diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-03 14:33:05 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-03 17:48:31 +0100 |
| commit | f39815aa87272849f8e0c808099c4cee780c2a81 (patch) | |
| tree | d3f59ae226591252e17737e12bae7f90be278b7b /docs/reference | |
| parent | bad0c7caff62aa90225ae8acee43b297bdc28b25 (diff) | |
Static documentation rebuilt by pkgdown::build_site()
Using pkgdown with PR hadley/pkgdown#212
Diffstat (limited to 'docs/reference')
38 files changed, 473 insertions, 428 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3b8e0e03..e05cdc29 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -113,10 +118,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='DFOP.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -136,7 +138,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4ea16d10..fe39ce6e 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -102,10 +107,7 @@ <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</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>) @@ -113,14 +115,12 @@ #> model B C #> FOMC List,42 List,42 #> attr(,"class") -#> [1] "mmkin" -#> </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B #> SFO List,42 #> FOMC List,42 #> attr(,"class") -#> [1] "mmkin" -#> </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#> $par +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#> $par #> parent_0 log_alpha log_beta #> 99.666193 2.549849 5.050586 #> @@ -193,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.26 0.00 0.26 +#> 0.256 0.000 0.256 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5421f48> +#> <environment: 0x5b47f50> #> #> $cost_notrans #> function (P) @@ -401,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5421f48> +#> <environment: 0x5b47f50> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,16 +467,14 @@ #> 99.66619 #> #> $date -#> [1] "Wed Oct 26 23:50:33 2016" +#> [1] "Thu Nov 3 17:46:18 2016" #> #> attr(,"class") -#> [1] "mkinfit" "modFit" -#> </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B #> SFO List,42 #> attr(,"class") -#> [1] "mmkin" -#> </div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#> $par +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#> $par #> parent_0 log_k_parent_sink #> 99.174072 -2.549028 #> @@ -735,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $cost_notrans #> function (P) @@ -757,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -820,11 +818,10 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:50:32 2016" +#> [1] "Thu Nov 3 17:46:18 2016" #> #> attr(,"class") -#> [1] "mkinfit" "modFit" -#> </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] +#> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] #> $par #> parent_0 log_k_parent_sink #> 99.174072 -2.549028 @@ -1084,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $cost_notrans #> function (P) @@ -1106,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x2b30d68> +#> <environment: 0x46881c0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1169,11 +1166,10 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:50:32 2016" +#> [1] "Thu Nov 3 17:46:18 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" -#> #> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -1195,7 +1191,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 6f071674..9f098ff3 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -110,10 +115,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -132,7 +134,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d721b2d9..e45463ba 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -109,10 +114,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -131,7 +133,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 11fcea7c..247c3e00 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -110,10 +115,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -132,7 +134,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 17c34f0f..006a3876 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -108,10 +113,7 @@ in this fit.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -130,7 +132,7 @@ in this fit.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c5bdae8b..c2501a7f 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -101,10 +106,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#> name time value #> 1 parent 0 85.1 #> 2 parent 1 57.9 @@ -114,8 +116,7 @@ #> 6 parent 28 6.6 #> 7 parent 63 4.0 #> 8 parent 91 3.9 -#> 9 parent 119 0.6 -#> </div></pre> +#> 9 parent 119 0.6</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -133,7 +134,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index a2e84ce0..1fbf7741 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -125,10 +130,7 @@ Technology</em> <b>24</b>, 1032-1038</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='FOMC.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -150,7 +152,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index e41b7b6a..2cecda28 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -111,10 +116,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='HS.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -134,7 +136,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index c39e7818..68b7be44 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -112,10 +117,7 @@ Media</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='IORE.solution-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='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'>fit.iore</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -125,13 +127,11 @@ <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS. #> model par 1 85.87489063 85.874891 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 -#> model par 3 0.65096665 1.949403 1.949403 -#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, +#> model par 3 0.65096665 1.949403 1.949403</div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 -#> iore.deS 1.785233 15.1479 4.559973 -#> </div></pre> +#> iore.deS 1.785233 15.1479 4.559973</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -152,7 +152,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 3ce813bf..51c35eee 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -104,10 +109,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -127,7 +129,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 942fa576..2f7dcb5d 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -113,10 +118,7 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -136,7 +138,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 2500e092..82a0b039 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -135,13 +140,10 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># The kinetic model</span> <span class='no'>m_SFO_SFO</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='st'>"M1"</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <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='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'># Generate a prediction for a specific set of parameters</span> <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) @@ -200,7 +202,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 73d7e746..6ff7ac36 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -96,7 +101,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + <p>The function is used internally by <code>summary.mkinfit</code>.