diff options
author | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 06:41:44 +0200 |
---|---|---|
committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 06:41:44 +0200 |
commit | dd65f3503e9d091c82aedcf91635fcf40f778bf9 (patch) | |
tree | 3857ad242a85815b45dbe6529a26ab8d0931a233 | |
parent | a5e2712cafd57239f69d58b8c7f16a1b2f4b7490 (diff) |
Static documentation rebuilt by pkgdown
Also update test log
52 files changed, 150 insertions, 132 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 0afabe7f..195570b1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-06</h4> + <h4 class="date">2018-09-14</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index a42c6e38..f7bbf961 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-06</h4> + <h4 class="date">2018-09-14</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -108,17 +108,17 @@ <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:50 2018 -## Date of summary: Thu Sep 6 13:35:50 2018 +## Date of fit: Fri Sep 14 06:39:28 2018 +## Date of summary: Fri Sep 14 06:39:28 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.086 s +## Fitted with method Port using 37 model solutions performed in 0.091 s ## ## Weighting: none ## @@ -199,17 +199,17 @@ <a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:52 2018 -## Date of summary: Thu Sep 6 13:35:52 2018 +## Date of fit: Fri Sep 14 06:39:30 2018 +## Date of summary: Fri Sep 14 06:39:30 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.35 s +## Fitted with method Port using 611 model solutions performed in 1.333 s ## ## Weighting: none ## @@ -294,17 +294,17 @@ <a class="sourceLine" id="cb11-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:52 2018 -## Date of summary: Thu Sep 6 13:35:53 2018 +## Date of fit: Fri Sep 14 06:39:30 2018 +## Date of summary: Fri Sep 14 06:39:30 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.175 s +## Fitted with method Port using 81 model solutions performed in 0.172 s ## ## Weighting: none ## @@ -365,10 +365,10 @@ <a class="sourceLine" id="cb14-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:53 2018 -## Date of summary: Thu Sep 6 13:35:53 2018 +## Date of fit: Fri Sep 14 06:39:31 2018 +## Date of summary: Fri Sep 14 06:39:31 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.746 s +## Fitted with method Port using 336 model solutions performed in 0.742 s ## ## Weighting: none ## @@ -457,10 +457,10 @@ <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:54 2018 -## Date of summary: Thu Sep 6 13:35:55 2018 +## Date of fit: Fri Sep 14 06:39:32 2018 +## Date of summary: Fri Sep 14 06:39:32 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -469,7 +469,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.324 s +## Fitted with method Port using 137 model solutions performed in 0.312 s ## ## Weighting: none ## @@ -558,17 +558,17 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:55 2018 -## Date of summary: Thu Sep 6 13:35:55 2018 +## Date of fit: Fri Sep 14 06:39:33 2018 +## Date of summary: Fri Sep 14 06:39:33 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.107 s +## Fitted with method Port using 46 model solutions performed in 0.097 s ## ## Weighting: none ## @@ -618,17 +618,17 @@ ## DT50 DT90 ## parent 106 352</code></pre> <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.2 +<pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Thu Sep 6 13:35:55 2018 -## Date of summary: Thu Sep 6 13:35:55 2018 +## Date of fit: Fri Sep 14 06:39:33 2018 +## Date of summary: Fri Sep 14 06:39:33 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.161 s +## Fitted with method Port using 66 model solutions performed in 0.143 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index 6e7707f8..9753abd6 100644 --- a/docs/articles/FOCUS_Z.html +++ b/docs/articles/FOCUS_Z.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-06</h4> + <h4 class="date">2018-09-14</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 16059fcb..d93fe9e1 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-06</h4> + <h4 class="date">2018-09-14</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -125,9 +125,9 @@ <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.218 1.000 2.217 0 -## 1 deSolve, not compiled 3 16.654 7.509 16.646 0 -## 2 Eigenvalue based 3 2.724 1.228 2.722 0 +## 3 deSolve, compiled 3 2.110 1.000 2.108 0 +## 1 deSolve, not compiled 3 16.442 7.792 16.433 0 +## 2 Eigenvalue based 3 2.593 1.229 2.592 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -156,13 +156,13 @@ <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.780 1.000 3.777 0 -## 1 deSolve, not compiled 3 35.169 9.304 35.152 0 +## 2 deSolve, compiled 3 3.781 1.000 3.778 0 +## 1 deSolve, not compiled 3 34.742 9.189 34.725 