a character value, retaining any implicit information on precision that may be present.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. For the Freundlich exponent, the capital letter <code>N</code> is used in order to facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.</p> + </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - </ul> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 34befc3..20ee17d 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -1,174 +1,115 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Calculate the geometric mean — geomean • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<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 +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE (default). 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If negative values are present, it gives an error message. +If at least one element of the vector is 0, it returns 0."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">pfm</a> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Calculate the geometric mean</h1> - <div class="hidden name"><code>geomean.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculate the geometric mean</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/geomean.R" class="external-link"><code>R/geomean.R</code></a></small> + <div class="d-none name"><code>geomean.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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> +<a href="http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in" class="external-link">http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. If at least one element of the vector is 0, it returns 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'>FALSE</span>)</pre> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">geomean</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>Vector of numbers</p></dd> - <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> - <th>x</th> - <td><p>Vector of numbers</p></td> - </tr> - <tr> - <th>na.rm</th> - <td><p>Should NA values be omitted?</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>na.rm</dt> +<dd><p>Should NA values be omitted?</p></dd> - <p>The geometric mean</p> +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] NA</div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> +<p>The geometric mean</p> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3</span> +<span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="cn">NA</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="op">-</span><span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span> <span class="co"># returns an error</span></span></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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class="external-link"><code>R/PEC_soil.R</code></a></small> + <div class="d-none name"><code>get_vertex.Rd</code></div> </div> - <div class="ref-description"> - + <div class="ref-description section level2"> <p>This was inspired by an answer on stackoverflow https://stackoverflow.com/a/717791</p> - </div> - <pre class="usage"><span class='fu'>get_vertex</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre> - - <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> - <th>x</th> - <td><p>Three x coordinates</p></td> - </tr> - <tr> - <th>y</th> - <td><p>Three y coordinates</p></td> - </tr> - </table> - + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_vertex</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div> + </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>Three x coordinates</p></dd> - </div> -</div> +<dt>y</dt> +<dd><p>Three y coordinates</p></dd> + +</dl></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site 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<main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function reference</h1> </div> - <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> - <h2 id="general-utility-functions">General utility functions <a href="#general-utility-functions" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> - </th> - </tr></tbody><tbody><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><tr><td> - <p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p> - </td> - <td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td> - </tr><tr><td> - <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> </p> - </td> - <td><p>Objects exported from other packages</p></td> - </tr><tr><td> - <p><code><a href="TSCF.html">TSCF()</a></code> </p> - </td> - <td><p>Estimation of the transpiration stream concentration factor</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil <a href="#predicted-environmental-concentrations-in-soil" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><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="PEC_soil_mets.html">PEC_soil_mets()</a></code> </p> - </td> - <td><p>Calculate initial and accumulation PEC soil for a set of metabolites</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><tr><td> - <p><code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </p> - </td> - <td><p>Properties of the predefined scenarios from the EFSA guidance from 2017</p></td> - </tr><tr><td> - <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p> - </td> - <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td> - </tr><tr><td> - <p><code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> </p> - </td> - <td><p>Subset of EFSA crop washoff default values</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater <a href="#predicted-environmental-concentrations-in-groundwater" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><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="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> </p> - </td> - <td><p>Subset of EFSA crop interception default values for groundwater modelling</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water <a href="#predicted-environmental-concentrations-in-surface-water" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><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_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="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="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="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="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </p> - </td> - <td><p>Calculate PEC surface water due to drainage as in Exposit 3</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="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="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> - </td> - <td><p>R6 class for holding TOXSWA water 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="classifications-and-indicators">Classifications and indicators <a href="#classifications-and-indicators" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Evaluating environmental fate properties</p> - </th> - </tr></tbody><tbody><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><tbody><tr><th