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diff --git a/docs/reference/index.html b/docs/reference/index.html index dbcd5ba0..e047f75d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -100,7 +100,7 @@ <div class="page-header"> <h1> Reference - <small>version 0.9.46.3</small> + <small>version 0.9.47.1</small> </h1> </div> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 9ff18876..8a148870 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -122,7 +122,7 @@ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing datasets in the form internally used by the 'gmkin' package. - The list has twelfe components. Each of the components is one dataset that has, + The list has twelve components. Each of the components is one dataset that has, among others, the following components</p><dl class='dl-horizontal'> <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> diff --git a/docs/reference/test_data_from_UBA_2014-16.png b/docs/reference/test_data_from_UBA_2014-16.png Binary files differnew file mode 100644 index 00000000..e5346b43 --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014-16.png diff --git a/docs/reference/test_data_from_UBA_2014-6.png b/docs/reference/test_data_from_UBA_2014-6.png Binary files differnew file mode 100644 index 00000000..e7fe4f0c --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014-6.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html new file mode 100644 index 00000000..601f148c --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014.html @@ -0,0 +1,411 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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>Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> + <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"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Three experimental datasets from two water sediment systems and one soil</h1> + </div> + + + <p>The datasets were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014).</p> + + + <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>. + Each dataset has, among others, the following components</p><dl class='dl-horizontal'> + <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> + <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> + </dl> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span> + <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span> + <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span> + <span class='co'># generally considered deprecated due to the frequent occurrence of such</span> + <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> + <span class='co'># model).</span> + <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), + <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</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'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 2371.755 +#> Model cost at call 3 : 2371.755 +#> Model cost at call 7 : 457.5705 +#> Model cost at call 10 : 457.5608 +#> Model cost at call 14 : 297.2882 +#> Model cost at call 16 : 297.2882 +#> Model cost at call 18 : 297.2881 +#> Model cost at call 21 : 275.6034 +#> Model cost at call 23 : 275.6034 +#> Model cost at call 27 : 268.2102 +#> Model cost at call 29 : 268.2101 +#> Model cost at call 33 : 255.941 +#> Model cost at call 35 : 255.941 +#> Model cost at call 39 : 246.486 +#> Model cost at call 41 : 246.486 +#> Model cost at call 45 : 231.4275 +#> Model cost at call 47 : 231.4275 +#> Model cost at call 51 : 212.4338 +#> Model cost at call 52 : 212.4338 +#> Model cost at call 53 : 212.4337 +#> Model cost at call 57 : 203.7185 +#> Model cost at call 58 : 203.7185 +#> Model cost at call 63 : 198.3304 +#> Model cost at call 69 : 198.3304 +#> Model cost at call 70 : 195.794 +#> Model cost at call 72 : 195.7939 +#> Model cost at call 76 : 195.2477 +#> Model cost at call 77 : 195.2477 +#> Model cost at call 82 : 191.6184 +#> Model cost at call 84 : 191.6184 +#> Model cost at call 88 : 189.9011 +#> Model cost at call 90 : 189.9011 +#> Model cost at call 91 : 189.9011 +#> Model cost at call 94 : 189.223 +#> Model cost at call 95 : 189.223 +#> Model cost at call 100 : 188.8728 +#> Model cost at call 101 : 188.8728 +#> Model cost at call 103 : 188.8728 +#> Model cost at call 106 : 188.2057 +#> Model cost at