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> <p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.47.2 on</p> +<p>This vignette was built with mkin 0.9.47.3 on</p> <pre><code>## R version 3.5.1 (2018-07-02) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> diff --git a/docs/articles/index.html b/docs/articles/index.html index 7902c611..dcaf33b8 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 234c6885..4d62b50d 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-06</h4> + <h4 class="date">2018-09-14</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 1a8a7eb2..2952e887 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-06</h4> + <h4 class="date">2018-09-14</h4> <div class="hidden name"><code>twa.Rmd</code></div> diff --git a/docs/authors.html b/docs/authors.html index b60e270c..20849b4a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/index.html b/docs/index.html index 11a699ff..ba838a39 100644 --- a/docs/index.html +++ b/docs/index.html @@ -36,7 +36,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -139,7 +139,7 @@ <div id="news" class="section level2"> <h2 class="hasAnchor"> <a href="#news" class="anchor"></a>News</h2> -<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.html">github master branch</a>.</p> +<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.html">github master branch</a>.</p> </div> <div id="credits-and-historical-remarks" class="section level2"> <h2 class="hasAnchor"> diff --git a/docs/news/index.html b/docs/news/index.html index 71390917..b76ca884 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -117,6 +117,15 @@ </div> + <div id="mkin-0-9-47-3-2018-09-13" class="section level1"> +<h1 class="page-header"> +<a href="#mkin-0-9-47-3-2018-09-13" class="anchor"></a>mkin 0.9.47.3 (2018-09-13)<small> Unreleased </small> +</h1> +<ul> +<li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’</p></li> +<li><p>Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’</p></li> +</ul> +</div> <div id="mkin-0-9-47-2-2018-07-19" class="section level1"> <h1 class="page-header"> <a href="#mkin-0-9-47-2-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)<small> 2018-07-19 </small> @@ -131,7 +140,7 @@ <a href="#mkin-0-9-47-1-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)<small> 2018-02-06 </small> </h1> <ul> -<li><p>Skip some test on CRAN and winbuilder to avoid timeouts</p></li> +<li><p>Skip some tests on CRAN and winbuilder to avoid timeouts</p></li> <li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> <li><p>‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.</p></li> <li><p>‘mkinfit’: Work around a bug in the current FME version that prevented the convergence message to be returned in the case of non-convergence.</p></li> @@ -639,6 +648,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> + <li><a href="#mkin-0-9-47-3-2018-09-13">0.9.47.3</a></li> <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li> <li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li> <li><a href="#mkin-0-9-46-3-2017-11-16">0.9.46.3</a></li> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index c1177306..22709123 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 8771b53b..94c4d336 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.171 0.001 0.171 +#> 0.165 0.000 0.165 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd7f970> -#> <environment: 0x55555bc8fca8> +#> <bytecode: 0x55555bd36378> +#> <environment: 0x55555bd42bc8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555ca84338> -#> <environment: 0x55555bc8fca8> +#> <bytecode: 0x55555c995188> +#> <environment: 0x55555bd42bc8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,10 +558,10 @@ #> 99.17407 #> #> $date -#> [1] "Thu Sep 6 13:35:24 2018" +#> [1] "Fri Sep 14 06:38:57 2018" #> #> $version -#> [1] "0.9.47.2" +#> [1] "0.9.47.3" #> #> $Rversion #> [1] "3.5.1" 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 6888c0ba..2b6886ff 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> 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 624f3908..73b2450b 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> 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 c089e5e7..e5621863 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> 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 e6846a38..872d68a9 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 42ff6926..232be6f3 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 9f7db6c1..c4f3158d 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 87ee2d20..8f1ff8de 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 18c8a751..ae09fcf7 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index ac26f950..f4e8eb42 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index bb782104..e568bd5a 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 9d71c18c..99871884 