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Diffstat (limited to 'docs/articles')
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diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 376acee2..e63feb07 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -156,18 +156,20 @@ ## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with +## value of zero were removed from the data</code></pre> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></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" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:39 2019 -## Date of summary: Mon Mar 4 14:06:39 2019 +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:31 2019 +## Date of summary: Wed Apr 10 10:11:31 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -175,16 +177,18 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.693 s +## Fitted with method using 396 model solutions performed in 1.048 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 100.7500 state -## k_parent_sink 0.1000 deparm -## k_parent_m1 0.1001 deparm -## k_m1_sink 0.1002 deparm +## value type +## parent_0 100.750000 state +## k_parent_sink 0.100000 deparm +## k_parent_m1 0.100100 deparm +## k_m1_sink 0.100200 deparm +## sigma 3.125504 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -192,6 +196,7 @@ ## log_k_parent_sink -2.302585 -Inf Inf ## log_k_parent_m1 -2.301586 -Inf Inf ## log_k_m1_sink -2.300587 -Inf Inf +## sigma 3.125504 0 Inf ## ## Fixed parameter values: ## value type @@ -199,29 +204,36 @@ ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## parent_0 99.600 1.61400 96.330 102.900 -## log_k_parent_sink -3.038 0.07826 -3.197 -2.879 -## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 -## log_k_m1_sink -5.248 0.13610 -5.523 -4.972 +## parent_0 99.600 1.57000 96.400 102.800 +## log_k_parent_sink -3.038 0.07626 -3.193 -2.883 +## log_k_parent_m1 -2.980 0.04033 -3.062 -2.898 +## log_k_m1_sink -5.248 0.13320 -5.518 -4.977 +## sigma 3.126 0.35850 2.396 3.855 ## ## Parameter correlation: -## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -## parent_0 1.00000 0.6075 -0.06625 -0.1701 -## log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 -## log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 -## log_k_m1_sink -0.17006 -0.6253 0.47164 1.0000 -## -## Residual standard error: 3.211 on 36 degrees of freedom +## parent_0 log_k_parent_sink log_k_parent_m1 +## parent_0 1.000e+00 6.067e-01 -6.372e-02 +## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 +## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 +## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 +## sigma -3.368e-07 3.365e-08 8.420e-07 +## log_k_m1_sink sigma +## parent_0 -1.688e-01 -3.368e-07 +## log_k_parent_sink -6.252e-01 3.365e-08 +## log_k_parent_m1 4.731e-01 8.420e-07 +## log_k_m1_sink 1.000e+00 1.958e-08 +## sigma 1.958e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper -## parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 -## k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02 -## k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02 -## k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 +## k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02 +## k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02 +## k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03 +## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -246,10 +258,10 @@ ## 0 parent 102.04 99.59848 2.442e+00 ## 1 parent 93.50 90.23787 3.262e+00 ## 1 parent 92.50 90.23787 2.262e+00 -## 3 parent 63.23 74.07320 -1.084e+01 -## 3 parent 68.99 74.07320 -5.083e+00 -## 7 parent 52.32 49.91207 2.408e+00 -## 7 parent 55.13 49.91207 5.218e+00 +## 3 parent 63.23 74.07319 -1.084e+01 +## 3 parent 68.99 74.07319 -5.083e+00 +## 7 parent 52.32 49.91206 2.408e+00 +## 7 parent 55.13 49.91206 5.218e+00 ## 14 parent 27.27 25.01257 2.257e+00 ## 14 parent 26.64 25.01257 1.627e+00 ## 21 parent 11.50 12.53462 -1.035e+00 @@ -259,23 +271,21 @@ ## 50 parent 0.69 0.71624 -2.624e-02 ## 50 parent 0.63 0.71624 -8.624e-02 ## 75 parent 0.05 0.06074 -1.074e-02 -## 75 parent 0.06 0.06074 -7.382e-04 -## 0 m1 0.00 0.00000 0.000e+00 -## 0 m1 0.00 0.00000 0.000e+00 +## 75 parent 0.06 0.06074 -7.381e-04 ## 1 m1 4.84 4.80296 3.704e-02 ## 1 m1 5.64 4.80296 8.370e-01 ## 3 m1 12.91 13.02400 -1.140e-01 ## 3 m1 12.96 13.02400 -6.400e-02 ## 7 m1 22.97 25.04476 -2.075e+00 ## 7 m1 24.47 25.04476 -5.748e-01 -## 14 m1 41.69 36.69002 5.000e+00 -## 14 m1 33.21 36.69002 -3.480e+00 +## 14 m1 41.69 36.69003 5.000e+00 +## 14 m1 33.21 36.69003 -3.480e+00 ## 21 m1 44.37 41.65310 2.717e+00 ## 21 m1 46.44 41.65310 4.787e+00 ## 35 m1 41.22 43.31312 -2.093e+00 ## 35 m1 37.95 43.31312 -5.363e+00 -## 50 m1 41.19 41.21831 -2.831e-02 -## 50 m1 40.01 41.21831 -1.208e+00 +## 50 m1 41.19 41.21832 -2.832e-02 +## 50 m1 40.01 41.21832 -1.208e+00 ## 75 m1 40.09 36.44704 3.643e+00 ## 75 m1 33.85 36.44704 -2.597e+00 ## 100 m1 31.04 31.98163 -9.416e-01 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 differindex c0fab72d..b8f2fe94 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ 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 differindex 47916477..79ec3aaf 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ 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 5dac9999..8af99f6c 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -112,52 +112,56 @@ <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:41 2019 -## Date of summary: Mon Mar 4 14:06:41 2019 +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:33 2019 +## Date of summary: Wed Apr 10 10:11:33 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.095 s +## Fitted with method using 133 model solutions performed in 0.344 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.85 state -## k_parent_sink 0.10 deparm +## value type +## parent_0 89.850000 state +## k_parent_sink 0.100000 deparm +## sigma 2.779827 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_k_parent_sink -2.302585 -Inf Inf +## sigma 2.779827 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## parent_0 92.470 1.36800 89.570 95.370 -## log_k_parent_sink -2.347 0.04057 -2.433 -2.261 +## parent_0 92.470 1.28200 89.740 95.200 +## log_k_parent_sink -2.347 0.03763 -2.428 -2.267 +## sigma 2.780 0.46330 1.792 3.767 ## ## Parameter correlation: -## parent_0 log_k_parent_sink -## parent_0 1.0000 0.6248 -## log_k_parent_sink 0.6248 1.0000 -## -## Residual standard error: 2.948 on 16 degrees of freedom +## parent_0 log_k_parent_sink sigma +## parent_0 1.000e+00 6.186e-01 -1.712e-09 +## log_k_parent_sink 6.186e-01 1.000e+00 -3.237e-09 +## sigma -1.712e-09 -3.237e-09 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper -## parent_0 92.47000 67.58 2.170e-21 89.57000 95.3700 -## k_parent_sink 0.09561 24.65 1.867e-14 0.08773 0.1042 +## parent_0 92.47000 72.13 8.824e-21 89.74000 95.2000 +## k_parent_sink 0.09561 26.57 2.487e-14 0.08824 0.1036 +## sigma 2.78000 6.00 1.216e-05 1.79200 3.7670 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -199,61 +203,76 @@ <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><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>)</a></code></pre></div> <p><img src="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" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb6-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge: +## false convergence (8)</code></pre> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:43 2019 -## Date of summary: Mon Mar 4 14:06:43 2019 +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</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>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:34 2019 +## Date of summary: Wed Apr 10 10:11:34 2019 +## +## +## Warning: Optimisation did not converge: +## false convergence (8) +## ## ## 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 1.502 s +## Fitted with method using 344 model