colspan="2"> - <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information <a href="#work-with-chent-objects-containing-relevant-information" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p> - </td> - <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="utilities">Utilities <a href="#utilities" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="get_vertex.html">get_vertex()</a></code> </p> - </td> - <td><p>Fit a parabola through three points</p></td> - </tr></tbody></table></div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + <div class="section level2"> + <h2 id="general-utility-functions">General utility functions<a class="anchor" aria-label="anchor" href="#general-utility-functions"></a></h2> + + <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="geomean.html">geomean()</a></code> + </dt> + <dd>Calculate the geometric mean</dd> + </dl><dl><dt> + + <code><a href="one_box.html">one_box()</a></code> + </dt> + <dd>Create a time series of decline data</dd> + </dl><dl><dt> + + <code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> + </dt> + <dd>Plot time series of decline data</dd> + </dl><dl><dt> + + <code><a href="sawtooth.html">sawtooth()</a></code> + </dt> + <dd>Create decline time series for multiple applications</dd> + </dl><dl><dt> + + <code><a href="twa.html">twa()</a></code> + </dt> + <dd>Calculate a time weighted average concentration</dd> + </dl><dl><dt> + + <code><a href="max_twa.html">max_twa()</a></code> + </dt> + <dd>The maximum time weighted average concentration for a moving window</dd> + </dl><dl><dt> + + <code><a href="pfm_degradation.html">pfm_degradation()</a></code> + </dt> + <dd>Calculate a time course of relative concentrations based on an mkinmod model</dd> + </dl><dl><dt> + + <code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> + </dt> + <dd>Actual and maximum moving window time average concentrations for SFO kinetics</dd> + </dl><dl><dt> + + <code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> + </dt> + <dd>Actual and maximum moving window time average concentrations for FOMC kinetics</dd> + </dl><dl><dt> + + <code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> + </dt> + <dd>Objects exported from other packages</dd> + </dl><dl><dt> + + <code><a href="TSCF.html">TSCF()</a></code> + </dt> + <dd>Estimation of the transpiration stream concentration factor</dd> + </dl></div><div class="section level2"> + <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-soil"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="PEC_soil.html">PEC_soil()</a></code> + </dt> + <dd>Calculate predicted environmental concentrations in soil</dd> + </dl><dl><dt> + + <code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> + </dt> + <dd>Calculate initial and accumulation PEC soil for a set of metabolites</dd> + </dl><dl><dt> + + <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> + </dt> + <dd>Properties of the predefined scenarios from the EFSA guidance from 2015</dd> + </dl><dl><dt> + + <code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> + </dt> + <dd>Properties of the predefined scenarios from the EFSA guidance from 2017</dd> + </dl><dl><dt> + + <code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> + </dt> + <dd>Get the relative accumulation of an FOMC model over multiples of an interval</dd> + </dl><dl><dt> + + <code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> + </dt> + <dd>Subset of EFSA crop washoff default values</dd> + </dl></div><div class="section level2"> + <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-groundwater"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> + </dt> + <dd>A very small subset of the FOCUS Groundwater scenario definitions</dd> + </dl><dl><dt> + + <code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> + </dt> + <dd>Subset of EFSA crop interception default values for groundwater modelling</dd> + </dl></div><div class="section level2"> + <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-surface-water"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> + </dt> + <dd>Calculate predicted environmental concentrations in surface water due to drift</dd> + </dl><dl><dt> + + <code><a href="drift_data_JKI.html">drift_data_JKI</a></code> + </dt> + <dd>Deposition from spray drift expressed as percent of the applied dose as +published by the JKI</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> + </dt> + <dd>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> + </dt> + <dd>Calculate predicted environmental concentrations in sediment from surface +water concentrations</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> + </dt> + <dd>Calculate PEC surface water at FOCUS Step 1</dd> + </dl><dl><dt> + + <code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> + </dt> + <dd>Create a chemical compound object for FOCUS Step 1 calculations</dd> + </dl><dl><dt> + + <code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> + </dt> + <dd>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> + </dt> + <dd>Calculate PEC surface water due to drainage as in Exposit 3</dd> + </dl><dl><dt> + + <code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> + </dt> + <dd>Calculate PEC surface water due to runoff and erosion as in Exposit 3</dd> + </dl><dl><dt> + + <code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> + </dt> + <dd>Runoff loss percentages as used in Exposit 3</dd> + </dl><dl><dt> + + <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> + </dt> + <dd>Runoff reduction percentages as used in Exposit</dd> + </dl><dl><dt> + + <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> + </dt> + <dd>R6 class for holding TOXSWA water concentration data and associated statistics</dd> + </dl><dl><dt> + + <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> + </dt> + <dd>Read TOXSWA surface water concentrations</dd> + </dl><dl><dt> + + <code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> + </dt> + <dd>Plot TOXSWA surface water concentrations</dd> + </dl></div><div class="section level2"> + <h2 id="classifications-and-indicators">Classifications and indicators<a class="anchor" aria-label="anchor" href="#classifications-and-indicators"></a></h2> + + <p class="section-desc"></p><p>Evaluating environmental fate properties</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> + </dt> + <dd>Determine the SSLRC mobility classification for a chemical substance from its Koc</dd> + </dl><dl><dt> + + <code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> + </dt> + <dd>Groundwater ubiquity score based on Gustafson (1989)</dd> + </dl></div><div class="section level2"> + <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information<a class="anchor" aria-label="anchor" href="#work-with-chent-objects-containing-relevant-information"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> + </dt> + <dd>Retrieve endpoint information from the chyaml field of a chent object</dd> + </dl></div><div class="section level2"> + <h2 id="utilities">Utilities<a