diff options
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 40 |
1 files changed, 19 insertions, 21 deletions
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"> |