solutions performed in 0.778 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.85 state -## alpha 1.00 deparm -## beta 10.00 deparm +## value type +## parent_0 89.85000 state +## alpha 1.00000 deparm +## beta 10.00000 deparm +## sigma 2.77987 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf +## sigma 2.779870 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 92.47 1.482 89.31 95.63 -## log_alpha 11.25 598.200 -1264.00 1286.00 -## log_beta 13.60 598.200 -1261.00 1289.00 +## Estimate Std. Error Lower Upper +## parent_0 92.47 1.2810 89.720 95.220 +## log_alpha 10.60 NaN NaN NaN +## log_beta 12.95 NaN NaN NaN +## sigma 2.78 0.4554 1.803 3.757 ## ## Parameter correlation: -## parent_0 log_alpha log_beta -## parent_0 1.0000 -0.3016 -0.3016 -## log_alpha -0.3016 1.0000 1.0000 -## log_beta -0.3016 1.0000 1.0000 -## -## Residual standard error: 3.045 on 15 degrees of freedom +## parent_0 log_alpha log_beta sigma +## parent_0 1.000000 NaN NaN 0.008714 +## log_alpha NaN 1 NaN NaN +## log_beta NaN NaN 1 NaN +## sigma 0.008714 NaN NaN 1.000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. -## Estimate t value Pr(>t) Lower Upper -## parent_0 92.47 64.45000 4.757e-20 89.31 95.63 -## alpha 76830.00 0.02852 4.888e-01 0.00 Inf -## beta 803500.00 0.02852 4.888e-01 0.00 Inf +## Estimate t value Pr(>t) Lower Upper +## parent_0 92.47 72.13000 1.052e-19 89.720 95.220 +## alpha 40090.00 0.02388 4.906e-01 NA NA +## beta 419300.00 0.02388 4.906e-01 NA NA +## sigma 2.78 6.00000 1.628e-05 1.803 3.757 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -262,7 +281,7 @@ ## ## Estimated disappearance times: ## DT50 DT90 DT50back -## parent 7.249 24.08 7.249</code></pre> +## parent 7.249 24.08 7.25</code></pre> <p>We get a warning that the default optimisation algorithm <code>Port</code> did not converge, which is an indication that the model is overparameterised, <em>i.e.</em> contains too many parameters that are ill-defined as a consequence.</p> <p>And in fact, due to the higher number of parameters, and the lower number of degrees of freedom of the fit, the <span class="math inline">\(\chi^2\)</span> error level is actually higher for the FOMC model (3.6%) than for the SFO model (3.4%). Additionally, the parameters <code>log_alpha</code> and <code>log_beta</code> internally fitted in the model have excessive confidence intervals, that span more than 25 orders of magnitude (!) when backtransformed to the scale of <code>alpha</code> and <code>beta</code>. Also, the t-test for significant difference from zero does not indicate such a significant difference, with p-values greater than 0.1, and finally, the parameter correlation of <code>log_alpha</code> and <code>log_beta</code> is 1.000, clearly indicating that the model is overparameterised.</p> <p>The <span class="math inline">\(\chi^2\)</span> error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same <span class="math inline">\(\chi^2\)</span> error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of <span class="math inline">\(\chi^2\)</span> error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt <span class="citation">(Ranke 2014)</span>.</p> @@ -271,19 +290,19 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l2" class="anchor"></a>Laboratory Data L2</h1> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">FOCUS_<span class="dv">2006</span>_L2 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb9-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>), <span class="dt">each =</span> <span class="dv">2</span>),</a> -<a class="sourceLine" id="cb9-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>,</a> -<a class="sourceLine" id="cb9-4" title="4"> <span class="fl">19.3</span>, <span class="fl">22.3</span>, <span class="fl">4.6</span>, <span class="fl">4.6</span>,</a> -<a class="sourceLine" id="cb9-5" title="5"> <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>))</a> -<a class="sourceLine" id="cb9-6" title="6">FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L2)</a></code></pre></div> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">FOCUS_<span class="dv">2006</span>_L2 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb14-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>), <span class="dt">each =</span> <span class="dv">2</span>),</a> +<a class="sourceLine" id="cb14-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>,</a> +<a class="sourceLine" id="cb14-4" title="4"> <span class="fl">19.3</span>, <span class="fl">22.3</span>, <span class="fl">4.6</span>, <span class="fl">4.6</span>,</a> +<a class="sourceLine" id="cb14-5" title="5"> <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>))</a> +<a class="sourceLine" id="cb14-6" title="6">FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L2)</a></code></pre></div> <div id="sfo-fit-for-l2" class="section level2"> <h2 class="hasAnchor"> <a href="#sfo-fit-for-l2" class="anchor"></a>SFO fit for L2</h2> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">m.L2.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>_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb10-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></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>,</a> -<a class="sourceLine" id="cb10-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">m.L2.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>_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></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>,</a> +<a class="sourceLine" id="cb15-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</a></code></pre></div> <p><img src="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> @@ -293,62 +312,66 @@ <h2 class="hasAnchor"> <a href="#fomc-fit-for-l2" class="anchor"></a>FOMC fit for L2</h2> <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" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb11-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>,</a> -<a class="sourceLine" id="cb11-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb16-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>,</a> +<a class="sourceLine" id="cb16-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:43 2019 -## Date of summary: Mon Mar 4 14:06:43 2019 +<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://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:35 2019 +## Date of summary: Wed Apr 10 10:11:35 2019 ## ## 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 0.196 s +## Fitted with method using 240 model solutions performed in 0.564 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 93.95 state -## alpha 1.00 deparm -## beta 10.00 deparm +## value type +## parent_0 93.950000 state +## alpha 1.000000 deparm +## beta 10.000000 deparm +## sigma 2.275722 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 93.950000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf +## sigma 2.275722 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 93.7700 1.8560 89.5700 97.9700 -## log_alpha 0.3180 0.1867 -0.1044 0.7405 -## log_beta 0.2102 0.2943 -0.4555 0.8759 +## Estimate Std. Error Lower Upper +## parent_0 93.7700 1.6130 90.05000 97.4900 +## log_alpha 0.3180 0.1559 -0.04149 0.6776 +## log_beta 0.2102 0.2493 -0.36460 0.7850 +## sigma 2.2760 0.4645 1.20500 3.3470 ## ## Parameter correlation: -## parent_0 log_alpha log_beta -## parent_0 1.00000 -0.09553 -0.1863 -## log_alpha -0.09553 1.00000 0.9757 -## log_beta -0.18628 0.97567 1.0000 -## -## Residual standard error: 2.628 on 9 degrees of freedom +## parent_0 log_alpha log_beta sigma +## parent_0 1.000e+00 -1.151e-01 -2.085e-01 1.606e-08 +## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.168e-07 +## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.029e-07 +## sigma 1.606e-08 -1.168e-07 -1.029e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper -## parent_0 93.770 50.510 1.173e-12 89.5700 97.970 -## alpha 1.374 5.355 2.296e-04 0.9009 2.097 -## beta 1.234 3.398 3.949e-03 0.6341 2.401 +## parent_0 93.770 58.120 4.267e-12 90.0500 97.490 +## alpha 1.374 6.414 1.030e-04 0.9594 1.969 +## beta 1.234 4.012 1.942e-03 0.6945 2.192 +## sigma 2.276 4.899 5.977e-04 1.2050 3.347 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -364,17 +387,15 @@ <h2 class="hasAnchor"> <a href="#dfop-fit-for-l2" class="anchor"></a>DFOP fit for L2</h2> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb14-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></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>,</a> -<a class="sourceLine" id="cb14-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb19-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></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>,</a> +<a class="sourceLine" id="cb19-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.L2.DFOP, data = FALSE): Could not estimate -## covariance matrix; singular system.