class="anchor" aria-label="anchor" href="#utilities"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + <dl><dt> + + <code><a href="get_vertex.html">get_vertex()</a></code> + </dt> + <dd>Fit a parabola through three points</dd> + </dl></div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + 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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><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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of type <code><a href='one_box.html'>one_box</a></code></p></td> - </tr> - <tr> - <th>window</th> - <td><p>The size of the moving window</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> + + +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The method working directly on fitted <code>mkinfit</code> objects uses the equations given in the PEC soil section of the FOCUS guidance and is restricted SFO, FOMC and DFOP models and to the parent compound</p> - - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <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> - <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) -<span class='fu'>max_twa</span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max -#> parent -#> 0.9537545 -#> -#> $window_start -#> parent -#> 0 -#> -#> $window_end -#> parent -#> 21 -#> </div><div class='input'><span class='no'>pred_FOMC</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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='fu'>max_twa</span>(<span class='no'>pred_FOMC</span>)</div><div class='output co'>#> 21 -#> 18.22124 </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#details">Details</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#see-also">See also</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> + <div class="dont-index"><p><code><a href="twa.html">twa</a></code></p></div> + </div> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0.9537545 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="va">pred_FOMC</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred_FOMC</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> 18.22124 </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png Binary files differindex 10bc9f7..b280532 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 9cbb045..8c8188c 100644 --- a/docs/reference/one_box-2.png +++ 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</div> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <div class="ref-description section level2"> + <p>Create a time series of decline data</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, <span class="va">ini</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for character</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">parms</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="st">"model"</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>When numeric, this is the half-life to be used for an exponential +decline. When a character string specifying a parent decline model is given +e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding parameters. +If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, the decline is calculated from this +object.</p></dd> +<dt>ini</dt> +<dd><p>The initial amount. If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, and +ini is 'model', the fitted initial concentrations are used. Otherwise, ini +must be numeric. If it has length one, it is used for the parent and +initial values of metabolites are zero, otherwise, it must give values for +all observed variables.</p></dd> -<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" /> +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> +<dt>t_end</dt> +<dd><p>End of the time series</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>res</dt> +<dd><p>Resolution of the time series</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>parms</dt> +<dd><p>A named numeric vector containing the model parameters</p></dd> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Create a time series of decline data</h1> +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - <div class="hidden name"><code>one_box.Rd</code></div> - </div> - <div class="ref-description"> - <p>Create a time series of decline data</p> +<p>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</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>) - -<span class='co'># S3 method for numeric</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</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>) - -<span class='co'># S3 method for character</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</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>) - -<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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>When numeric, this is the half-life to be used for an exponential -decline. When a character string specifying a parent decline model is given -e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding parameters. -If x is an <code>mkinfit</code> object, the decline is calculated from this -object.</p></td> - </tr> - <tr> - <th>ini</th> - <td><p>The initial amount. If x is an <code>mkinfit</code> object, and -ini is 'model', the fitted initial concentrations are used. Otherwise, ini -must be numeric. If it has length one, it is used for the parent and -initial values of metabolites are zero, otherwise, it must give values for -all observed variables.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - <tr> - <th>t_end</th> - <td><p>End of the time series</p></td> - </tr> - <tr> - <th>res</th> - <td><p>Resolution of the time series</p></td> - </tr> - <tr> - <th>parms</th> - <td><p>A named numeric vector containing the model parameters</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code>one_box</code>, inheriting from <code><a href='https://rdrr.io/r/stats/ts.html'>ts</a></code>.</p> - - <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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>mkin</span>) -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinfit.html'>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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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='https://pkgdown.jrwb.de/mkin/reference/mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinsub.html'>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='https://pkgdown.jrwb.de/mkin/reference/mkinsub.html'>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='https://pkgdown.jrwb.de/mkin/reference/mkinfit.html'>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>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Only use a half-life</span></span></span> +<span class="r-in"><span><span class="va">pred_0</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_0</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/" class="external-link">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_1</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_1</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a