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -123,7 +128,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 62a9163f..a4b661e2 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -94,14 +99,8 @@ <p>The geometric mean.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> - <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</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'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA -#> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051 -#> </div></pre> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</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'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA</div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -118,7 +117,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 82accca4..d2551059 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -107,31 +112,17 @@ <p>Another implementation can be found in R package <code>robCompositions</code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Order matters</span> -<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079 -#> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079 -#> </div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> -<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> [1] 0 0 -#> </div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> [1] -0.2034219 0.1174457 -#> </div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> -<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01 -#> </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01 -#> </div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> -<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01 -#> </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04 -#> </div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'>sum</span>(<span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> [1] 1 -#> </div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> +<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> +<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> +<span class='fu'>sum</span>(<span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> <span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>) <span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>) -<span class='fu'>length</span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> [1] 4 -#> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5 -#> </div></pre> +<span class='fu'>length</span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -156,7 +147,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/index.html b/docs/reference/index.html index 6fcf39c8..23eb608b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -80,175 +85,180 @@ <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2> <p class="section-desc"><p>Essential functionality</p></p> - <p><a href="mkinfit.html"> -</a></p> + + <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p> <ul> <li><code><a href="mkinfit.html">mkinfit</a></code></li> </ul> - <p><a href="mkinmod.html"> -</a></p> + + <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p> <ul> <li><code><a href="mkinmod.html">mkinmod</a></code></li> </ul> - <p><a href="mmkin.html"> -</a></p> + + <p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p> <ul> <li><code><a href="mmkin.html">mmkin</a></code></li> </ul> <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> <p class="section-desc"><p>Functions working with mkinfit objects</p></p> - <p><a href="endpoints.html"> -</a></p> + + <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p> <ul> <li><code><a href="endpoints.html">endpoints</a></code></li> </ul> - <p><a href="mkinerrmin.html"> -</a></p> + + <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p> <ul> <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li> </ul> - <p><a href="mkinparplot.html"> -</a></p> + + <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using + mkinfit</a></p> <ul> <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> </ul> - <p><a href="mkinresplot.html"> -</a></p> + + <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p> <ul> <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> </ul> - <p><a href="plot.mkinfit.html"> -</a></p> - <ul> - <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li> - </ul> - <p><a href="summary.mkinfit.html"> -</a></p> - <ul> - <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li> - </ul> <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> <p class="section-desc"><p>Functions working with aggregated results</p></p> + <p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p> <ul> <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li> </ul> - <p><a href="plot.mmkin.html"> -</a></p> + + <p><a href="plot.mmkin.html">Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</a></p> <ul> <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li> </ul> <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2> <p class="section-desc"></p> - <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html"> -</a></p> + + <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li> </ul> - <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html"> -</a></p> + + <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li> </ul> - <p><a href="FOCUS_2006_HS_ref_A_to_F.html"> -</a></p> + + <p><a href="FOCUS_2006_HS_ref_A_to_F.html">Results of fitting the HS model to Datasets A to F of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li> </ul> - <p><a href="FOCUS_2006_SFO_ref_A_to_F.html"> -</a></p> + + <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p> <ul> <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li> </ul> - <p><a href="mccall81_245T.html"> -</a></p> + + <p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p> <ul> <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li> </ul> - <p><a href="schaefer07_complex_case.html"> -</a></p> + + <p><a href="mkinds.html">A dataset class for mkin</a></p> <ul> - <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li> + <li><code><a href="mkinds.html">mkinds</a></code></li> </ul> - <p><a href="synthetic_data_for_UBA.html"> -</a></p> + + <p><a href="print.mkinds.html">Print mkinds objects</a></p> + <ul> + <li><code><a href="print.mkinds.html">print.mkinds</a></code></li> + </ul> + + <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p> <ul> <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li> </ul> <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> <p class="section-desc"></p> - <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p> + + <p><a href="geometric_mean.html">Calculate the geometric mean</a></p> <ul> <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> </ul> - <p><a href="ilr.html"> -</a></p> + + <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p> <ul> - <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> + <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> </ul> - <p><a href="mkin_long_to_wide.html"> -</a></p> + + <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p> <ul> - <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> + <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> </ul> - <p><a href="mkinpredict.html"> -</a></p> + + <p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p> <ul> <li><code><a