</code></pre> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:44 2019 -## Date of summary: Mon Mar 4 14:06:44 2019 +<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:37 2019 +## Date of summary: Wed Apr 10 10:11:37 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -383,16 +404,18 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.84 s +## Fitted with method using 585 model solutions performed in 1.296 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 93.95 state -## k1 0.10 deparm -## k2 0.01 deparm -## g 0.50 deparm +## value type +## parent_0 93.950000 state +## k1 0.100000 deparm +## k2 0.010000 deparm +## g 0.500000 deparm +## sigma 1.413899 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -400,30 +423,37 @@ ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf ## g_ilr 0.000000 -Inf Inf +## sigma 1.413899 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 93.9500 NA NA NA -## log_k1 3.1370 NA NA NA -## log_k2 -1.0880 NA NA NA -## g_ilr -0.2821 NA NA NA +## Estimate Std. Error Lower Upper +## parent_0 93.9500 9.998e-01 91.5900 96.3100 +## log_k1 3.1350 2.336e+03 -5522.0000 5528.0000 +## log_k2 -1.0880 6.285e-02 -1.2370 -0.9394 +## g_ilr -0.2821 7.033e-02 -0.4484 -0.1158 +## sigma 1.4140 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: -## Could not estimate covariance matrix; singular system. -## Residual standard error: 1.732 on 8 degrees of freedom +## parent_0 log_k1 log_k2 g_ilr sigma +## parent_0 1.000e+00 5.247e-07 -1.026e-10 2.665e-01 -8.076e-11 +## log_k1 5.247e-07 1.000e+00 8.592e-05 -1.690e-04 -7.938e-06 +## log_k2 -1.026e-10 8.592e-05 1.000e+00 -7.903e-01 5.048e-10 +## g_ilr 2.665e-01 -1.690e-04 -7.903e-01 1.000e+00 -6.476e-10 +## sigma -8.076e-11 -7.938e-06 5.048e-10 -6.476e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. -## Estimate t value Pr(>t) Lower Upper -## parent_0 93.9500 NA NA NA NA -## k1 23.0400 NA NA NA NA -## k2 0.3369 NA NA NA NA -## g 0.4016 NA NA NA NA +## Estimate t value Pr(>t) Lower Upper +## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 +## k1 23.0000 4.377e-04 4.998e-01 0.0000 Inf +## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909 +## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591 +## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -432,7 +462,7 @@ ## ## Estimated disappearance times: ## DT50 DT90 DT50_k1 DT50_k2 -## parent 0.5335 5.311 0.03009 2.058</code></pre> +## parent 0.5335 5.311 0.03014 2.058</code></pre> <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p> </div> </div> @@ -440,18 +470,18 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l3" class="anchor"></a>Laboratory Data L3</h1> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> -<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">FOCUS_<span class="dv">2006</span>_L3 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb18-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>),</a> -<a class="sourceLine" id="cb18-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>))</a> -<a class="sourceLine" id="cb18-4" title="4">FOCUS_<span class="dv">2006</span>_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L3)</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">FOCUS_<span class="dv">2006</span>_L3 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb22-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>),</a> +<a class="sourceLine" id="cb22-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>))</a> +<a class="sourceLine" id="cb22-4" title="4">FOCUS_<span class="dv">2006</span>_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L3)</a></code></pre></div> <div id="fit-multiple-models" class="section level2"> <h2 class="hasAnchor"> <a href="#fit-multiple-models" class="anchor"></a>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" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> -<a class="sourceLine" id="cb19-2" title="2">mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>,</a> -<a class="sourceLine" id="cb19-3" title="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb19-4" title="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3)</a></code></pre></div> +<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> +<a class="sourceLine" id="cb23-2" title="2">mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>,</a> +<a class="sourceLine" id="cb23-3" title="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb23-4" title="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="700"></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> @@ -460,11 +490,11 @@ <a href="#accessing-mmkin-objects" class="anchor"></a>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" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:45 2019 -## Date of summary: Mon Mar 4 14:06:46 2019 +<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:39 2019 +## Date of summary: Wed Apr 10 10:11:39 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -473,16 +503,18 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.343 s +## Fitted with method using 372 model solutions performed in 0.809 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 97.80 state -## k1 0.10 deparm -## k2 0.01 deparm -## g 0.50 deparm +## value type +## parent_0 97.800000 state +## k1 0.100000 deparm +## k2 0.010000 deparm +## g 0.500000 deparm +## sigma 1.017292 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -490,35 +522,37 @@ ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf ## g_ilr 0.000000 -Inf Inf +## sigma 1.017292 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 97.7500 1.43800 93.7500 101.70000 -## log_k1 -0.6612 0.13340 -1.0310 -0.29100 -## log_k2 -4.2860 0.05902 -4.4500 -4.12200 -## g_ilr -0.1229 0.05121 -0.2651 0.01925 +## Estimate Std. Error Lower Upper +## parent_0 97.7500 1.01900 94.5000 101.000000 +## log_k1 -0.6612 0.10050 -0.9812 -0.341300 +## log_k2 -4.2860 0.04322 -4.4230 -4.148000 +## g_ilr -0.1229 0.03727 -0.2415 -0.004343 +## sigma 1.0170 0.25430 0.2079 1.827000 ## ## Parameter correlation: -## parent_0 log_k1 log_k2 g_ilr -## parent_0 1.00000 0.1640 0.01315 0.4253 -## log_k1 0.16400 1.0000 0.46478 -0.5526 -## log_k2 0.01315 0.4648 1.00000 -0.6631 -## g_ilr 0.42526 -0.5526 -0.66310 1.0000 -## -## Residual standard error: 1.439 on 4 degrees of freedom +## parent_0 log_k1 log_k2 g_ilr sigma +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 1.656e-07 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 6.759e-08 +## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 3.867e-07 +## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -3.839e-07 +## sigma 1.656e-07 6.759e-08 3.867e-07 -3.839e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper -## parent_0 97.75000 67.970 1.404e-07 93.75000 101.70000 -## k1 0.51620 7.499 8.460e-04 0.35650 0.74750 -## k2 0.01376 16.940 3.557e-05 0.01168 0.01621 -## g 0.45660 25.410 7.121e-06 0.40730 0.50680 +## parent_0 97.75000 95.960 1.248e-06 94.50000 101.00000 +## k1 0.51620 9.947 