model with more than one observed variable</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="st">"model"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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src="" class="logo" alt=""><h1>Runoff loss percentages as used in Exposit 3</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit_runoff.R" class="external-link"><code>R/PEC_sw_exposit_runoff.R</code></a></small> + <div class="d-none name"><code>perc_runoff_exposit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame with percentage values for the dissolved fraction and the fraction - bound to eroding particles, with Koc classes used as row names</p><dl'> - <dt>Koc_lower_bound</dt><dd><p>The lower bound of the Koc class</p></dd> - <dt>dissolved</dt><dd><p>The percentage of the applied substance transferred to an + bound to eroding particles, with Koc classes used as row names</p><dl><dt>Koc_lower_bound</dt> +<dd><p>The lower bound of the Koc class</p></dd> + + <dt>dissolved</dt> +<dd><p>The percentage of the applied substance transferred to an adjacent water body in the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The percentage of the applied substance transferred to an - adjacent water body bound to eroding particles</p></dd> - -</dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt>bound</dt> +<dd><p>The percentage of the applied substance transferred to an + adjacent water body bound to eroding particles</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>perc_runoff_exposit</span>)</div><div class='output co'>#> Koc_lower_bound dissolved bound -#> 0-20 0 0.110 0.000 -#> >20-50 20 0.151 0.000 -#> >50-100 50 0.197 0.000 -#> >100-200 100 0.248 0.001 -#> >200-500 200 0.224 0.004 -#> >500-1000 500 0.184 0.020 -#> >1000-2000 1000 0.133 0.042 -#> >2000-5000 2000 0.084 0.091 -#> >5000-10000 5000 0.037 0.159 -#> >10000-20000 10000 0.031 0.192 -#> >20000-50000 20000 0.014 0.291 -#> >50000 50000 0.001 0.451</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <a href="https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html" class="external-link">https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">perc_runoff_exposit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Koc_lower_bound dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> 0-20 0 0.110 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >20-50 20 0.151 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >50-100 50 0.197 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >100-200 100 0.248 0.001</span> +<span class="r-out co"><span class="r-pr">#></span> >200-500 200 0.224 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> >500-1000 500 0.184 0.020</span> +<span class="r-out co"><span class="r-pr">#></span> >1000-2000 1000 0.133 0.042</span> +<span class="r-out co"><span class="r-pr">#></span> >2000-5000 2000 0.084 0.091</span> +<span class="r-out co"><span class="r-pr">#></span> >5000-10000 5000 0.037 0.159</span> +<span class="r-out co"><span class="r-pr">#></span> >10000-20000 10000 0.031 0.192</span> +<span class="r-out co"><span class="r-pr">#></span> >20000-50000 20000 0.014 0.291</span> +<span class="r-out co"><span class="r-pr">#></span> >50000 50000 0.001 0.451</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index dd37f4b..f398ca1 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -1,191 +1,125 @@ -<!-- Generated by pkgdown: do not edit 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class="external-link"><code>R/PEC_sw_exposit_runoff.R</code></a></small> + <div class="d-none name"><code>perc_runoff_reduction_exposit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> </div> - <pre class="usage"><span class='va'>perc_runoff_reduction_exposit</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_reduction_exposit</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A named list of data frames with reduction percentage values for the dissolved fraction and the fraction bound to eroding particles, with vegetated buffer widths as row names. The names of the list items are the Exposit versions -from which the values were taken.</p><dl> - <dt>dissolved</dt><dd><p>The reduction percentage for the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The reduction percentage for the particulate phase</p></dd> - -</dl> +from which the values were taken.</p><dl><dt>dissolved</dt> +<dd><p>The reduction percentage for the dissolved phase</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt>bound</dt> +<dd><p>The reduction percentage for the particulate phase</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> + <a href="https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html" class="external-link">https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> <p>Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>perc_runoff_reduction_exposit</span><span class='op'>)</span> -</div><div class='output co'>#> $`3.02` -#> dissolved bound -#> No buffer 0 0 -#> 5 m 40 40 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`3.01a` -#> dissolved bound -#> No buffer 0 0 -#> 3 m 25 30 -#> 5 m 40 40 -#> 6 m 45 55 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`3.01a2` -#> dissolved bound -#> No buffer 0 0 -#> 3 m 25 25 -#> -#> $`2.0` -#> dissolved bound -#> No buffer 0.0 0.0 -#> 20 m 97.5 97.5 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">perc_runoff_reduction_exposit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`3.02`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 40 40</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 60 85</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 80 95</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`3.01a`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 25 30</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 40 40</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 45 55</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 60 85</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 80 95</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`3.01a2`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 25 25</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`2.0`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.0 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 97.5 97.5</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git 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pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="ref-description section level2"> + <p>Calculate a time course of relative concentrations based on an mkinmod model</p> + </div> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pfm_degradation</span><span class="op">(</span></span> +<span> model <span class="op">=</span> <span class="st">"SFO"</span>,</span> +<span> DT50 <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="va">DT50</span><span class="op">)</span>,</span> +<span> years <span class="op">=</span> <span class="fl">1</span>,</span> +<span> step_days <span class="op">=</span> <span class="fl">1</span>,</span> +<span> times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="va">years</span> <span class="op">*</span> <span class="fl">365</span>, by <span class="op">=</span> <span class="va">step_days</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>model</dt> +<dd><p>The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object</p></dd> -<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" /> +<dt>DT50</dt> +<dd><p>The half-life. This is only used when simple exponential decline +is calculated (SFO model).