diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-11-01 12:19:03 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-11-01 12:19:03 +0100 |
| commit | bbb74d4f60033899cd5cdd36aa70f157bc52209e (patch) | |
| tree | ca0f620ba0ffd59ff242071260d2346e4ca254ff /docs/articles/web_only | |
| parent | 70e48e8360875f22970174d409c46cb3f076fa99 (diff) | |
Fix bug in yesterdays release, add methods for BIC
Diffstat (limited to 'docs/articles/web_only')
14 files changed, 37 insertions, 62 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 5ea0b256..14234785 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -90,7 +90,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -244,36 +244,7 @@ <div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> <div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> -<pre><code>## Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink -## Z0_0 3.8375e+00 5.4918e-03 3.0584e-02 1.2969e-01 -## log_k_Z0_Z1 5.4918e-03 2.7613e-03 -1.8820e-04 2.6634e-04 -## log_k_Z1_Z2 3.0584e-02 -1.8820e-04 3.3807e-03 3.2177e-03 -## log_k_Z2_sink 1.2969e-01 2.6634e-04 3.2177e-03 3.4256e-02 -## log_k_Z2_Z3_free -2.4223e-02 -2.6169e-04 -1.1845e-03 -8.1134e-03 -## log_k_Z3_free_sink -6.5467e-02 -4.0815e-04 -3.2978e-03 -3.6010e-02 -## log_k_Z3_free_bound -6.0659e-02 -4.4768e-04 -3.0588e-03 -3.9074e-02 -## log_k_Z3_bound_free 5.2844e-01 4.5458e-03 7.9800e-03 4.6274e-02 -## sigma 2.0366e-10 -3.4658e-10 8.9910e-11 -2.5946e-10 -## log_k_Z2_Z3_free log_k_Z3_free_sink -## Z0_0 -2.4223e-02 -6.5467e-02 -## log_k_Z0_Z1 -2.6169e-04 -4.0815e-04 -## log_k_Z1_Z2 -1.1845e-03 -3.2978e-03 -## log_k_Z2_sink -8.1134e-03 -3.6010e-02 -## log_k_Z2_Z3_free 1.5500e-02 2.1583e-02 -## log_k_Z3_free_sink 2.1583e-02 7.5705e-02 -## log_k_Z3_free_bound 2.5836e-02 1.1964e-01 -## log_k_Z3_bound_free 5.2534e-02 2.9441e-01 -## sigma 1.3063e-10 3.4170e-10 -## log_k_Z3_free_bound log_k_Z3_bound_free sigma -## Z0_0 -6.0659e-02 5.2844e-01 2.0366e-10 -## log_k_Z0_Z1 -4.4768e-04 4.5458e-03 -3.4658e-10 -## log_k_Z1_Z2 -3.0588e-03 7.9800e-03 8.9910e-11 -## log_k_Z2_sink -3.9074e-02 4.6274e-02 -2.5946e-10 -## log_k_Z2_Z3_free 2.5836e-02 5.2534e-02 1.3063e-10 -## log_k_Z3_free_sink 1.1964e-01 2.9441e-01 3.4170e-10 -## log_k_Z3_free_bound 6.5902e-01 5.4737e+00 -6.7704e-10 -## log_k_Z3_bound_free 5.4737e+00 2.8722e+08 7.2421e-02 -## sigma -6.7704e-10 7.2421e-02 1.4170e-01</code></pre> +<pre><code>## NULL</code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> <div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> <a class="sourceLine" id="cb44-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> @@ -358,6 +329,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex 471db177..76826836 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differindex 3c983f21..25249a9a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex 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a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png Binary files differindex 0d3b4d1a..891d95e1 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 898e6190..ea4f89e6 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 0476acf8..fecbe3b1 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -90,7 +90,7 @@ <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -414,8 +414,8 @@ <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p9b)</a></code></pre></div> @@ -628,8 +628,8 @@ <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p12b)</a></code></pre></div> @@ -680,8 +680,8 @@ <div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p13)</a></code></pre></div> @@ -733,8 +733,8 @@ <div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p14)</a></code></pre></div> @@ -787,8 +787,8 @@ <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15a)</a></code></pre></div> @@ -835,8 +835,8 @@ <div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15b)</a></code></pre></div> @@ -951,6 +951,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index c0682cb0..4fb76fa2 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -90,7 +90,7 @@ <h1>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>benchmarks.Rmd</code></div> @@ -204,82 +204,83 @@ ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.005 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.901 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.266 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.164 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.559 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.510 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.574 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 30.849 ## t5 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.659 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.545 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.634 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.563 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.324 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.252 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.233 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.865 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.376 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.195 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.058 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.729 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 11.133</code></pre> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.787</code></pre> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/save.html">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 6df504ed..363f0c38 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -90,7 +90,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -165,9 +165,9 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.171 1.000 3.170 0 -## 1 deSolve, not compiled 3 29.012 9.149 28.996 0 -## 2 Eigenvalue based 3 4.473 1.411 4.470 0 +## 3 deSolve, compiled 3 3.143 1.000 3.142 0 +## 1 deSolve, not compiled 3 29.169 9.281 29.154 0 +## 2 Eigenvalue based 3 4.358 1.387 4.356 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -216,8 +216,8 @@ ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.913 1.000 4.909 0 -## 1 deSolve, not compiled 3 53.418 10.873 53.393 0 +## 2 deSolve, compiled 3 4.840 1.000 4.837 0 +## 1 deSolve, not compiled 3 54.338 11.227 54.309 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> @@ -231,6 +231,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> |
