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Diffstat (limited to 'docs/articles')
| -rw-r--r-- | docs/articles/FOCUS_D.html | 12 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 60 | ||||
| -rw-r--r-- | docs/articles/FOCUS_Z.html | 4 | ||||
| -rw-r--r-- | docs/articles/compiled_models.html | 18 | ||||
| -rw-r--r-- | docs/articles/index.html | 2 | ||||
| -rw-r--r-- | docs/articles/mkin.html | 4 | ||||
| -rw-r--r-- | docs/articles/twa.html | 4 |
7 files changed, 52 insertions, 52 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 8a1f51d1..630b1d02 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</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">2018-06-06</h4> + <h4 class="date">2018-07-18</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -161,9 +161,9 @@ <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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:49 2018 -## Date of summary: Wed Jun 6 01:21:50 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 14:52:30 2018 +## Date of summary: Wed Jul 18 14:52:31 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -171,7 +171,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.633 s +## Fitted with method Port using 153 model solutions performed in 0.604 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index fcd0719d..72c293b9 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</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">2018-06-06</h4> + <h4 class="date">2018-07-18</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -109,16 +109,16 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <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_<span class="dv">2006</span>_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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:52 2018 -## Date of summary: Wed Jun 6 01:21:52 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:17 2018 +## Date of summary: Wed Jul 18 15:16:17 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 0.094 s +## Fitted with method Port using 37 model solutions performed in 0.081 s ## ## Weighting: none ## @@ -200,16 +200,16 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:53 2018 -## Date of summary: Wed Jun 6 01:21:53 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:19 2018 +## Date of summary: Wed Jul 18 15:16:19 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 1.369 s +## Fitted with method Port using 611 model solutions performed in 1.304 s ## ## Weighting: none ## @@ -295,16 +295,16 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:54 2018 -## Date of summary: Wed Jun 6 01:21:54 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:19 2018 +## Date of summary: Wed Jul 18 15:16:19 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 0.173 s +## Fitted with method Port using 81 model solutions performed in 0.175 s ## ## Weighting: none ## @@ -366,9 +366,9 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:55 2018 -## Date of summary: Wed Jun 6 01:21:55 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:20 2018 +## Date of summary: Wed Jul 18 15:16:20 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.76 s +## Fitted with method Port using 336 model solutions performed in 0.721 s ## ## Weighting: none ## @@ -458,9 +458,9 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:56 2018 -## Date of summary: Wed Jun 6 01:21:56 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:21 2018 +## Date of summary: Wed Jul 18 15:16:21 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -469,7 +469,7 @@ 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 0.33 s +## Fitted with method Port using 137 model solutions performed in 0.294 s ## ## Weighting: none ## @@ -559,16 +559,16 @@ 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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:56 2018 -## Date of summary: Wed Jun 6 01:21:57 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:22 2018 +## Date of summary: Wed Jul 18 15:16:22 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 0.099 s +## Fitted with method Port using 46 model solutions performed in 0.092 s ## ## Weighting: none ## @@ -619,16 +619,16 @@ 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 used for fitting: 0.9.47.1 -## R version used for fitting: 3.5.0 -## Date of fit: Wed Jun 6 01:21:57 2018 -## Date of summary: Wed Jun 6 01:21:57 2018 +## R version used for fitting: 3.5.1 +## Date of fit: Wed Jul 18 15:16:22 2018 +## Date of summary: Wed Jul 18 15:16:22 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 0.146 s +## Fitted with method Port using 66 model solutions performed in 0.137 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index 61425745..d8b9c961 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-06-06</h4> + <h4 class="date">2018-07-18</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 379176bf..183c9658 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</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">2018-06-06</h4> + <h4 class="date">2018-07-18</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -125,14 +125,14 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</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 2.335 1.000 2.333 0 -## 1 deSolve, not compiled 3 16.810 7.199 16.801 0 -## 2 Eigenvalue based 3 2.882 1.234 2.879 0 +## 3 deSolve, compiled 3 2.044 1.000 2.043 0 +## 1 deSolve, not compiled 3 16.571 8.107 16.565 0 +## 2 Eigenvalue based 3 2.499 1.223 2.496 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 ## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 7 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 around 8 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> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> @@ -156,14 +156,14 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</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 3.766 1.000 3.764 0 -## 1 deSolve, not compiled 3 37.119 9.856 37.097 0 +## 2 deSolve, compiled 3 3.592 1.000 3.589 0 +## 1 deSolve, not compiled 3 35.340 9.839 35.324 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> <p>Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.47.1 on</p> -<pre><code>## R version 3.5.0 (2018-04-23) +<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> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> diff --git a/docs/articles/index.html b/docs/articles/index.html index 59bd221d..7902c611 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 28186062..14a2f9b9 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span> </span> </div> @@ -84,7 +84,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-06-06</h4> + <h4 class="date">2018-07-18</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 53afcca3..0c5fe558 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">0.9.47.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</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">2018-06-06</h4> + <h4 class="date">2018-07-18</h4> <div class="hidden name"><code>twa.Rmd</code></div> |