1.081e-03 0.37490 0.71090 +## k2 0.01376 23.140 8.840e-05 0.01199 0.01579 +## g 0.45660 34.920 2.581e-05 0.41540 0.49850 +## sigma 1.01700 4.000 1.400e-02 0.20790 1.82700 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -539,7 +573,7 @@ ## 60 parent 22.0 23.26 -1.25919 ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395</code></pre> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></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> @@ -549,65 +583,69 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l4" class="anchor"></a>Laboratory Data L4</h1> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> -<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">FOCUS_<span class="dv">2006</span>_L4 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb23-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>),</a> -<a class="sourceLine" id="cb23-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span>))</a> -<a class="sourceLine" id="cb23-4" title="4">FOCUS_<span class="dv">2006</span>_L4_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L4)</a></code></pre></div> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1">FOCUS_<span class="dv">2006</span>_L4 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb27-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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>),</a> +<a class="sourceLine" id="cb27-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span>))</a> +<a class="sourceLine" id="cb27-4" title="4">FOCUS_<span class="dv">2006</span>_L4_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L4)</a></code></pre></div> <p>Fits of the SFO and FOMC models, plots and summaries are produced below:</p> -<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> -<a class="sourceLine" id="cb24-2" title="2">mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>), <span class="dt">cores =</span> <span class="dv">1</span>,</a> -<a class="sourceLine" id="cb24-3" title="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L4_mkin),</a> -<a class="sourceLine" id="cb24-4" title="4"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb24-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L4)</a></code></pre></div> +<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> +<a class="sourceLine" id="cb28-2" title="2">mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>), <span class="dt">cores =</span> <span class="dv">1</span>,</a> +<a class="sourceLine" id="cb28-3" title="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L4_mkin),</a> +<a class="sourceLine" id="cb28-4" title="4"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb28-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L4)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:46 2019 -## Date of summary: Mon Mar 4 14:06:46 2019 +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:39 2019 +## Date of summary: Wed Apr 10 10:11:40 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.111 s +## Fitted with method using 146 model solutions performed in 0.306 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 96.6 state -## k_parent_sink 0.1 deparm +## value type +## parent_0 96.60000 state +## k_parent_sink 0.10000 deparm +## sigma 3.16181 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 96.600000 -Inf Inf ## log_k_parent_sink -2.302585 -Inf Inf +## sigma 3.161810 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## parent_0 96.44 1.94900 91.670 101.200 -## log_k_parent_sink -5.03 0.07999 -5.225 -4.834 +## parent_0 96.440 1.69900 92.070 100.800 +## log_k_parent_sink -5.030 0.07059 -5.211 -4.848 +## sigma 3.162 0.79050 1.130 5.194 ## ## Parameter correlation: -## parent_0 log_k_parent_sink -## parent_0 1.0000 0.5865 -## log_k_parent_sink 0.5865 1.0000 -## -## Residual standard error: 3.651 on 6 degrees of freedom +## parent_0 log_k_parent_sink sigma +## parent_0 1.000e+00 5.938e-01 5.612e-10 +## log_k_parent_sink 5.938e-01 1.000e+00 -4.994e-10 +## sigma 5.612e-10 -4.994e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper -## parent_0 96.440000 49.49 2.283e-09 91.670000 1.012e+02 -## k_parent_sink 0.006541 12.50 8.008e-06 0.005378 7.955e-03 +## parent_0 96.440000 56.77 1.604e-08 92.070000 1.008e+02 +## k_parent_sink 0.006541 14.17 1.578e-05 0.005455 7.842e-03 +## sigma 3.162000 4.00 5.162e-03 1.130000 5.194e+00 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -621,58 +659,62 @@ ## Estimated disappearance times: ## DT50 DT90 ## parent 106 352</code></pre> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.48.1 -## R version used for fitting: 3.5.2 -## Date of fit: Mon Mar 4 14:06:46 2019 -## Date of summary: Mon Mar 4 14:06:46 2019 +<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> +<pre><code>## mkin version used for fitting: 0.9.49.4 +## R version used for fitting: 3.5.3 +## Date of fit: Wed Apr 10 10:11:40 2019 +## Date of summary: Wed Apr 10 10:11:40 2019 ## ## 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 0.173 s +## Fitted with method using 224 model solutions performed in 0.478 s ## -## Weighting: none +## Error model: +## NULL ## ## Starting values for parameters to be optimised: -## value type -## parent_0 96.6 state -## alpha 1.0 deparm -## beta 10.0 deparm +## value type +## parent_0 96.600000 state +## alpha 1.000000 deparm +## beta 10.000000 deparm +## sigma 1.830055 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 96.600000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf +## sigma 1.830055 0 Inf ## ## Fixed parameter values: ## None ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 99.1400 1.6800 94.820 103.5000 -## log_alpha -0.3506 0.3725 -1.308 0.6068 -## log_beta 4.1740 0.5635 2.726 5.6230 +## Estimate Std. Error Lower Upper +## parent_0 99.1400 1.2670 95.6300 102.7000 +## log_alpha -0.3506 0.2616 -1.0770 0.3756 +## log_beta 4.1740 0.3938 3.0810 5.2670 +## sigma 1.8300 0.4575 0.5598 3.1000 ## ## Parameter correlation: -## parent_0 log_alpha log_beta -## parent_0 1.0000 -0.5365 -0.6083 -## log_alpha -0.5365 1.0000 0.9913 -## log_beta -0.6083 0.9913 1.0000 -## -## Residual standard error: 2.315 on 5 degrees of freedom +## parent_0 log_alpha log_beta sigma +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.460e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.351e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 5.079e-08 +## sigma -2.460e-07 2.351e-08 5.079e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper -## parent_0 99.1400 59.020 1.322e-08 94.8200 103.500 -## alpha 0.7042 2.685 2.178e-02 0.2703 1.835 -## beta 64.9800 1.775 6.807e-02 15.2600 276.600 +## parent_0 99.1400 78.250 7.993e-08 95.6300 102.700 +## alpha 0.7042 3.823 9.365e-03 0.3407 1.456 +## beta 64.9800 2.540 3.201e-02 21.7800 193.900 +## sigma 1.8300 4.000 8.065e-03 0.5598 3.100 ## ## Chi2 error levels in percent: ## err.min n.optim df 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 differindex 770db292..6e4ccb9d 100644 --- 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 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 differindex ee225461..0a403808 100644 --- 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 diff --git a/docs/articles/index.html b/docs/articles/index.html index 9381dedb..eb2d55ef 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,7 +60,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -132,6 +132,7 @@ <li><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></li> <li><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></li> <li><a href="web_only/NAFTA_examples.html">Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</a></li> + <li><a href="web_only/benchmarks.html">Benchmark timings for mkin on various systems</a></li> <li><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> </ul> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 93ad4b56..2e5cd759 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index f58814e3..cdcea4d3 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>twa.Rmd</code></div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 79e39e55..33d0c90f 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -125,87 +125,97 @@ <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">Z<span class="fl">.2</span>a <-<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">"SFO"</span>, <span class="st">"Z1"</span>),</a> <a class="sourceLine" id="cb2-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations +## with value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.2a, data = FALSE): Could not estimate -## covariance matrix; singular system.