</p></dd> +<dt>parms</dt> +<dd><p>The parameters used for the degradation model</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>years</dt> +<dd><p>For how many years should the degradation be predicted?</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>step_days</dt> +<dd><p>What step size in days should the output have?</p></dd> - - </header> +<dt>times</dt> +<dd><p>The output times</p></dd> -<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> - - <div class="hidden name"><code>pfm_degradation.Rd</code></div> +</dl></div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> + <p>Johannes Ranke</p> </div> - <div class="ref-description"> - <p>Calculate a time course of relative concentrations based on an mkinmod model</p> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in head(pfm_degradation("SFO", DT50 = 10)):</span> could not find function "head"</span> +</code></pre></div> </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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></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'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>model</th> - <td><p>The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The half-life. This is only used when simple exponential decline -is calculated (SFO model).</p></td> - </tr> - <tr> - <th>parms</th> - <td><p>The parameters used for the degradation model</p></td> - </tr> - <tr> - <th>years</th> - <td><p>For how many years should the degradation be predicted?</p></td> - </tr> - <tr> - <th>step_days</th> - <td><p>What step size in days should the output have?</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#> time parent -#> 0 0 1.0000000 -#> 1 1 0.9330330 -#> 2 2 0.8705506 -#> 3 3 0.8122524 -#> 4 4 0.7578583 -#> 5 5 0.7071068</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png Binary files differindex c6a278a..19dfbe6 100644 --- a/docs/reference/plot.TOXSWA_cwa-1.png +++ 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class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/TOXSWA_cwa.R" class="external-link"><code>R/TOXSWA_cwa.R</code></a></small> + <div class="d-none name"><code>plot.TOXSWA_cwa.Rd</code></div> + </div> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <div class="ref-description section level2"> + <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body.</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for TOXSWA_cwa</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> time_column <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"datetime"</span>, <span class="st">"t"</span>, <span class="st">"t_firstjan"</span>, <span class="st">"t_rel_to_max"</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> add <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> threshold_factor <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> thin_low <span class="op">=</span> <span class="fl">1</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> LC_TIME <span class="op">=</span> <span class="st">"C"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>The TOXSWA_cwa object to be plotted.</p></dd> +<dt>time_column</dt> +<dd><p>What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.</p></dd> -<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" /> +<dt>xlab, ylab</dt> +<dd><p>Labels for x and y axis.</p></dd> +<dt>add</dt> +<dd><p>Should we add to an existing plot?</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>threshold_factor</dt> +<dd><p>The factor by which the data have to be lower than the maximum +in order to get thinned for plotting (see next argument).</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>thin_low</dt> +<dd><p>If an integer greater than 1, the data close to zero (smaller than +1/threshold_factor of the maximum) in the series will be thinned by this factor +in order to decrease the amount of data that is included in the plots</p></dd> - - </header> +<dt>total</dt> +<dd><p>Should the total concentration in water be plotted, including substance sorbed +to suspended matter?</p></dd> -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Plot TOXSWA surface water concentrations</h1> - - <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> +<dt>LC_TIME</dt> +<dd><p>Specification of the locale used to format dates</p></dd> - <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>, <span class='st'>"t_rel_to_max"</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>The TOXSWA_cwa object to be plotted.</p></td> - </tr> - <tr> - <th>time_column</th> - <td><p>What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.</p></td> - </tr> - <tr> - <th>xlab, ylab</th> - <td><p>Labels for x and y axis.</p></td> - </tr> - <tr> - <th>add</th> - <td><p>Should we add to an existing plot?</p></td> - </tr> - <tr> - <th>threshold_factor</th> - <td><p>The factor by which the data have to be lower than the maximum -in order to get thinned for plotting (see next argument).</p></td> - </tr> - <tr> - <th>thin_low</th> - <td><p>If an integer greater than 1, the data close to zero (smaller than -1/threshold_factor of the maximum) in the series will be thinned by this factor -in order to decrease the amount of data that is included in the plots</p></td> - </tr> - <tr> - <th>total</th> - <td><p>Should the total concentration in water be plotted, including substance sorbed -to suspended matter?</p></td> - </tr> - <tr> - <th>LC_TIME</th> - <td><p>Specification of the locale used to format dates</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <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'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> + +<dt>...</dt> +<dd><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_firstjan"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-5.