href="mkinpredict.html">mkinpredict</a></code></li> </ul> - <p><a href="mkinsub.html"> -</a></p> + + <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p> <ul> <li><code><a href="mkinsub.html">mkinsub</a></code></li> </ul> - <p><a href="mkin_wide_to_long.html"> -</a></p> - <ul> - <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> - </ul> - <p><a href="print.mkinmod.html"> -</a></p> + + <p><a href="print.mkinmod.html">Print mkinmod objects</a></p> <ul> <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> </ul> - <p><a href="transform_odeparms.html"> -</a></p> - <ul> - <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li> - </ul> <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> <p class="section-desc"><p>Parent only model solutions</p></p> - <p><a href="DFOP.solution.html"> -</a></p> + + <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p> <ul> <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li> </ul> - <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p> + + <p><a href="FOMC.solution.html">First-Order Multi-Compartment kinetics</a></p> <ul> <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li> </ul> - <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p> + + <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p> <ul> <li><code><a href="HS.solution.html">HS.solution</a></code></li> </ul> - <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p> + + <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p> <ul> <li><code><a href="IORE.solution.html">IORE.solution</a></code></li> </ul> - <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p> + + <p><a href="SFO.solution.html">Single First-Order kinetics</a></p> + <ul> + <li><code><a href="SFO.solution.html">SFO.solution</a></code></li> + </ul> + + <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p> <ul> <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li> </ul> + <h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2> + <p class="section-desc"></p> + + + <p><a href="add_err.html">Add normally distributed errors to simulated kinetic degradation data</a></p> + <ul> + <li><code><a href="add_err.html">add_err</a></code></li> + </ul> <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2> <p class="section-desc"><p>Functions that have been superseeded</p></p> - <p><a href="mkinplot.html"> -</a></p> + + <p><a href="mkinplot.html">Plot the observed data and the fitted model of an mkinfit object</a></p> <ul> <li><code><a href="mkinplot.html">mkinplot</a></code></li> </ul> @@ -265,6 +275,7 @@ <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li> <li><a href="#section-helper-functions">Helper functions</a></li> <li><a href="#section-analytical-solutions">Analytical solutions</a></li> + <li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li> <li><a href="#section-deprecated-functions">Deprecated functions</a></li> </ul> </div> @@ -272,7 +283,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 74b9c088..8309a23e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -105,13 +110,10 @@ <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</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'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</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'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='co'>## Not run: ------------------------------------</span> <span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> <span class='co'># summary(fit.1, data = FALSE)</span> <span class='co'># </span> @@ -121,9 +123,9 @@ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:40 2016 -#> Date of summary: Wed Oct 26 23:50:40 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:24 2016 +#> Date of summary: Thu Nov 3 17:46:24 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +135,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.43 s +#> Fitted with method Port using 246 model solutions performed in 1.662 s #> #> Weighting: none #> @@ -213,8 +215,7 @@ #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 -#> anisole 103.784 344.763 -#> </div></pre> +#> anisole 103.784 344.763</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -232,7 +233,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index cc50bf7d..0385ccbb 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -108,10 +113,7 @@ <p>Dataframe in wide format.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> time parent m1 #> 1 0 99.46 0.00 #> 2 0 102.04 0.00 @@ -134,8 +136,7 @@ #> 19 100 NA 31.04 #> 20 100 NA 33.13 #> 21 120 NA 25.15 -#> 22 120 NA 33.31 -#> </div></pre> +#> 22 120 NA 33.31</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -156,7 +157,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index bce6d6a4..965262ce 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -102,10 +107,7 @@ <p>Dataframe in long format as needed for <code>modCost</code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>)) <span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#> name time value #> 1 x 1 1 @@ -113,8 +115,7 @@ #> 3 x 3 7 #> 4 y 1 3 #> 5 y 2 4 -#> 6 y 3 5 -#> </div></pre> +#> 6 y 3 5</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -135,7 +136,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index e5d99fd5..522aab33 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -100,10 +105,7 @@ in order to be compatible with mkinfit</dd> </dl></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -122,7 +124,7 @@ in order to be compatible with mkinfit</dd> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 5b437b08..4e1be39c 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -105,7 +110,7 @@ as defined in the FOCUS kinetics report from 2006.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + <p>This function is used internally by <code>summary.mkinfit</code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> @@ -116,24 +121,19 @@ as defined in the FOCUS kinetics report from 2006.</p> <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>SFO_SFO</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'>list</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'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <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'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.0640 4 15 #> parent 0.0646 2 7 -#> m1 0.0469 2 8 -#> </div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +#> m1 0.0469 2 8</div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.1544 4 13 #> parent 0.1659 2 7 -#> m1 0.1095 2 6 -#> </div></pre> +#> m1 0.1095 2 6</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -154,7 +154,7 @@ as defined in the FOCUS kinetics report from 2006.</p> <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 6bfb9352..867fb9ff 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -251,7 +256,7 @@ to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the - <code><a href='ilr.html'>ilr</a></code> transformation. + <code>ilr</code> transformation. </dd> <dt>plot</dt> <dd> @@ -327,11 +332,11 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + A summary can be obtained by <code>summary.mkinfit</code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and + <p>Plotting methods <code>plot.mkinfit</code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> <p>Fitting of several models to several datasets in a single call to <code><a href='mmkin.html'>mmkin</a></code>.