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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-05-05 12:46:31 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-05-05 12:46:31 +0200 |
| commit | ccc70e82af4ba435f0a71ba1ae4e0e92045c3852 (patch) | |
| tree | d8ffd99be771f47eae876f244b049742481bdd25 /docs/reference/mmkin.html | |
| parent | 1c7dbeec335c404377381157d34db6e219ce3f21 (diff) | |
Static docs except articles rebuilt with current pkgdown
Diffstat (limited to 'docs/reference/mmkin.html')
| -rw-r--r-- | docs/reference/mmkin.html | 91 |
1 files changed, 48 insertions, 43 deletions
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 67397827..fe10c88f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mmkin • mkin</title> +<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -26,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<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> @@ -71,6 +72,9 @@ <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> @@ -96,8 +100,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> </div> @@ -105,37 +108,38 @@ specified in its first two arguments.</p> - <pre><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, + <pre class="usage"><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>models</dt> - <dd> - Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> - objects. - </dd> - <dt>datasets</dt> - <dd> - An optionally named list of datasets suitable as observed data for - <code><a href='mkinfit.html'>mkinfit</a></code>. - </dd> - <dt>cores</dt> - <dd> - The number of cores to be used for multicore processing. This is only - used when the <code>cluster</code> argument is <code>NULL</code>. - </dd> - <dt>cluster</dt> - <dd> - A cluster as returned by <code>makeCluster</code> to be used for parallel - execution. - </dd> - <dt>…</dt> - <dd> - Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. - </dd> - </dl> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>models</th> + <td><p>Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> + objects.</p></td> + </tr> + <tr> + <th>datasets</th> + <td><p>An optionally named list of datasets suitable as observed data for + <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + </tr> + <tr> + <th>cores</th> + <td><p>The number of cores to be used for multicore processing. This is only + used when the <code>cluster</code> argument is <code>NULL</code>.</p></td> + </tr> + <tr> + <th>cluster</th> + <td><p>A cluster as returned by <code>makeCluster</code> to be used for parallel + execution.</p></td> + </tr> + <tr> + <th>…</th> + <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -144,7 +148,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> + <p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -160,11 +164,12 @@ <span class='fu'>names</span>(<span class='no'>datasets</span>) <span class='kw'><-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) <span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) -<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) - +<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> +#> <span class='warning'>Convergence code is 1</span></div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> +#> <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='no'>time_default</span></div><div class='output co'>#> user system elapsed -#> 16.360 0.128 9.017 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 21.888 0.004 21.892 </div><div class='input'> +#> 16.092 0.132 11.761 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed +#> 25.004 0.000 25.000 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340479 0.2659521 0.7505687 0.2494313 @@ -174,17 +179,17 @@ #> #> $distimes #> DT50 DT90 -#> parent 0.8777688 2.915885 +#> parent 0.8777689 2.915885 #> M1 2.3257456 7.725960 -#> M2 33.7200881 112.015708 +#> M2 33.7200862 112.015702 #> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-12.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-15.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-17.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-19.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> <span class='co'># by plot.mkinfit and can be plotted using plot_sep</span> -<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-18.png' alt='' width='540' height='400' /><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]]) +<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-21.png' alt='' width='540' height='400' /><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]]) <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> <span class='co'># allow to plot the observed variables separately</span> -<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-23.png' alt='' width='540' height='400' /><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |