diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-04 15:38:09 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-04 15:38:09 +0100 |
| commit | 09f4f904af23a34d68d5d78482a5b9e12d9a9494 (patch) | |
| tree | 60b61d802985e6a4328c57e32099e66217403026 /docs/reference | |
| parent | db73a6bab3a60de98d020442e4ad103f47df9ab0 (diff) | |
Static documentation rebuilt by pkgdown::build_site()
With updated pkgdown with my PR
Diffstat (limited to 'docs/reference')
38 files changed, 104 insertions, 269 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index e05cdc29..7d036804 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index fe39ce6e..cfe6329b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,12 +60,7 @@ </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 --> @@ -193,7 +188,7 @@ #> #> $time #> user system elapsed -#> 0.256 0.000 0.256 +#> 0.316 0.000 0.317 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +374,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5b47f50> +#> <environment: 0x5d4a3b0> #> #> $cost_notrans #> function (P) @@ -401,7 +396,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5b47f50> +#> <environment: 0x5d4a3b0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,7 +462,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:31 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 @@ -546,7 +541,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.070 +#> 0.076 0.000 0.077 #> #> $mkinmod #> <mkinmod> model generated with @@ -733,7 +728,7 @@ #> } #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $cost_notrans #> function (P) @@ -755,7 +750,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -818,7 +813,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:30 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]] @@ -894,7 +889,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.070 +#> 0.076 0.000 0.077 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +1076,7 @@ #> } #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $cost_notrans #> function (P) @@ -1103,7 +1098,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +1161,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:30 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" 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 9f098ff3..97af2f9c 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -61,12 +61,7 @@ </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 --> 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 e45463ba..1487e2c9 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -61,12 +61,7 @@ </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 --> 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 247c3e00..4571c175 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -61,12 +61,7 @@ </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 --> 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 006a3876..7003fa0e 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c2501a7f..83edd323 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 1fbf7741..83bca886 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2cecda28..13db29aa 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 68b7be44..56c2b48e 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 51c35eee..8ff5b5ba 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 2f7dcb5d..43b6028a 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 82a0b039..8e491bc9 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 6ff7ac36..a3716060 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -61,12 +61,7 @@ </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 --> @@ -101,7 +96,7 @@ 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>summary.mkinfit</code>.</p> + <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index a4b661e2..633e0865 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d2551059..955b5c58 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/index.html b/docs/reference/index.html index 23eb608b..b7d59a21 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,12 +60,7 @@ </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 --> @@ -115,7 +110,7 @@ </ul> <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using - mkinfit</a></p> + list(list("mkinfit"))</a></p> <ul> <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> </ul> @@ -124,6 +119,16 @@ <ul> <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> </ul> + + <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</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">Summary method for class "mkinfit"</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> @@ -176,6 +181,11 @@ <li><code><a href="print.mkinds.html">print.mkinds</a></code></li> </ul> + <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</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> + </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> @@ -189,6 +199,11 @@ <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> </ul> + <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p> + <ul> + <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> + </ul> + <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p> <ul> <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> @@ -213,6 +228,11 @@ <ul> <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> </ul> + + <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</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> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 8309a23e..d32acb5b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -61,12 +61,7 @@ </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 --> @@ -124,8 +119,8 @@ <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: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:24 2016 -#> Date of summary: Thu Nov 3 17:46:24 2016 +#> Date of fit: Fri Nov 4 15:36:38 2016 +#> Date of summary: Fri Nov 4 15:36:38 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -135,7 +130,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.662 s +#> Fitted with method Port using 246 model solutions performed in 1.886 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 0385ccbb..21a8a8f8 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 965262ce..fe6e47e4 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 522aab33..f5dd4c88 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,12 +60,7 @@ </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 --> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 4e1be39c..8d420165 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -61,12 +61,7 @@ </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 --> @@ -110,7 +105,7 @@ 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>summary.mkinfit</code>.</p> + <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 867fb9ff..b298d90a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -61,12 +61,7 @@ </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 --> @@ -256,7 +251,7 @@ 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>ilr</code> transformation. + <code><a href='ilr.html'>ilr</a></code> transformation. </dd> <dt>plot</dt> <dd> @@ -332,11 +327,11 @@ <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>summary.mkinfit</code>.</p> + A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Plotting methods <code>plot.mkinfit</code> and + <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></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> @@ -361,15 +356,15 @@ <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: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:27 2016 -#> Date of summary: Thu Nov 3 17:46:27 2016 +#> Date of fit: Fri Nov 4 15:36:41 2016 +#> Date of summary: Fri Nov 4 15:36:41 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 0.147 s +#> Fitted with method Port using 64 model solutions performed in 0.156 s #> #> Weighting: none #> @@ -438,7 +433,7 @@ <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 -#> 1.204 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 +#> 1.244 1.208 0.933 </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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index bdfd0e09..7dba1b6d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f8151c16..923abc6d 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 9ed92dd0..5fe94a8a 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,12 +61,7 @@ </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 +78,7 @@ </div> - <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> + <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> @@ -96,7 +91,7 @@ </dd> <dt>&#8230;</dt> <dd> - further arguments passed to <code>plot.mkinfit</code>. + further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. </dd> </dl> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 57bb747c..f7eb950a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -61,12 +61,7 @@ </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 --> @@ -277,17 +272,17 @@ <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 -#> 0.004 0.024 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.008 0.024 0.005 </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 -#> 0.004 0.016 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.000 0.020 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 -#> 0.036 0.000 0.033 </div></pre> +#> 0.036 0.000 0.037 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 53c4f62f..a0dcd06d 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -61,12 +61,7 @@ </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 --> @@ -85,7 +80,7 @@ <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>plot.mkinfit</code> + model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the argument <code>show_residuals = TRUE</code>.</p> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 86374e4b..8424eaab 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 21461986..5613a720 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 61a597e7..e7158180 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index b107ca70..ef5c04b7 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -61,12 +61,7 @@ </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 --> @@ -124,7 +119,7 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments passed to <code>plot.mkinfit</code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. + Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> </dl> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 9bd088b1..c578f4ee 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 11b96036..3f653971 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 526dde10..c63ba490 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 46d078bf..241964a7 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -61,12 +61,7 @@ </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 --> @@ -144,15 +139,15 @@ <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: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:35 2016 -#> Date of summary: Thu Nov 3 17:46:35 2016 +#> Date of fit: Fri Nov 4 15:36:49 2016 +#> Date of summary: Fri Nov 4 15:36:49 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.08 s +#> Fitted with method Port using 35 model solutions performed in 0.086 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index a46a5781..333b3dbf 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -61,12 +61,7 @@ </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 --> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index ccd56ca4..5ee1e9cc 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -61,12 +61,7 @@ </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 --> @@ -88,7 +83,7 @@ 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>ilr</code> transformation is used.</p> + negative, the <code><a href='ilr.html'>ilr</a></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. @@ -114,7 +109,7 @@ <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>ilr</code> transformation, the parameter names and + before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and the information if the pathway to sink is included in the model. </dd> <dt>transform_rates</dt> @@ -133,7 +128,7 @@ 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>ilr</code> + transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> transformation. </dd> </dl> @@ -151,8 +146,8 @@ <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: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:36 2016 -#> Date of summary: Thu Nov 3 17:46:36 2016 +#> Date of fit: Fri Nov 4 15:36:50 2016 +#> Date of summary: Fri Nov 4 15:36:50 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -160,7 +155,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.657 s +#> Fitted with method Port using 153 model solutions performed in 0.663 s #> #> Weighting: none #> |