</code></pre> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 9.7015e+01 3.553140 2.7304e+01 1.6793e-21 NA NA -## k_Z0_sink 1.2790e-11 0.226895 5.6368e-11 5.0000e-01 NA NA -## k_Z0_Z1 2.2360e+00 0.165073 1.3546e+01 7.3938e-14 NA NA -## k_Z1_sink 4.8212e-01 0.065854 7.3212e+00 3.5520e-08 NA NA</code></pre> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 9.7015e+01 3.39373 2.8587e+01 6.4606e-21 91.66556 102.3642 +## k_Z0_sink 4.0181e-10 0.22534 1.7831e-09 5.0000e-01 0.00000 Inf +## k_Z0_Z1 2.2360e+00 0.15915 1.4050e+01 1.1387e-13 1.95303 2.5600 +## k_Z1_sink 4.8212e-01 0.06547 7.3641e+00 5.1396e-08 0.40341 0.5762 +## sigma 4.8041e+00 0.63763 7.5343e+00 3.4444e-08 3.52677 6.0815</code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">Z<span class="fl">.2</span>a.ff <-<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">"SFO"</span>, <span class="st">"Z1"</span>),</a> -<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">Z<span class="fl">.2</span>a.ff <-<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">"SFO"</span>, <span class="st">"Z1"</span>),</a> +<a class="sourceLine" id="cb9-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb9-3" title="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb10-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations +## with value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> -<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.2a.ff, data = FALSE): Could not estimate -## covariance matrix; singular system.</code></pre> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 3.553145 27.3039 1.6793e-21 NA NA -## k_Z0 2.23601 0.216849 10.3114 3.6623e-11 NA NA -## k_Z1 0.48212 0.065854 7.3211 3.5520e-08 NA NA -## f_Z0_to_Z1 1.00000 0.101473 9.8548 9.7068e-11 NA NA</code></pre> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 +## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 +## k_Z1 0.48212 0.063265 7.6207 2.8155e-08 0.40341 0.5762 +## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000 +## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre> <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> <p>A simplified model is obtained by removing the pathway to the sink. </p> <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">Z<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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb14-2" 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="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">Z<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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb16-2" 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="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb16-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> +<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with +## value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> -<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://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 2.681772 36.176 2.3636e-25 91.52152 102.508 -## k_Z0 2.23601 0.146861 15.225 2.2464e-15 1.95453 2.558 -## k_Z1 0.48212 0.042687 11.294 3.0686e-12 0.40216 0.578</code></pre> +<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538 +## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593 +## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760 +## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</code></pre> <p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> </div> <div id="metabolites-z2-and-z3" class="section level1"> <h1 class="hasAnchor"> <a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1> <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">Z<span class="fl">.5</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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb19-2" 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> -<a class="sourceLine" id="cb19-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">Z<span class="fl">.5</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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb23-2" 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> +<a class="sourceLine" id="cb23-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb21-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with +## value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">Z.FOCUS <-<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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb22-2" 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> -<a class="sourceLine" id="cb22-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb22-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb22-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1">Z.FOCUS <-<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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb28-2" 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> +<a class="sourceLine" id="cb28-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb28-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb28-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb24-2" title="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb24-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> -<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge: +<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb30-2" title="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb30-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z. +## 5$bparms.ode, : Observations with value of zero were removed from the data</code></pre> +<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge: ## false convergence (8)</code></pre> -<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.837112 2.058861 47.0343 5.5877e-44 92.703779 100.970445 -## k_Z0 2.215368 0.118098 18.7587 7.6563e-25 1.990525 2.465609 -## k_Z1 0.478302 0.029289 16.3302 3.3408e-22 0.422977 0.540864 -## k_Z2 0.451617 0.044214 10.2144 3.1133e-14 0.371034 0.549702 -## k_Z3 0.058693 0.014296 4.1056 7.2924e-05 0.035994 0.095705 -## f_Z2_to_Z3 0.471516 0.057057 8.2639 2.8156e-11 0.360381 0.585548</code></pre> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> +## Z0_0 96.838619 1.994272 48.5584 4.0282e-42 92.826596 100.850642 +## k_Z0 2.215408 0.118459 18.7018 1.0415e-23 1.989468 2.467007 +## k_Z1 0.478300 0.028257 16.9267 6.2407e-22 0.424701 0.538663 +## k_Z2 0.451618 0.042138 10.7177 1.6308e-14 0.374327 0.544869 +## k_Z3 0.058693 0.015246 3.8498 1.7805e-04 0.034804 0.098981 +## f_Z2_to_Z3 0.471508 0.058352 8.0804 9.6647e-11 0.357725 0.588332 +## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> +<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> <pre><code>## $ff ## Z2_Z3 Z2_sink -## 0.47152 0.52848 +## 0.47151 0.52849 ## ## $SFORB ## logical(0) @@ -213,9 +223,9 @@ ## $distimes ## DT50 DT90 ## Z0 0.31288 1.0394 -## Z1 1.44918 4.8141 +## Z1 1.44919 4.8141 ## Z2 1.53481 5.0985 -## Z3 11.80973 39.2311</code></pre> +## Z3 11.80962 39.2307</code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> <div id="using-the-sforb-model" class="section level1"> @@ -223,77 +233,116 @@ <a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1">Z.mkin<span class="fl">.1</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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb31-2" 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> -<a class="sourceLine" id="cb31-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb31-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">Z.mkin<span class="fl">.1</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">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb38-2" 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> +<a class="sourceLine" id="cb38-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb38-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb33-2" title="2"><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> +<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations +## with value of zero were removed from the data</code></pre> +<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="../../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="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(m.Z.mkin.1, data = FALSE): Could not estimate -## covariance matrix; singular system.