call 107 : 188.2057 +#> Model cost at call 112 : 187.8429 +#> Model cost at call 118 : 187.6219 +#> Model cost at call 119 : 187.3931 +#> Model cost at call 121 : 187.3931 +#> Model cost at call 125 : 187.1236 +#> Model cost at call 126 : 187.1236 +#> Model cost at call 131 : 186.9995 +#> Model cost at call 137 : 186.927 +#> Model cost at call 139 : 186.927 +#> Model cost at call 143 : 186.8909 +#> Model cost at call 146 : 186.8909 +#> Model cost at call 150 : 186.8708 +#> Model cost at call 152 : 186.8708 +#> Model cost at call 157 : 186.8606 +#> Model cost at call 159 : 186.8606 +#> Model cost at call 161 : 186.8606 +#> Model cost at call 162 : 186.8606 +#> Model cost at call 167 : 186.8551 +#> Model cost at call 169 : 186.8551 +#> Model cost at call 176 : 186.8519 +#> Model cost at call 177 : 186.8519 +#> Model cost at call 180 : 186.8519 +#> Model cost at call 181 : 186.8519 +#> Model cost at call 186 : 186.8504 +#> Model cost at call 187 : 186.8504 +#> Model cost at call 196 : 186.8496 +#> Model cost at call 197 : 186.8496 +#> Model cost at call 200 : 186.8496 +#> Model cost at call 206 : 186.8493 +#> Model cost at call 211 : 186.8493 +#> Model cost at call 215 : 186.8493 +#> Model cost at call 216 : 186.8491 +#> Model cost at call 225 : 186.8491 +#> Model cost at call 226 : 186.849 +#> Model cost at call 236 : 186.8489 +#> Model cost at call 246 : 186.8489 +#> Model cost at call 254 : 186.8489 +#> Model cost at call 257 : 186.8489 +#> Model cost at call 265 : 186.8489 +#> Model cost at call 268 : 186.8489 +#> Model cost at call 276 : 186.8489 +#> Model cost at call 279 : 186.8489 +#> Model cost at call 287 : 186.8489 +#> Model cost at call 290 : 186.8489 +#> Model cost at call 298 : 186.8489 +#> Model cost at call 301 : 186.8489 +#> Model cost at call 309 : 186.8489 +#> Model cost at call 312 : 186.8489 +#> Model cost at call 320 : 186.8489 +#> Model cost at call 323 : 186.8489 +#> Model cost at call 331 : 186.8489 +#> Model cost at call 334 : 186.8489 +#> Model cost at call 342 : 186.8489 +#> Model cost at call 345 : 186.8489 +#> Model cost at call 353 : 186.8489 +#> Model cost at call 356 : 186.8489 +#> Model cost at call 367 : 186.8489 +#> Model cost at call 374 : 186.8489 +#> Model cost at call 375 : 186.8489 +#> Model cost at call 380 : 186.8489 +#> Model cost at call 382 : 186.8489 +#> Model cost at call 383 : 186.8489 +#> Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'>plot</span>(<span class='no'>f_river</span>)</div><img src='test_data_from_UBA_2014-6.png' alt='' width='540' height='400' /><div class='input'> + <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_w_0 9.598567e+01 2.33959810 4.102657e+01 9.568973e-19 NA +#> k_parent_w_sink 3.603743e-01 0.03497716 1.030313e+01 4.988281e-09 NA +#> k_parent_w_parent_s 6.031370e-02 0.01746026 3.454342e+00 1.514738e-03 NA +#> k_parent_s_sink 5.099834e-11 0.10381939 4.912217e-10 5.000000e-01 NA +#> k_parent_s_parent_w 7.419672e-02 0.11338174 6.543974e-01 2.608057e-01 NA +#> Upper +#> parent_w_0 NA +#> k_parent_w_sink NA +#> k_parent_w_parent_s NA +#> k_parent_s_sink NA +#> k_parent_s_parent_w NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09246946 5 6 +#> parent_w 0.06377096 3 3 +#> parent_s 0.20882324 2 3</div><div class='input'> + <span class='co'># This is the evaluation used for the validation of software packages</span> + <span class='co'># in the expertise from 2014</span> + <span class='no'>m_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), + <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 340.115 +#> Model cost at call 3 : 340.115 +#> Model cost at call 12 : 278.5521 +#> Model cost at call 14 : 278.5499 +#> Model cost at call 22 : 244.4153 +#> Model cost at call 24 : 244.4152 +#> Model cost at call 32 : 211.0249 +#> Model cost at call 34 : 211.0247 +#> Model cost at call 42 : 151.2576 +#> Model cost at call 44 : 151.2575 +#> Model cost at call 46 : 151.2574 +#> Model cost at call 52 : 109.7633 +#> Model cost at call 53 : 100.8415 +#> Model cost at call 58 : 100.8412 +#> Model cost at call 61 : 100.8412 +#> Model cost at call 62 : 100.8411 +#> Model cost at call 64 : 70.07576 +#> Model cost at call 66 : 70.07568 +#> Model cost at call 76 : 64.29488 +#> Model cost at call 78 : 64.29487 +#> Model cost at call 86 : 