diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-03 14:33:05 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-03 17:48:31 +0100 |
| commit | f39815aa87272849f8e0c808099c4cee780c2a81 (patch) | |
| tree | d3f59ae226591252e17737e12bae7f90be278b7b /docs/articles | |
| parent | bad0c7caff62aa90225ae8acee43b297bdc28b25 (diff) | |
Static documentation rebuilt by pkgdown::build_site()
Using pkgdown with PR hadley/pkgdown#212
Diffstat (limited to 'docs/articles')
35 files changed, 102 insertions, 82 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index df259e21..726c8378 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -105,16 +108,16 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(fit, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>)</code></pre></div> -<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-5-1.png" width="672"></p> +<p><img src="FOCUS_D_files/figure-html/plot-1.png" width="672"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</code></pre></div> -<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-6-1.png" width="672"></p> +<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="672"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:10 2016 -## Date of summary: Wed Oct 26 23:18:10 2016 +## R version: 3.3.2 +## Date of fit: Wed Nov 2 16:25:22 2016 +## Date of summary: Wed Nov 2 16:25:22 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -122,7 +125,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.628 s +## Fitted with method Port using 153 model solutions performed in 0.665 s ## ## Weighting: none ## @@ -243,7 +246,7 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData Binary files differnew file mode 100644 index 00000000..969644fa --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.rdb b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.rdb index e69de29b..e69de29b 100644 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.rdb +++ b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.rdb diff --git a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.rdx b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.rdx diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData Binary files differnew file mode 100644 index 00000000..17db087e --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb Binary files differnew file mode 100644 index 00000000..42cdbaff --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx Binary files differnew file mode 100644 index 00000000..5cced058 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData Binary files differnew file mode 100644 index 00000000..b170a652 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb Binary files differnew file mode 100644 index 00000000..5aae8d68 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx Binary files differnew file mode 100644 index 00000000..9ecc2d70 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData Binary files differnew file mode 100644 index 00000000..95ceef43 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.rdb b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.rdb diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.rdx b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.rdx diff --git a/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData Binary files differnew file mode 100644 index 00000000..f04428b9 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.rdb b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.rdb diff --git a/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.rdx b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.rdx diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.RData Binary files differdeleted file mode 100644 index ab5bdfb2..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.RData +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData Binary files differnew file mode 100644 index 00000000..30ad4f31 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.rdb b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.rdb diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.rdx diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differnew file mode 100644 index 00000000..c0b0c2db --- /dev/null +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differnew file mode 100644 index 00000000..6700e527 --- /dev/null +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index cb3096e0..55caa22e 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -59,16 +62,16 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:11 2016 -## Date of summary: Wed Oct 26 23:18:11 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:48 2016 +## Date of summary: Thu Nov 3 17:47:48 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.089 s +## Fitted with method Port using 37 model solutions performed in 0.093 s ## ## Weighting: none ## @@ -152,9 +155,9 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:12 2016 -## Date of summary: Wed Oct 26 23:18:12 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:49 2016 +## Date of summary: Thu Nov 3 17:47:49 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -166,7 +169,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.434 s +## Fitted with method Port using 188 model solutions performed in 0.447 s ## ## Weighting: none ## @@ -249,16 +252,16 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:12 2016 -## Date of summary: Wed Oct 26 23:18:12 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:49 2016 +## Date of summary: Thu Nov 3 17:47:49 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.191 s +## Fitted with method Port using 81 model solutions performed in 0.189 s ## ## Weighting: none ## @@ -319,9 +322,9 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:13 2016 -## Date of summary: Wed Oct 26 23:18:14 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:50 2016 +## Date of summary: Thu Nov 3 17:47:50 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -330,7 +333,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.803 s +## Fitted with method Port using 336 model solutions performed in 0.836 s ## ## Weighting: none ## @@ -392,8 +395,8 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>), <span class="dt">parent =</span> <span class="kw">c</span>(<span class="fl">97.8</span>, <span class="dv">60</span>, <span class="dv">51</span>, <span class="dv">43</span>, <span class="dv">35</span>, <span class="dv">22</span>, <span class="dv">15</span>, <span class="dv">12</span>)) FOCUS_2006_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_2006_L3)</code></pre></div> -<div id="use-mmkin-to-fit-multiple-models" class="section level2"> -<h2 class="hasAnchor"><html><body><a href="#use-mmkin-to-fit-multiple-models" class="anchor"> </a></body></html>Use mmkin to fit multiple models</h2> +<div