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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
| commit | a77a10ea6c607346778ba0700b3b66ac393101a2 (patch) | |
| tree | e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/schaefer07_complex_case.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/schaefer07_complex_case.html')
| -rw-r--r-- | docs/dev/reference/schaefer07_complex_case.html | 239 |
1 files changed, 239 insertions, 0 deletions
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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">mkin</a> + <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + </span> + </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 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--> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Metabolism data set used for checking the software quality of KinGUI</h1> + + <div class="hidden name"><code>schaefer07_complex_case.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the + software quality of KinGUI in the original publication (Schäfer et al., 2007). + The results from the fitting are also included.</p> + </div> + + <pre class="usage"><span class='no'>schaefer07_complex_case</span></pre> + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl'> + <dt><code>time</code></dt><dd><p>a numeric vector</p></dd> + <dt><code>parent</code></dt><dd><p>a numeric vector</p></dd> + <dt><code>A1</code></dt><dd><p>a numeric vector</p></dd> + <dt><code>B1</code></dt><dd><p>a numeric vector</p></dd> + <dt><code>C1</code></dt><dd><p>a numeric vector</p></dd> + <dt><code>A2</code></dt><dd><p>a numeric vector</p></dd> + +</dl><p>The results are a data frame with 14 results for different parameter values</p> + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic + software tool for evaluations according to FOCUS degradation kinetics. In: Del + Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII + Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) +<span class='no'>model</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='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), + <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</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='co'># \dontrun{</span> + <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink +#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479609 0.5520391 +#> +#> $distimes +#> DT50 DT90 +#> parent 13.95078 46.34350 +#> A1 49.75343 165.27733 +#> B1 37.26907 123.80517 +#> C1 11.23131 37.30959 +#> A2 28.50638 94.69614 +#> </div><div class='input'> <span class='co'># }</span> + <span class='co'># Compare with the results obtained in the original publication</span> + <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation +#> 1 parent degradation rate 0.0496 0.0506 2.0 +#> 2 parent DT50 13.9900 13.6900 2.2 +#> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9 +#> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2 +#> 5 metabolite A1 DT50 49.9600 50.8900 1.8 +#> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6 +#> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7 +#> 8 metabolite B1 DT50 39.6100 40.2400 1.6 +#> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5 +#> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9 +#> 11 metabolite C1 DT50 10.8700 9.9000 9.8 +#> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7 +#> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4 +#> 14 metabolite A2 DT50 28.2400 28.4500 0.7</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> + + + <footer> + <div class="copyright"> + <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> + + </footer> + </div> + + + + + </body> +</html> + + |