</p> @@ -351,23 +356,20 @@ internal rate transformation.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:42 2016 -#> Date of summary: Wed Oct 26 23:50:42 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:27 2016 +#> Date of summary: Thu Nov 3 17:46:27 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.168 s +#> Fitted with method Port using 64 model solutions performed in 0.147 s #> #> Weighting: none #> @@ -428,19 +430,16 @@ #> 28 parent 6.6 4.754 1.8460 #> 63 parent 4.0 2.102 1.8977 #> 91 parent 3.9 1.441 2.4590 -#> 119 parent 0.6 1.092 -0.4919 -#> </div><div class='input'> +#> 119 parent 0.6 1.092 -0.4919</div><div class='input'> <span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> <span class='no'>SFO_SFO</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='st'>"m1"</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>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</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>))</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'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.272 1.204 0.943 -#> </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 99.59848 -3.03822 -2.98030 -5.24750 -#> </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 +#> 1.204 1.244 0.932 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 99.59848 -3.03822 -2.98030 -5.24750 </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_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -451,7 +450,6 @@ #> DT50 DT90 #> parent 7.022929 23.32967 #> m1 131.760712 437.69961 -#> #> </div><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, </span> @@ -535,7 +533,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 40381656..bdfd0e09 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -153,17 +158,14 @@ Media</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># One parent compound, one metabolite, both single first order</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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='st'>"m1"</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>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='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='co'>## Not run: ------------------------------------</span> <span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> <span class='co'># SFO_SFO <- mkinmod(</span> @@ -210,7 +212,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index dff30930..f8151c16 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -97,14 +102,11 @@ <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</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'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</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'>c</span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><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='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</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='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -126,7 +128,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index d3f0c1f6..9ed92dd0 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -78,7 +83,7 @@ </div> - <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> + <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> @@ -91,7 +96,7 @@ </dd> <dt>&#8230;</dt> <dd> - further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. + further arguments passed to <code>plot.mkinfit</code>. </dd> </dl> @@ -118,7 +123,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 31556527..57bb747c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -154,10 +159,7 @@ <p>A matrix in the same format as the output of <code>ode</code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, @@ -182,8 +184,7 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#> time degradinol #> 1 0 100.0000000 #> 2 1 74.0818221 @@ -205,8 +206,7 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> time degradinol #> 1 0 100.0000000 #> 2 1 74.0818221 @@ -228,8 +228,7 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#> time degradinol #> 1 0 100.0000000 #> 2 1 74.0818221 @@ -251,57 +250,44 @@ #> 18 17 0.6096747 #> 19 18 0.4516581 #> 20 19 0.3345965 -#> 21 20 0.2478752 -#> </div><div class='input'> +#> 21 20 0.2478752</div><div class='input'> <span class='co'># Compare integration methods to analytical solution</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, +#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol -#> 21 20 0.2480043 -#> </div><div class='input'> <span class='co'># rk4 is not as precise here</span> +#> 21 20 0.2480043</div><div class='input'> <span class='co'># rk4 is not as precise here</span> <span class='co'># The number of output times used to make a lot of difference until the</span> <span class='co'># default for atol was adjusted</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#> time degradinol -#> 201 20 0.2478752 -#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), +#> 201 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#> time degradinol -#> 2001 20 0.2478752 -#> </div><div class='input'> +#> 2001 20 0.2478752</div><div class='input'> <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span> <span class='no'>SFO_SFO</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'>list</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'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='fu'>system.time</span>( + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227 -#> </div><div class='output co'>#> user system elapsed -#> 0.028 0.004 0.004 -#> </div><div class='input'> <span class='fu'>system.time</span>( +#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed +#> 0.004 0.024 0.004 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227 -#> </div><div class='output co'>#> user system elapsed -#> 0.016 0.004 0.002 -#> </div><div class='input'> <span class='fu'>system.time</span>( +#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed +#> 0.004 0.016 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227 -#> </div><div class='output co'>#> user system elapsed -#> 0.052 0.000 0.052 -#> </div></pre> +#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed +#> 0.036 0.000 0.033 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -322,7 +308,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index d8c84191..53c4f62f 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -80,7 +85,7 @@ <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted - model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> + model and the residuals can be obtained using <code>plot.mkinfit</code> using the argument <code>show_residuals = TRUE</code>.</p> @@ -142,11 +147,8 @@ mkinfit object.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> - <pre class="examples"><div class='input'><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='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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><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'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><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='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='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</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><img src='mkinresplot-4.