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> 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+ + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot time series of decline data</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/twa.R" class="external-link"><code>R/twa.R</code></a></small> + <div class="d-none name"><code>plot.one_box.Rd</code></div> + </div> -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + <div class="ref-description section level2"> + <p>Plot time series of decline data</p> + </div> -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for one_box</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/time.html" class="external-link">time</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> max_twa <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> max_twa_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> +<dt>xlim</dt> +<dd><p>Limits for the x axis</p></dd> -<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" /> +<dt>ylim</dt> +<dd><p>Limits for the y axis</p></dd> +<dt>xlab</dt> +<dd><p>Label for the x axis</p></dd> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> +<dt>ylab</dt> +<dd><p>Label for the y axis</p></dd> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<dt>max_twa</dt> +<dd><p>If a numeric value is given, the maximum time weighted +average concentration(s) is/are shown in the graph.</p></dd> - - </header> +<dt>max_twa_var</dt> +<dd><p>Variable for which the maximum time weighted average should +be shown if max_twa is not NULL.</p></dd> -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Plot time series of decline data</h1> - - <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> +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> - <pre class="usage"><span class='co'># S3 method for one_box</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</span>)), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></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'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>The object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>Limits for the x axis</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>Limits for the y axis</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis</p></td> - </tr> - <tr> - <th>max_twa</th> - <td><p>If a numeric value is given, the maximum time weighted -average concentration(s) is/are shown in the graph.</p></td> - </tr> - <tr> - <th>max_twa_var</th> - <td><p>Variable for which the maximum time weighted average should -be shown if max_twa is not NULL.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <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'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><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'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> + <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> + </div> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dfop_pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="st">"DFOP"</span>, parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pred</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">dfop_pred</span>, <span class="fl">3</span>, <span class="fl">7</span><span class="op">)</span>, max_twa <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes 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Per default, the data for the last +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). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">pfm</a> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> + </ul></div> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Read TOXSWA surface water concentrations</h1> - <div class="hidden name"><code>read.TOXSWA_cwa.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Read TOXSWA surface water concentrations</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/TOXSWA_cwa.R" class="external-link"><code>R/TOXSWA_cwa.R</code></a></small> + <div class="d-none name"><code>read.TOXSWA_cwa.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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 segment are imported. As TOXSWA 4 reports the values at the end of the hour @@ -119,103 +61,99 @@ of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was renamed to ConLiqWatLay in the out file.</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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>filename</th> - <td><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></td> - </tr> - <tr> - <th>basedir</th> - <td><p>The path to the directory where the cwa file resides.</p></td> - </tr> - <tr> - <th>zipfile</th> - <td><p>Optional path to a zip file containing the cwa file.</p></td> - </tr> - <tr> - <th>segment</th> - <td><p>The segment for which the data should be read. Either "last", or -the segment number.</p></td> - </tr> - <tr> - <th>substance</th> - <td><p>For .out files, the default value "parent" leads + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read.TOXSWA_cwa</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> basedir <span class="op">=</span> <span class="st">"."</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> windows <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> thresholds <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>filename</dt> +<dd><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></dd> + + +<dt>basedir</dt> +<dd><p>The path to the directory where the cwa file resides.</p></dd> + + +<dt>zipfile</dt> +<dd><p>Optional path to a zip file containing the cwa file.</p></dd> + + +<dt>segment</dt> +<dd><p>The segment for which the data should be read. Either "last", or +the segment number.</p></dd> + + +<dt>substance</dt> +<dd><p>For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.</p></td> - </tr> - <tr> - <th>total</th> - <td><p>Set this to TRUE in order to read total concentrations as well. This is +of interested can be selected by its code name.</p></dd> + + +<dt>total</dt> +<dd><p>Set this to TRUE in order to read total concentrations as well. This is only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.</p></td> - </tr> - <tr> - <th>windows</th> - <td><p>Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.</p></td> - </tr> - <tr> - <th>thresholds</th> - <td><p>Numeric vector of threshold concentrations in µg/L for -generating event statistics.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An instance of an R6 object of class -<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'>read.TOXSWA_cwa</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'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> +files. For .cwa files, the total concentration is always read as well.</p></dd> + + +<dt>windows</dt> +<dd><p>Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.</p></dd> + + +<dt>thresholds</dt> +<dd><p>Numeric vector of threshold concentrations in µg/L for +generating event statistics.</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + + +<p>An instance of an R6 object of class +<code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu">read.TOXSWA_cwa</span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 2f410e4..a98a861 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,5 +1,12 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Objects exported from other packages — reexports • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Objects exported from other packages — reexports"><meta property="og:description" content="These objects are imported from other packages. Follow the links +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These objects are imported from other packages. 