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 46cb10e1..e39d1c15 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 091e65ea..a5c63aeb 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 34edfc08..ec49468a 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index d9705ce3..af7642e6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 447d9fda..8d31b0d2 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -65,7 +65,7 @@ guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 9894f8eb..cea92155 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -164,10 +164,10 @@ <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</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'>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 used for fitting: 0.9.47.2 + <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 used for fitting: 0.9.47.3 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 13:35:34 2018 -#> Date of summary: Thu Sep 6 13:35:34 2018 +#> Date of fit: Fri Sep 14 06:39:07 2018 +#> Date of summary: Fri Sep 14 06:39:07 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -177,7 +177,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.549 s +#> Fitted with method Port using 246 model solutions performed in 1.423 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 2bf67d39..8d53bc1b 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 3e0f10f7..e7342cee 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 3f4a84ec..16086f3e 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 44fc1e51..c8fd8272 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index f9c6c117..b1c42168 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -161,7 +161,7 @@ <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"none"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>), + <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"none"</span>, <span class='st'>"manual"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>), <span class='kw'>tc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>sigma_low</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>rsd_high</span> <span class='kw'>=</span> <span class='fl'>0.07</span>), <span class='kw'>scaleVar</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, @@ -326,7 +326,8 @@ <th>weight</th> <td><p>only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none", "std", "mean", see details of <code>modCost</code>, or "tc" for the - two component error model.</p></td> + two component error model. The option "manual" is available for + the case that <code>err</code>!=<code>NULL</code>, but it is not necessary to specify it.</p></td> </tr> <tr> <th>tc</th> @@ -431,17 +432,17 @@ <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 used for fitting: 0.9.47.2 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.3 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 13:35:36 2018 -#> Date of summary: Thu Sep 6 13:35:36 2018 +#> Date of fit: Fri Sep 14 06:39:09 2018 +#> Date of summary: Fri Sep 14 06:39:09 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.144 s +#> Fitted with method Port using 64 model solutions performed in 0.157 s #> #> Weighting: none #> @@ -510,7 +511,7 @@ <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 verstrichen -#> 0.919 0.000 0.920 </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 +#> 0.892 0.000 0.892 </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 a9c6bb26..a0eade3b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 33eeefbd..75d22288 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 71437181..6aa67e5b 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 59b67a5d..6c2ba992 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -321,17 +321,17 @@ <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 verstrichen -#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.000 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='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.001 0.000 0.002 </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 verstrichen -#> 0.037 0.000 0.038 </div></pre> +#> 0.035 0.000 0.036 </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 e73b4905..4ba540b2 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 85345135..65de0664 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 2a060628..557da0d7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 07fc4854..765f1628 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -66,7 +66,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 829105bd..0599907d 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -65,7 +65,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 70c4f768..86bb58e5 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 141dd1c9..bc4c644a 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 18f3b78f..b212aa53 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 8bf1d5f6..c8000ae5 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 7b7b0a31..28447e64 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -204,17 +204,17 @@ <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'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.47.2 + <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'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.47.3 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 13:35:46 2018 -#> Date of summary: Thu Sep 6 13:35:46 2018 +#> Date of fit: Fri Sep 14 06:39:24 2018 +#> Date of summary: Fri Sep 14 06:39:24 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.075 s +#> Fitted with method Port using 35 model solutions performed in 0.081 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 9d9404e5..dd44a450 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 5b683283..f9032c84 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 1b94d319..a31b075e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> </span> </div> @@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <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 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 used for fitting: 0.9.47.2 +<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 used for fitting: 0.9.47.3 #> R version used for fitting: 3.5.1 -#> Date of fit: Thu Sep 6 13:35:48 2018 -#> Date of summary: Thu Sep 6 13:35:48 2018 +#> Date of fit: Fri Sep 14 06:39:25 2018 +#> Date of summary: Fri Sep 14 06:39:25 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.619 s +#> Fitted with method Port using 153 model solutions performed in 0.642 s #> #> Weighting: none #> @@ -1,14 +1,21 @@ Loading mkin Loading required package: testthat Testing mkin -Calculation of FOCUS chi2 error levels: .. -Results for FOCUS D established in expertise for UBA (Ranke 2014): ...... -The t-test for significant difference from zero: .. -Iteratively reweighed least squares (IRLS) fitting: .. -Model predictions with mkinpredict: ... -Fitting of parent only models: ..................... -Complex test case from Schaefer et al. (2007) Piacenza paper: .. -Results for synthetic data established in expertise for UBA (Ranke 2014): .... -Calculation of maximum time weighted average concentrations (TWAs): ... +✔ | OK F W S | Context +
⠏ | 0 | Calculation of FOCUS chi2 error levels
⠋ | 1 | Calculation of FOCUS chi2 error levels
⠙ | 2 | Calculation of FOCUS chi2 error levels
✔ | 2 | Calculation of FOCUS chi2 error levels [2.4 s] +
⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.3 s] +
⠏ | 0 | The t-test for significant difference from zero
⠋ | 1 | The t-test for significant difference from zero
⠙ | 2 | The t-test for significant difference from zero
✔ | 2 | The t-test for significant difference from zero [4.2 s] +
⠏ | 0 | Iteratively reweighed least squares (IRLS) fitting
⠋ | 1 | Iteratively reweighed least squares (IRLS) fitting
⠙ | 2 | Iteratively reweighed least squares (IRLS) fitting
⠹ | 3 | Iteratively reweighed least squares (IRLS) fitting
✔ | 3 | Iteratively reweighed least squares (IRLS) fitting [36.3 s] +
⠏ | 0 | Model predictions with mkinpredict
⠋ | 1 | Model predictions with mkinpredict
⠙ | 2 | Model predictions with mkinpredict
⠹ | 3 | Model predictions with mkinpredict
✔ | 3 | Model predictions with mkinpredict [0.3 s] +
⠏ | 0 | Fitting of parent only models
⠋ | 1 | Fitting of parent only models
⠙ | 2 | Fitting of parent only models
⠹ | 3 | Fitting of parent only models
⠸ | 4 | Fitting of parent only models
⠼ | 5 | Fitting of parent only models
⠴ | 6 | Fitting of parent only models
⠦ | 7 | Fitting of parent only models
⠧ | 8 | Fitting of parent only models
⠇ | 9 | Fitting of parent only models
⠏ | 10 | Fitting of parent only models
⠋ | 11 | Fitting of parent only models
⠙ | 12 | Fitting of parent only models
⠹ | 13 | Fitting of parent only models
⠸ | 14 | Fitting of parent only models
⠼ | 15 | Fitting of parent only models
⠴ | 16 | Fitting of parent only models
⠦ | 17 | Fitting of parent only models
⠧ | 18 | Fitting of parent only models
⠇ | 19 | Fitting of parent only models
⠏ | 20 | Fitting of parent only models
⠋ | 21 | Fitting of parent only models
✔ | 21 | Fitting of parent only models [21.6 s] +
⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] +
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.7 s] +
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 3 | Calculation of maximum time weighted average concentrations (TWAs) [4.6 s] -DONE =========================================================================== +══ Results ═════════════════════════════════════════════════════════════════════ +Duration: 83.9 s + +OK: 46 +Failed: 0 +Warnings: 0 +Skipped: 0 |