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -170,7 +172,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 89387468..86374e4b 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -115,22 +120,19 @@ <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='no'>SFO_SFO</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'>list</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'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='co'># The same model using mkinsub</span> <span class='no'>SFO_SFO.2</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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <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='co'># Now supplying full names</span> <span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div></pre> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -151,7 +153,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index a6e74b8a..21461986 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -124,10 +129,7 @@ <p><code><a href='[.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> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> <span class='co'># M1 = mkinsub("SFO", "M2"),</span> @@ -182,7 +184,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4eb7369a..61a597e7 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -199,14 +204,11 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> <span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span> <span class='no'>SFO_SFO</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='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</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='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Show the observed variables separately</span> <span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><div class='input'> @@ -235,7 +237,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index e0a20f3d..b107ca70 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -119,7 +124,7 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. + Further arguments passed to <code>plot.mkinfit</code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> </dl> @@ -128,10 +133,7 @@ <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed</span> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</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='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) @@ -160,7 +162,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index a586a103..9bd088b1 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -109,7 +114,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 73bfd60e..11b96036 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -109,7 +114,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 4714747a..526dde10 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -106,17 +111,14 @@ Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <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'>list</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'>c</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'>list</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'>list</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'>list</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'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> + <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</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'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -134,7 +136,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index b88a5469..46d078bf 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -136,21 +141,18 @@ <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:50 2016 -#> Date of summary: Wed Oct 26 23:50:50 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:35 2016 +#> Date of summary: Thu Nov 3 17:46:35 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.083 s +#> Fitted with method Port using 35 model solutions performed in 0.08 s #> #> Weighting: none #> @@ -209,8 +211,7 @@ #> 30 parent 29.71 35.738 -6.0283 #> 62 parent 5.98 10.862 -4.8818 #> 90 parent 1.54 3.831 -2.2911 -#> 118 parent 0.39 1.351 -0.9613 -#> </div></pre> +#> 118 parent 0.39 1.351 -0.9613</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -233,7 +234,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 45d5f53a..a46a5781 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -117,10 +122,7 @@ measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> <span class='co'># M1 = list(type = "SFO", to = "M2"),</span> @@ -160,7 +162,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index ab5ce062..ccd56ca4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -83,7 +88,7 @@ constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be - negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> + negative, the <code>ilr</code> transformation is used.</p> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. @@ -109,7 +114,7 @@ <dd> The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of the model variables that are needed for grouping the formation fractions - before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and + before <code>ilr</code> transformation, the parameter names and the information if the pathway to sink is included in the model. </dd> <dt>transform_rates</dt> @@ -128,7 +133,7 @@ assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> + transformation used for these transformations is the <code>ilr</code> transformation. </dd> </dl> @@ -139,18 +144,15 @@ as the original parameters.</p> - <h2 class="hasAnchor" id="examples"> - <a class="anchor" href="#examples"></a> - Examples - </h2> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>SFO_SFO</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'>list</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'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:50:51 2016 -#> Date of summary: Wed Oct 26 23:50:51 2016 +#> R version: 3.3.2 +#> Date of fit: Thu Nov 3 17:46:36 2016 +#> Date of summary: Thu Nov 3 17:46:36 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -158,7 +160,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.629 s +#> Fitted with method Port using 153 model solutions performed in 0.657 s #> #> Weighting: none #> @@ -221,8 +223,7 @@ #> Estimated disappearance times: #> DT50 DT90 #> parent 7.023 23.33 -#> m1 131.761 437.70 -#> </div><div class='input'> +#> m1 131.761 437.70</div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> <span class='co'># summary(fit.2, data=FALSE) </span> @@ -233,10 +234,8 @@ <span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> <span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>) <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 100.750000 -2.302585 -2.301586 -2.300587 -#> </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink -#> 100.7500 0.1000 0.1001 0.1002 -#> </div><div class='input'> +#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># # The case of formation fractions</span> <span class='co'># SFO_SFO.ff <- mkinmod(</span> @@ -280,7 +279,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> |