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Follow the links below to see their documentation. mkin @@ -9,44 +16,47 @@ set_nd_nq, set_nd_nq_focus "><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.0</span> - </span> - </div> + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> -</li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small> - + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Objects exported from other packages</h1> - <div class="hidden name"><code>reexports.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Objects exported from other packages</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/reexports.R" class="external-link"><code>R/reexports.R</code></a></small> + <div class="d-none name"><code>reexports.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>These objects are imported from other packages. Follow the links below to see their documentation.</p> <dl><dt>mkin</dt> @@ -57,26 +67,21 @@ below to see their documentation.</p> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 2952433..6cf67ed 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 87da954..5c9fbcc 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applications</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/twa.R" class="external-link"><code>R/twa.R</code></a></small> + <div class="d-none name"><code>sawtooth.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>If the application pattern is specified in <code>applications</code>, <code>n</code> and <code>i</code> are disregarded.</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'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>A <code><a href='one_box.html'>one_box</a></code> object</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of applications. If <code>applications</code> is specified, <code>n</code> is ignored</p></td> - </tr> - <tr> - <th>i</th> - <td><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> -is ignored</p></td> - </tr> - <tr> - <th>applications</th> - <td><p>A data frame holding the application times in the first column and -the corresponding amounts applied in the second column.</p></td> - </tr> - </table> - - - <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'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/plot.html'>plot</a></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>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><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'><a href='https://rdrr.io/r/base/plot.html'>plot</a></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 -#> -#> $window_start -#> parent m1 -#> 0.00 26.85 -#> -#> $window_end -#> parent m1 -#> 21.00 47.85 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sawtooth</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>,</span> +<span> i <span class="op">=</span> <span class="fl">365</span>,</span> +<span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="op">(</span><span class="va">n</span> <span class="op">-</span> <span class="fl">1</span><span class="op">)</span> <span class="op">*</span> <span class="va">i</span>, length.out <span class="op">=</span> <span class="va">n</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>A <code><a href="one_box.html">one_box</a></code> object</p></dd> + + +<dt>n</dt> +<dd><p>The number of applications. If <code>applications</code> is specified, <code>n</code> is ignored</p></dd> + + +<dt>i</dt> +<dd><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> +is ignored</p></dd> + + +<dt>applications</dt> +<dd><p>A data frame holding the application times in the first column and +the corresponding amounts applied in the second column.</p></dd> + +</dl></div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">applications</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">14</span>, by <span class="op">=</span> <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred</span>, applications <span class="op">=</span> <span class="va">applications</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sawtooth-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sawtooth-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred_2_saw</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.7834481 0.8617049 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.00 26.85 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 21.00 47.85 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site 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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> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 doi:10.2903/j.efsa.2015.4093</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>( - <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>), - <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>), - <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>), - <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>), - <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>), - <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>), - <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>), - <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>), - <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>), - <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>), - <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>) - ) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>) -} - -<span class='co'># And this is the resulting dataframe</span> -<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce -#> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 -#> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 -#> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 -#> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 -#> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 -#> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 -#> f_mod -#> CTN 2 -#> CTC 2 -#> CTS 2 -#> CLN 4 -#> CLC 4 -#> CLS 4</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to define the data</span></span></span> +<span class="r-in"><span> <span class="va">soil_scenario_data_EFSA_2015</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> Zone <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"Central"</span>, <span class="st">"South"</span><span class="op">)</span>, <span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Country <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Estonia"</span>, <span class="st">"Germany"</span>, <span class="st">"France"</span>, <span class="st">"Denmark"</span>, <span class="st">"Czech Republik"</span>, <span class="st">"Spain"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> T_arit <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">4.7</span>, <span class="fl">8.0</span>, <span class="fl">11.0</span>, <span class="fl">8.2</span>, <span class="fl">9.1</span>, <span class="fl">12.8</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> T_arr <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7.0</span>, <span