id="fit-multiple-models" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#fit-multiple-models" class="anchor"> </a></body></html>Fit multiple models</h2> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Only use one core here, not to offend the CRAN checks</span> mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw">c</span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="dt">cores =</span> <span class="dv">1</span>, @@ -402,15 +405,15 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> -<div id="accessing-elements-of-mmkin-objects" class="section level2"> -<h2 class="hasAnchor"><html><body><a href="#accessing-elements-of-mmkin-objects" class="anchor"> </a></body></html>Accessing elements of mmkin objects</h2> +<div id="accessing-mmkin-objects" class="section level2"> +<h2 class="hasAnchor"><html><body><a href="#accessing-mmkin-objects" class="anchor"> </a></body></html>Accessing mmkin objects</h2> <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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:15 2016 -## Date of summary: Wed Oct 26 23:18:15 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:51 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -419,7 +422,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.323 s +## Fitted with method Port using 137 model solutions performed in 0.328 s ## ## Weighting: none ## @@ -508,16 +511,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:15 2016 -## Date of summary: Wed Oct 26 23:18:16 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:52 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.108 s +## Fitted with method Port using 46 model solutions performed in 0.107 s ## ## Weighting: none ## @@ -568,16 +571,16 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## parent 106 352</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 -## R version: 3.3.1 -## Date of fit: Wed Oct 26 23:18:16 2016 -## Date of summary: Wed Oct 26 23:18:16 2016 +## R version: 3.3.2 +## Date of fit: Thu Nov 3 17:47:52 2016 +## Date of summary: Thu Nov 3 17:47:52 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.151 s +## Fitted with method Port using 66 model solutions performed in 0.148 s ## ## Weighting: none ## @@ -647,8 +650,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <li><a href="#fomc-fit-for-l2">FOMC fit for L2</a></li> <li><a href="#dfop-fit-for-l2">DFOP fit for L2</a></li> </ul></li> - <li><a href="#laboratory-data-l3">Laboratory Data L3</a><ul class="nav nav-pills nav-stacked"><li><a href="#use-mmkin-to-fit-multiple-models">Use mmkin to fit multiple models</a></li> - <li><a href="#accessing-elements-of-mmkin-objects">Accessing elements of mmkin objects</a></li> + <li><a href="#laboratory-data-l3">Laboratory Data L3</a><ul class="nav nav-pills nav-stacked"><li><a href="#fit-multiple-models">Fit multiple models</a></li> + <li><a href="#accessing-mmkin-objects">Accessing mmkin objects</a></li> </ul></li> <li><a href="#laboratory-data-l4">Laboratory Data L4</a></li> <li><a href="#references">References</a></li> @@ -659,7 +662,7 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf Binary files differindex bc37c873..6f71d018 100644 --- a/docs/articles/FOCUS_Z.pdf +++ b/docs/articles/FOCUS_Z.pdf diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index e02b9cf3..5a04168e 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -75,21 +78,21 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6298.7342 6308.6792 6343.9668 6318.6243 6366.5831 -## Eigenvalue based 871.7379 880.7757 903.5267 889.8135 919.4211 -## deSolve, compiled 724.9025 730.6729 732.9837 736.4432 737.0243 +## deSolve, not compiled 6306.4527 6340.7895 6403.5937 6375.1264 6452.1643 +## Eigenvalue based 918.0808 929.7217 948.9742 941.3626 964.4210 +## deSolve, compiled 736.1337 753.6016 773.5605 771.0696 792.2739 ## max neval cld -## 6414.5420 3 c -## 949.0287 3 b -## 737.6054 3 a</code></pre> +## 6529.2022 3 b +## 987.4793 3 a +## 813.4783 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> -<p>We see that using the compiled model is by a factor of 8.6 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> +<p>We see that using the compiled model is by a factor of 8.3 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 8.579920 -## Eigenvalue based 1.208258 +## deSolve, not compiled 8.267900 +## Eigenvalue based 1.220853 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -111,20 +114,20 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds ## expr min lq mean median uq -## deSolve, not compiled 13.265212 13.330161 13.412053 13.395109 13.485473 -## deSolve, compiled 1.322466 1.326851 1.364827 1.331236 1.386007 +## deSolve, not compiled 13.604720 13.667244 13.689764 13.729768 13.732286 +## deSolve, compiled 1.305077 1.311124 1.328943 1.317172 1.340876 ## max neval cld -## 13.575837 3 b -## 1.440779 3 a</code></pre> +## 13.734804 3 b +## 1.364579 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<p>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.44.9000 on</p> -<pre><code>## R version 3.3.1 (2016-06-21) +<pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> <pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> @@ -144,7 +147,7 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png Binary files differindex bba259d6..eec55773 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png Binary files differindex 6b732075..b043c13b 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index 9994716d..cd6a7bea 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -49,16 +49,19 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -93,7 +96,7 @@ <footer> <div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 74d8ccca..dafaa0e4 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>mkin - Kinetic evaluation of chemical degradation data</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -67,7 +70,7 @@ d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../ref f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>) -<span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> +<span class="kw">plot_sep</span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> @@ -169,7 +172,7 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index c8b1e877..03ece635 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,8 +1,13 @@ base +datasets +utils +grDevices +graphics +stats knitr minpack.lm rootSolve +methods inline +parallel mkin -microbenchmark -ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData Binary files differnew file mode 100644 index 00000000..d11ccf31 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb Binary files differnew file mode 100644 index 00000000..5ac4f484 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx Binary files differnew file mode 100644 index 00000000..8983f69e --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex d34e3805..2e7e2244 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png |
