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| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/NAFTA_SOP_Attachment.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/NAFTA_SOP_Attachment.html')
| -rw-r--r-- | docs/reference/NAFTA_SOP_Attachment.html | 224 |
1 files changed, 84 insertions, 140 deletions
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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -72,13 +17,12 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -87,8 +31,7 @@ <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,6 +41,9 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -112,30 +58,23 @@ <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Example datasets from Attachment 1 to the NAFTA SOP published 2015</h1> @@ -147,91 +86,96 @@ <p>Data taken from from Attachment 1 of the SOP.</p> </div> - <pre class="usage"><span class='va'>NAFTA_SOP_Attachment</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">NAFTA_SOP_Attachment</span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable - for the evaluation with <code><a href='nafta.html'>nafta</a></code></p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + for the evaluation with <code><a href="nafta.html">nafta</a></code></p> + </div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>nafta_att_p5a</span> <span class='op'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Attachment</span><span class='op'>[[</span><span class='st'>"p5a"</span><span class='op'>]</span><span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><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'>nafta_att_p5a</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 465.21753 56.27506 32.06401 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 64.4304 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 95.8401 4.67e-21 92.245 99.4357 -#> k_parent 0.0102 3.92e-12 0.009 0.0117 -#> sigma 4.8230 3.81e-06 3.214 6.4318 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -#> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 -#> N_parent 2.57e+00 NA 2.25e+00 2.89e+00 -#> sigma 1.68e+00 NA 1.12e+00 2.24e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 -#> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.26e-12 5.00e-01 0.0000 Inf -#> g 6.47e-01 3.67e-06 0.6248 0.6677 -#> sigma 1.27e+00 8.91e-06 0.8395 1.6929 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 67.7 2.25e+02 6.77e+01 -#> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.59e+11 3.07e+11 -#> -#> Representative half-life: -#> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> -</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"> <span class="va">nafta_att_p5a</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The half-life obtained from the IORE model may be used</span> +<span class="r-in"> <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">nafta_att_p5a</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 465.21753 56.27506 32.06401 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 64.4304</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.8401 4.67e-21 92.245 99.4357</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0102 3.92e-12 0.009 0.0117</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.8230 3.81e-06 3.214 6.4318</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.68e+00 NA 1.12e+00 2.24e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> +<span class="r-out co"><span class="r-pr">#></span> k1 2.67e-02 5.05e-06 0.0243 0.0295</span> +<span class="r-out co"><span class="r-pr">#></span> k2 2.26e-12 5.00e-01 0.0000 Inf</span> +<span class="r-out co"><span class="r-pr">#></span> g 6.47e-01 3.67e-06 0.6248 0.6677</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 67.7 2.25e+02 6.77e+01</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 58.2 1.07e+03 3.22e+02</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 55.5 5.59e+11 3.07e+11</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 321.51</span> +<span class="r-in"> <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">nafta_att_p5a</span><span class="op">)</span></span> +<span class="r-plt img"><img src="NAFTA_SOP_Attachment-1.png" alt="" width="700" height="433"></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <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> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - 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