class="fl">10.1</span>, <span class="fl">12.3</span>, <span class="fl">9.8</span>, <span class="fl">11.2</span>, <span class="fl">14.7</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Texture <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Coarse"</span>, <span class="st">"Coarse"</span>, <span class="st">"Medium fine"</span>, <span class="st">"Medium"</span>, <span class="st">"Medium"</span>, <span class="st">"Medium"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> f_om <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.118</span>, <span class="fl">0.086</span>, <span class="fl">0.048</span>, <span class="fl">0.023</span>, <span class="fl">0.018</span>, <span class="fl">0.011</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> theta_fc <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.244</span>, <span class="fl">0.244</span>, <span class="fl">0.385</span>, <span class="fl">0.347</span>, <span class="fl">0.347</span>, <span class="fl">0.347</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> rho <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.95</span>, <span class="fl">1.05</span>, <span class="fl">1.22</span>, <span class="fl">1.39</span>, <span class="fl">1.43</span>, <span class="fl">1.51</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> f_sce <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">2</span>, <span class="fl">2</span>, <span class="fl">2</span>, <span class="fl">1.5</span>, <span class="fl">1.5</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> f_mod <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">2</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">4</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> row.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CTN"</span>, <span class="st">"CTC"</span>, <span class="st">"CTS"</span>, <span class="st">"CLN"</span>, <span class="st">"CLC"</span>, <span class="st">"CLS"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">soil_scenario_data_EFSA_2015</span>, file <span class="op">=</span> <span class="st">'../data/soil_scenario_data_EFSA_2015.RData'</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And this is the resulting dataframe</span></span></span> +<span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2015</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce</span> +<span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5</span> +<span class="r-out co"><span class="r-pr">#></span> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5</span> +<span class="r-out co"><span class="r-pr">#></span> f_mod</span> +<span class="r-out co"><span class="r-pr">#></span> CTN 2</span> +<span class="r-out co"><span class="r-pr">#></span> CTC 2</span> +<span class="r-out co"><span class="r-pr">#></span> CTS 2</span> +<span class="r-out co"><span class="r-pr">#></span> CLN 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLC 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLS 4</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index 7e8044e..8e5739e 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Also, the +scenario and model adjustment factors from p. 16 and p. 18 are included."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">pfm</a> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small> -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> - </span> - </div> + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> - <div class="hidden name"><code>soil_scenario_data_EFSA_2017.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/soil_scenario_data_EFSA_2017.R" class="external-link"><code>R/soil_scenario_data_EFSA_2017.R</code></a></small> + <div class="d-none name"><code>soil_scenario_data_EFSA_2017.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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 (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included.</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>EFSA (European Food Safety Authority) (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 doi:10.2903/j.efsa.2017.4982</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>soil_scenario_data_EFSA_2017</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod -#> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 -#> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 -#> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 -#> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 -#> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 -#> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 -#> FOCUS_zone prec -#> CTN Hamburg 639 -#> CTC Hamburg 617 -#> CTS Hamburg 667 -#> CLN Hamburg 602 -#> CLC Châteaudun 589 -#> CLS Sevilla 526</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2017</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod</span> +<span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> FOCUS_zone prec</span> +<span class="r-out co"><span class="r-pr">#></span> CTN Hamburg 639</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Hamburg 617</span> +<span class="r-out co"><span class="r-pr">#></span> CTS Hamburg 667</span> +<span class="r-out co"><span class="r-pr">#></span> CLN Hamburg 602</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Châteaudun 589</span> +<span class="r-out co"><span class="r-pr">#></span> CLS Sevilla 526</span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> diff --git a/docs/reference/twa.html b/docs/reference/twa.html index 2c21c67..fbcbe9a 100644 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class="external-link"><code>R/twa.R</code></a></small> + <div class="d-none name"><code>twa.Rd</code></div> </div> - <div class="ref-description"> - + <div class="ref-description section level2"> <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>) + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for one_box</span></span> +<span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> -<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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of type <code><a href='one_box.html'>one_box</a></code></p></td> - </tr> - <tr> - <th>window</th> - <td><p>The size of the moving window</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> - <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> - <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) -<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max -#> parent -#> 0.9537545 -#> -#> $window_start -#> parent -#> 0 -#> -#> $window_end -#> parent -#> 21 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#see-also">See also</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> - </div> -</div> +</dl></div> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> + <div class="dont-index"><p><code><a href="max_twa.html">max_twa</a></code></p></div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0.9537545 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +<div class="pkgdown-footer-right"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> |