</code></pre> -<pre><code>## NULL</code></pre> +<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</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 -6.0658e-02 -4.4768e-04 -3.0588e-03 -3.9074e-02 +## log_k_Z3_bound_free 4.7821e+00 5.5819e-03 1.0267e-01 1.1956e+00 +## sigma -1.4345e-08 8.6519e-11 -6.1861e-10 -4.7499e-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 -2.1303e-01 -9.0584e-01 +## sigma 5.8776e-10 1.0773e-09 +## log_k_Z3_free_bound log_k_Z3_bound_free sigma +## Z0_0 -6.0658e-02 4.7821e+00 -1.4345e-08 +## log_k_Z0_Z1 -4.4768e-04 5.5819e-03 8.6519e-11 +## log_k_Z1_Z2 -3.0588e-03 1.0267e-01 -6.1861e-10 +## log_k_Z2_sink -3.9074e-02 1.1956e+00 -4.7499e-10 +## log_k_Z2_Z3_free 2.5836e-02 -2.1303e-01 5.8776e-10 +## log_k_Z3_free_sink 1.1964e-01 -9.0584e-01 1.0773e-09 +## log_k_Z3_free_bound 6.5902e-01 4.2011e+00 2.1743e-09 +## log_k_Z3_bound_free 4.2011e+00 3.6036e+08 7.2404e-02 +## sigma 2.1743e-09 7.2404e-02 1.4170e-01</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="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" 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="cb37-2" 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> -<a class="sourceLine" id="cb37-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" 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="cb45-2" 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> +<a class="sourceLine" id="cb45-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" title="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb39-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations +## with value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> -<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1">Z.mkin<span class="fl">.4</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="cb40-2" 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> -<a class="sourceLine" id="cb40-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb40-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1">Z.mkin<span class="fl">.4</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="cb50-2" 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> +<a class="sourceLine" id="cb50-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb50-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb42-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb42-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb42-4" title="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> +<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb52-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb52-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. +## 3$bparms.ode, : Observations with value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">Z.mkin<span class="fl">.5</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="cb43-2" 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> -<a class="sourceLine" id="cb43-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb43-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1">Z.mkin<span class="fl">.5</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="cb55-2" 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> +<a class="sourceLine" id="cb55-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb55-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb45-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> -<a class="sourceLine" id="cb45-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb45-4" title="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb57-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> +<a class="sourceLine" id="cb57-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. +## 4$bparms.ode[1:4], : Observations with value of zero were removed from the +## data</code></pre> +<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> -<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb46-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> -<a class="sourceLine" id="cb46-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> -<a class="sourceLine" id="cb46-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> -<a class="sourceLine" id="cb46-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb46-6" title="6"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb60-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> +<a class="sourceLine" id="cb60-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> +<a class="sourceLine" id="cb60-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> +<a class="sourceLine" id="cb60-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin. +## 5$bparms.ode[1:7], : Observations with value of zero were removed from the +## data</code></pre> +<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> -<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> -<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <pre><code>## $ff ## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink ## 1.00000 1.00000 0.46344 0.53656 1.00000 ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471382 0.0075127 0.0800075 0.0000000 +## 2.4471355 0.0075125 0.0800068 0.0000000 ## ## $distimes ## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.28325 92.264 NA NA +## Z0 0.3043 1.1848 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA ## Z2 1.6414 5.4526 NA NA NA NA -## Z3 NA NA NA NA 8.6635 Inf</code></pre> +## Z3 NA NA NA NA 8.6636 Inf</code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> <div id="references" class="section level1"> 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 53f2ce85..f371827f 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 90eab945..3dfb6477 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 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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 e6ce97cd..27c51525 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 12e5d522..0bcfca27 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <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">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -111,13 +111,11 @@ <h2 class="hasAnchor"> <a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</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="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -128,28 +126,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 95.8401 1.10e-21 92.121 99.5597 -## k_parent_sink 0.0102 1.71e-12 0.009 0.0117 +## parent_0 95.8401 4.67e-21 92.245 99.4357 +## k_parent_sink 0.0102 3.92e-12 0.009 0.0117 +## sigma 4.8230 3.81e-06 3.214 6.4318 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 2.37e-26 9.89e+01 1.03e+02 -## k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05 -## N_parent 2.57e+00 1.14e-11 2.22e+00 2.92e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 NA 9.91e+01 1.02e+02 +## k__iore_parent_sink 1.54e-05 NA 