61.39756 +#> Model cost at call 88 : 61.39755 +#> Model cost at call 96 : 57.47933 +#> Model cost at call 98 : 57.47932 +#> Model cost at call 106 : 52.46647 +#> Model cost at call 108 : 52.46646 +#> Model cost at call 116 : 48.17301 +#> Model cost at call 118 : 48.173 +#> Model cost at call 126 : 45.15666 +#> Model cost at call 128 : 45.15665 +#> Model cost at call 137 : 44.55574 +#> Model cost at call 139 : 44.55573 +#> Model cost at call 143 : 44.55573 +#> Model cost at call 147 : 43.13847 +#> Model cost at call 149 : 43.13847 +#> Model cost at call 151 : 43.13847 +#> Model cost at call 158 : 43.11922 +#> Model cost at call 160 : 43.11922 +#> Model cost at call 168 : 42.29535 +#> Model cost at call 170 : 42.29535 +#> Model cost at call 178 : 42.03979 +#> Model cost at call 180 : 42.03979 +#> Model cost at call 189 : 41.56286 +#> Model cost at call 190 : 41.12187 +#> Model cost at call 191 : 39.73019 +#> Model cost at call 192 : 39.31762 +#> Model cost at call 193 : 39.31762 +#> Model cost at call 196 : 39.31762 +#> Model cost at call 203 : 38.6346 +#> Model cost at call 204 : 38.6346 +#> Model cost at call 205 : 38.63459 +#> Model cost at call 209 : 38.63459 +#> Model cost at call 210 : 38.63459 +#> Model cost at call 211 : 38.63459 +#> Model cost at call 213 : 38.12767 +#> Model cost at call 215 : 38.12767 +#> Model cost at call 223 : 38.04349 +#> Model cost at call 225 : 38.04349 +#> Model cost at call 229 : 38.04349 +#> Model cost at call 233 : 37.93963 +#> Model cost at call 236 : 37.93963 +#> Model cost at call 243 : 37.87645 +#> Model cost at call 244 : 37.87645 +#> Model cost at call 254 : 37.79144 +#> Model cost at call 256 : 37.79144 +#> Model cost at call 264 : 37.7493 +#> Model cost at call 269 : 37.7493 +#> Model cost at call 274 : 37.72466 +#> Model cost at call 275 : 37.72466 +#> Model cost at call 279 : 37.72466 +#> Model cost at call 283 : 37.72466 +#> Model cost at call 284 : 37.71402 +#> Model cost at call 285 : 37.71402 +#> Model cost at call 287 : 37.71402 +#> Model cost at call 294 : 37.70366 +#> Model cost at call 295 : 37.70366 +#> Model cost at call 296 : 37.70366 +#> Model cost at call 305 : 37.69553 +#> Model cost at call 306 : 37.69553 +#> Model cost at call 307 : 37.69553 +#> Model cost at call 315 : 37.6936 +#> Model cost at call 319 : 37.6936 +#> Model cost at call 321 : 37.6936 +#> Model cost at call 326 : 37.6924 +#> Model cost at call 328 : 37.6924 +#> Model cost at call 329 : 37.6924 +#> Model cost at call 336 : 37.69198 +#> Model cost at call 338 : 37.69198 +#> Model cost at call 344 : 37.69198 +#> Model cost at call 348 : 37.69197 +#> Model cost at call 350 : 37.69197 +#> Model cost at call 363 : 37.69197 +#> Model cost at call 364 : 37.69197 +#> Model cost at call 367 : 37.69197 +#> Model cost at call 382 : 37.69197 +#> Model cost at call 384 : 37.69197 +#> Model cost at call 387 : 37.69197 +#> Model cost at call 401 : 37.69197 +#> Model cost at call 420 : 37.69197 +#> Model cost at call 441 : 37.69197 +#> Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'>plot</span>(<span class='no'>f_soil</span>)</div><img src='test_data_from_UBA_2014-16.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_0 76.55425583 0.943443834 81.1434164 4.422340e-30 74.602593306 +#> k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257526 +#> k_M1 0.84258650 0.930121206 0.9058889 1.871937e-01 0.085876305 +#> k_M2 0.04210878 0.013729902 3.0669396 2.729137e-03 0.021450631 +#> k_M3 0.01122919 0.008044866 1.3958205 8.804914e-02 0.002550985 +#> f_parent_to_M1 0.32240199 0.278620411 1.1571370 1.295466e-01 NA +#> f_parent_to_M2 0.16099854 0.030548889 5.2701930 1.196191e-05 NA +#> f_M1_to_M3 0.27921500 0.314732717 0.8871496 1.920907e-01 0.015016888 +#> f_M2_to_M3 0.55641332 0.650247079 0.8556952 2.004966e-01 0.005360551 +#> Upper +#> parent_0 78.50591836 +#> k_parent 0.13120340 +#> k_M1 8.26714671 +#> k_M2 0.08266187 +#> k_M3 0.04942980 +#> f_parent_to_M1 NA +#> f_parent_to_M2 NA +#> f_M1_to_M3 0.90777217 +#> f_M2_to_M3 0.99658634</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09649963 9 20 +#> parent 0.04721283 2 6 +#> M1 0.26551209 2 5 +#> M2 0.20327575 2 5 +#> M3 0.05196549 3 4</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="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> |
