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Diffstat (limited to 'docs/articles')
18 files changed, 26 insertions, 26 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index bbfc36b6..02c3aa69 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -103,10 +103,10 @@ <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="/home/jranke/git/mkin/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.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="/home/jranke/git/mkin/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.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 diff --git a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png Binary files differdeleted file mode 100644 index c0b0c2db..00000000 --- a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png Binary files differdeleted file mode 100644 index 6700e527..00000000 --- a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 353f1484..5d586799 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -138,16 +138,16 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## 30 parent 4.0 5.251 -1.2513</code></pre> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(m.L1.SFO, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - SFO"</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinresplot.html">mkinresplot</a></span>(m.L1.SFO, <span class="dt">ylab =</span> <span class="st">"Observed"</span>, <span class="dt">xlab =</span> <span class="st">"Time"</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</code></pre></div> <pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge. ## Convergence code is 1</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/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 @@ -233,7 +233,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.SFO, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.</p> <p>In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.</p> <p>We may add that it is difficult to judge the random nature of the residuals just from the three samplings at days 0, 1 and 3. Also, it is not clear <em>a priori</em> why a consistent underestimation after the approximate DT90 should be irrelevant. However, this can be rationalised by the fact that the FOCUS fate models generally only implement SFO kinetics.</p> @@ -244,7 +244,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/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 @@ -314,7 +314,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.DFOP, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/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 @@ -397,7 +397,7 @@ FOCUS_2006_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../re 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>, <span class="kw">list</span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_2006_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(mm.L3)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="672"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/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"> @@ -484,7 +484,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="672"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="672"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> <p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter <code>g</code> is quite narrow.</p> </div> @@ -502,7 +502,7 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <span class="kw">list</span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_2006_L4_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(mm.L4)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></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"><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 diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png Binary files differdeleted file mode 100644 index bb174c01..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png Binary files differdeleted file mode 100644 index cab1f123..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png Binary files differdeleted file mode 100644 index 4ef79892..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png Binary files differdeleted file mode 100644 index b8eef14c..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png Binary files differdeleted file mode 100644 index 860ec47b..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png Binary files differdeleted file mode 100644 index 5131f700..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differdeleted file mode 100644 index 2908e5ea..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png Binary files differdeleted file mode 100644 index b4bcc8fc..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png Binary files differdeleted file mode 100644 index 21a8c2e3..00000000 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png +++ /dev/null diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 1eeb78c6..d2e1d87d 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -73,21 +73,21 @@ 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 6407.0333 6420.1971 6434.6510 6433.3609 6448.4598 -## Eigenvalue based 887.4338 891.8401 906.9270 896.2463 916.6735 -## deSolve, compiled 720.2433 727.8793 733.2019 735.5152 739.6812 +## deSolve, not compiled 6365.2773 6407.1609 6467.4083 6449.0446 6518.4738 +## Eigenvalue based 872.0339 912.6754 926.7178 953.3169 954.0597 +## deSolve, compiled 730.1252 740.7149 751.8881 751.3045 762.7695 ## max neval cld -## 6463.5587 3 c -## 937.1007 3 b -## 743.8472 3 a</code></pre> +## 6587.9031 3 b +## 954.8026 3 a +## 774.2345 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 8.7 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 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> <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 8.746741 -## Eigenvalue based 1.218529 +## deSolve, not compiled 8.583796 +## Eigenvalue based 1.268882 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -108,12 +108,12 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>) <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 13.501761 13.52142 13.697021 13.541086 13.794651 -## deSolve, compiled 1.359921 1.35996 1.366796 1.359999 1.370233 +## expr min lq mean median uq +## deSolve, not compiled 13.464194 13.498471 13.52712 13.532748 13.558577 +## deSolve, compiled 1.328628 1.342168 1.35224 1.355707 1.364046 ## max neval cld -## 14.048217 3 b -## 1.380468 3 a</code></pre> +## 13.584407 3 b +## 1.372385 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 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 e64a4b92..54420d5b 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 e19fbe7f..af90245e 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/mkin.html b/docs/articles/mkin.html index 44c9e9c5..c1b38794 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -66,7 +66,7 @@ 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> -<p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> +<p><img src="/home/jranke/git/mkin/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> <h1>Background</h1> 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 differdeleted file mode 100644 index d34e3805..00000000 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ /dev/null |