4.08e-06 5.84e-05 +## N_parent 2.57e+00 NA 2.25e+00 2.89e+00 +## sigma 1.68e+00 NA 1.12e+00 2.24e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.99e+01 4.33e-27 NA NA -## k1 2.67e-02 3.17e-05 NA NA -## k2 2.16e-12 5.00e-01 NA NA -## g 6.47e-01 2.13e-05 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 +## k1 2.67e-02 5.05e-06 0.0243 0.0295 +## k2 3.41e-12 5.00e-01 0.0000 Inf +## g 6.47e-01 3.67e-06 0.6248 0.6677 +## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.84e+11 3.21e+11 +## DFOP 55.5 3.70e+11 2.03e+11 ## ## Representative half-life: ## [1] 321.5119</code></pre> @@ -157,14 +158,12 @@ <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> <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="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -175,28 +174,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 96.497 2.62e-25 94.77653 98.21774 -## k_parent_sink 0.008 1.35e-14 0.00736 0.00871 +## parent_0 96.497 2.32e-24 94.85271 98.14155 +## k_parent_sink 0.008 3.42e-14 0.00737 0.00869 +## sigma 2.295 1.22e-05 1.47976 3.11036 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 1.02e-29 9.78e+01 9.93e+01 -## k__iore_parent_sink 1.53e-04 1.15e-02 6.60e-05 3.56e-04 -## N_parent 1.94e+00 8.18e-13 1.74e+00 2.14e+00 +## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01 +## k__iore_parent_sink 1.53e-04 6.50e-03 7.21e-05 3.26e-04 +## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00 +## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.84e+01 1.90e-28 NA NA -## k1 1.55e-02 2.83e-03 NA NA -## k2 8.17e-12 5.00e-01 NA NA -## g 6.89e-01 1.31e-02 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 +## k1 1.55e-02 4.10e-04 0.0143 0.0167 +## k2 1.09e-11 5.00e-01 0.0000 Inf +## g 6.89e-01 2.92e-03 0.6626 0.7142 +## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.39e+11 8.48e+10 +## DFOP 83.6 1.04e+11 6.34e+10 ## ## Representative half-life: ## [1] 215.8655</code></pre> @@ -204,14 +206,12 @@ <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> <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="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -222,28 +222,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 94.7759 1.25e-24 92.2558 97.2960 -## k_parent_sink 0.0179 2.35e-16 0.0166 0.0194 +## parent_0 94.7759 7.29e-24 92.3479 97.2039 +## k_parent_sink 0.0179 8.02e-16 0.0166 0.0194 +## sigma 3.0696 3.81e-06 2.0456 4.0936 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 97.12446 5.62e-27 95.49343 98.75549 -## k__iore_parent_sink 0.00252 3.54e-03 0.00126 0.00502 -## N_parent 1.49587 6.13e-13 1.32380 1.66794 +## parent_0 97.12446 2.63e-26 95.62461 98.62431 +## k__iore_parent_sink 0.00252 1.95e-03 0.00134 0.00472 +## N_parent 1.49587 4.07e-13 1.33896 1.65279 +## sigma 1.59698 5.05e-06 1.06169 2.13227 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.66e+01 4.17e-26 NA NA -## k1 2.55e-02 2.12e-05 NA NA -## k2 3.09e-11 5.00e-01 NA NA -## g 8.61e-01 2.10e-05 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 +## k1 2.55e-02 7.33e-06 0.0233 0.0278 +## k2 3.88e-11 5.00e-01 0.0000 Inf +## g 8.61e-01 7.55e-06 0.8314 0.8867 +## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 1.06e+10 2.24e+10 +## DFOP 34.1 8.42e+09 1.79e+10 ## ## Representative half-life: ## [1] 53.16582</code></pre> @@ -251,14 +254,12 @@ <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> <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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -269,28 +270,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 96.41796 1.52e-53 93.29554 99.54038 -## k_parent_sink 0.00735 3.59e-21 0.00641 0.00842 +## parent_0 96.41796 4.80e-53 93.32245 99.51347 +## k_parent_sink 0.00735 7.64e-21 0.00641 0.00843 +## sigma 7.94557 1.83e-15 6.46713 9.42401 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.92e+01 7.33e-49 9.53e+01 1.03e+02 -## k__iore_parent_sink 1.60e-05 3.47e-01 9.98e-08 2.57e-03 -## N_parent 2.45e+00 6.14e-05 1.26e+00 3.63e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.92e+01 NA 9.55e+01 1.03e+02 +## k__iore_parent_sink 1.60e-05 NA 1.45e-07 1.77e-03 +## N_parent 2.45e+00 NA 1.35e+00 3.54e+00 +## sigma 7.42e+00 NA 6.04e+00 8.80e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 8.13e-48 NA NA -## k1 1.81e-02 2.20e-01 NA NA -## k2 3.28e-10 5.00e-01 NA NA -## g 6.06e-01 2.60e-01 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 +## k1 1.81e-02 1.75e-01 0.0116 0.0281 +## k2 2.57e-10 5.00e-01 0.0000 Inf +## g 6.06e-01 2.19e-01 0.4826 0.7178 +## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 4.18e+09 2.11e+09 +## DFOP 96.4 5.32e+09 2.69e+09 ## ## Representative half-life: ## [1] 454.5528</code></pre> @@ -303,7 +307,7 @@ <h2 class="hasAnchor"> <a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; ## singular system. @@ -311,9 +315,9 @@ ## singular system.</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="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -327,12 +331,14 @@ ## parent_0 88.16549 NA NA NA ## k__iore_parent_sink 0.00100 NA NA NA ## k_parent_sink 0.00803 NA NA NA +## sigma 7.44786 NA NA NA ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 9.77e+01 1.05e-35 9.44e+01 1.01e+02 -## k__iore_parent_sink 6.14e-05 2.76e-02 2.21e-05 1.71e-04 -## N_parent 2.27e+00 6.00e-19 2.02e+00 2.53e+00 +## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 +## k__iore_parent_sink 6.14e-05 3.20e-02 2.12e-05 1.78e-04 +## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00 +## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper @@ -341,6 +347,7 @@ ## k1 0.02500 NA NA NA ## k2 0.00273 NA NA NA ## g 0.58835 NA NA NA +## sigma 3.90001 NA NA NA ## ## ## DTx values: @@ -359,14 +366,12 @@ <div id="example-on-page-9-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> -<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> <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="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<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="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -377,28 +382,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 88.1933 1.12e-12 79.7671 96.6195 -## k_parent_sink 0.0409 9.50e-08 0.0326 0.0513 +## parent_0 88.1933 3.06e-12 79.9447 96.4419 +## k_parent_sink 0.0409 2.07e-07 0.0324 0.0516 +## sigma 7.2429 3.92e-05 4.4768 10.0090 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 5.16e-17 9.50e+01 1.03e+02 -## k__iore_parent_sink 1.93e-05 1.48e-01 2.65e-06 1.40e-04 -## N_parent 2.91e+00 3.74e-09 2.43e+00 3.39e+00 +## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 +## k__iore_parent_sink 1.93e-05 1.13e-01 3.49e-06 1.06e-04 +## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00 +## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 1.31e-21 NA NA -## k1 1.38e-01 3.63e-09 NA NA -## k2 6.02e-13 5.00e-01 NA NA -## g 6.52e-01 1.50e-10 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 2.54e-20 97.390 99.672 +## k1 1.38e-01 3.52e-05 0.131 0.146 +## k2 5.75e-13 5.00e-01 0.000 Inf +## g 6.52e-01 8.13e-06 0.642 0.661 +## sigma 7.88e-01 6.13e-02 0.481 1.095 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 2.07e+12 1.15e+12 +## DFOP 10.5 2.17e+12 1.21e+12 ## ## Representative half-life: ## [1] 101.4264</code></pre> @@ -407,14 +415,17 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- +## finite result is doubtful</code></pre> <pre><code>## 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="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -424,22 +435,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 2.21e-20 93.0673 96.357 -## k_parent_sink 0.0389 1.48e-14 0.0369 0.041 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 2.15e-19 93.178 96.2464 +## k_parent_sink 0.0389 4.47e-14 0.037 0.0408 +## sigma 1.5957 1.28e-04 0.932 2.2595 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 93.863 2.91e-19 92.2996 95.426 -## k__iore_parent_sink 0.127 2.73e-02 0.0457 0.354 -## N_parent 0.711 3.13e-05 0.4605 0.961 +## parent_0 93.863 2.32e-18 92.4565 95.269 +## k__iore_parent_sink 0.127 1.85e-02 0.0504 0.321 +## N_parent 0.711 1.88e-05 0.4843 0.937 +## sigma 1.288 1.76e-04 0.7456 1.830 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 NA NA NA -## k1 0.0389 NA NA NA -## k2 0.0389 NA NA NA -## g 0.7742 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 1.61e-16 93.1355 96.2891 +## k1 0.0389 NaN 0.0316 0.0478 +## k2 0.0389 1.13e-08 0.0203 0.0743 +## g 0.7599 NaN NA NA +## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## ## DTx values: @@ -455,14 +469,12 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> <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="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -473,21 +485,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 4.95e-11 90.9683 112.4947 -## k_parent_sink 0.0495 3.40e-07 0.0393 0.0624 +## parent_0 101.7315 6.42e-11 91.9259 111.5371 +## k_parent_sink 0.0495 1.70e-07 0.0404 0.0607 +## sigma 8.0152 1.28e-04 4.6813 11.3491 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 96.86 2.71e-12 89.884 103.826 -## k__iore_parent_sink 2.96 1.31e-01 0.461 19.020 -## N_parent 0.00 5.00e-01 -0.473 0.473 +## parent_0 96.86 3.32e-12 90.848 102.863 +## k__iore_parent_sink 2.96 7.91e-02 0.687 12.761 +## N_parent 0.00 5.00e-01 -0.372 0.372 +## sigma 4.90 1.77e-04 2.837 6.968 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 NA NA NA -## k1 0.0495 NA NA NA -## k2 0.0495 NA NA NA -## g 0.6634 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 1.41e-09 91.6534 111.8097 +## k1 0.0495 6.41e-04 0.0303 0.0809 +## k2 0.0495 1.66e-02 0.0201 0.1219 +## g 0.6634 5.00e-01 0.0000 1.0000 +## sigma 8.0152 2.50e-04 4.5886 11.4418 ## ## ## DTx values: @@ -507,14 +522,12 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> <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="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -525,28 +538,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 96.15820 1.56e-13 89.91373 1.02e+02 -## k_parent_sink 0.00321 5.27e-05 0.00218 4.71e-03 +## parent_0 96.15820 4.83e-13 90.24934 1.02e+02 +## k_parent_sink 0.00321 4.71e-05 0.00222 4.64e-03 +## sigma 6.43473 1.28e-04 3.75822 9.11e+00 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 NA 9.80e+01 1.11e+02 -## k__iore_parent_sink 3.11e-17 NA 6.88e-25 1.41e-09 -## N_parent 8.36e+00 NA 4.40e+00 1.23e+01 +## parent_0 1.05e+02 NA 9.90e+01 1.10e+02 +## k__iore_parent_sink 3.11e-17 NA 1.35e-20 7.18e-14 +## N_parent 8.36e+00 NA 6.62e+00 1.01e+01 +## sigma 3.82e+00 NA 2.21e+00 5.44e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 7.50e-13 NA NA -## k1 4.41e-02 3.34e-02 NA NA -## k2 7.25e-13 5.00e-01 NA NA -## g 3.22e-01 7.87e-03 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 9.47e-13 99.9990 109.1224 +## k1 4.41e-02 5.95e-03 0.0296 0.0658 +## k2 9.20e-13 5.00e-01 0.0000 Inf +## g 3.22e-01 1.45e-03 0.2814 0.3650 +## sigma 3.22e+00 3.52e-04 1.8410 4.5906 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 2.16e+02 7.18e+02 2.16e+02 ## IORE 9.73e+02 1.37e+08 4.11e+07 -## DFOP 4.21e+11 2.64e+12 9.56e+11 +## DFOP 3.31e+11 2.08e+12 7.53e+11 ## ## Representative half-life: ## [1] 41148169</code></pre> @@ -560,9 +576,14 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; ## singular system.</code></pre> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- +## finite result is doubtful</code></pre> <pre><code>## 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="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> @@ -578,21 +599,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 100.521 5.61e-12 91.687 109.355 -## k_parent_sink 0.124 7.24e-08 0.102 0.152 +## parent_0 100.521 8.75e-12 92.461 108.581 +## k_parent_sink 0.124 3.61e-08 0.104 0.148 +## sigma 7.048 1.28e-04 4.116 9.980 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.823 1.24e-13 91.5691 102.078 -## k__iore_parent_sink 2.436 3.89e-02 0.7854 7.556 -## N_parent 0.263 3.64e-02 -0.0288 0.554 +## Estimate Pr(>t) Lower Upper +## parent_0 96.823 NA NA NA +## k__iore_parent_sink 2.436 NA NA NA +## N_parent 0.263 NA NA NA +## sigma 3.965 NA NA NA ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 NA NA NA -## k1 0.124 NA NA NA -## k2 0.124 NA NA NA -## g 0.877 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 2.74e-10 92.2366 108.805 +## k1 0.124 5.43e-06 0.0959 0.161 +## k2 0.124 6.45e-02 0.0315 0.490 +## g 0.880 NaN NA NA +## sigma 7.048 2.50e-04 4.0349 10.061 ## ## ## DTx values: @@ -608,13 +632,19 @@ <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> <div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- +## finite result is doubtful</code></pre> <pre><code>## 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="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -624,22 +654,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 5.36e-05 86.3205 109.0475 -## k_parent_sink 0.0589 9.87e-04 0.0432 0.0803 +## Estimate Pr(>t) Lower Upper +## parent_0 97.6840 0.00039 85.9388 109.4292 +## k_parent_sink 0.0589 0.00261 0.0431 0.0805 +## sigma 3.4323 0.04356 -1.2377 8.1023 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.523 0.000386 84.0963 106.95 -## k__iore_parent_sink 0.333 0.170886 0.0103 10.80 -## N_parent 0.568 0.054881 -0.3161 1.45 +## Estimate Pr(>t) Lower Upper +## parent_0 95.523 0.0055 74.539157 116.51 +## k__iore_parent_sink 0.333 0.1433 0.000717 154.57 +## N_parent 0.568 0.0677 -0.989464 2.13 +## sigma 1.953 0.0975 -5.893100 9.80 ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NA NA NA -## k1 0.0589 NA NA NA -## k2 0.0589 NA NA NA -## g 0.6902 NA NA NA +## parent_0 97.6840 NaN NaN NaN +## k1 0.0589 NaN NA NA +## k2 0.0589 NaN NA NA +## g 0.8275 NaN NA NA +## sigma 3.4323 NaN NaN NaN ## ## ## DTx values: @@ -654,14 +687,12 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" 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 summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" 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>## 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="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -671,22 +702,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 1.45e-17 89.3891 96.08094 -## k_parent_sink 0.00258 2.63e-09 0.0022 0.00303 +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 5.99e-17 89.61936 95.85065 +## k_parent_sink 0.00258 2.42e-09 0.00223 0.00299 +## sigma 3.41172 7.07e-05 2.05455 4.76888 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.6016 2.93e-16 88.08711 95.12 -## k__iore_parent_sink 0.0396 2.81e-01 0.00102 1.53 -## N_parent 0.3541 1.97e-01 -0.51943 1.23 +## Estimate Pr(>t) Lower Upper +## parent_0 91.6016 6.34e-16 88.53086 94.672 +## k__iore_parent_sink 0.0396 2.36e-01 0.00207 0.759 +## N_parent 0.3541 1.46e-01 -0.35153 1.060 +## sigma 3.0811 9.64e-05 1.84296 4.319 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 NA NA NA -## k1 0.00258 NA NA NA -## k2 0.00258 NA NA NA -## g 0.00442 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 +## k1 0.00258 4.28e-01 1.38e-08 4.82e+02 +## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 +## g 0.00442 5.00e-01 0.00e+00 1.00e+00 +## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 ## ## ## DTx values: @@ -702,14 +736,16 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- +## finite result is doubtful</code></pre> <pre><code>## 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="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -720,28 +756,31 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 99.47124 1.71e-31 98.37313 1.01e+02 -## k_parent_sink 0.00279 2.22e-15 0.00255 3.05e-03 +## parent_0 99.47124 2.06e-30 98.42254 1.01e+02 +## k_parent_sink 0.00279 3.75e-15 0.00256 3.04e-03 +## sigma 1.55616 3.81e-06 1.03704 2.08e+00 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 NA 9.93e+01 1.01e+02 -## k__iore_parent_sink 9.44e-08 NA 6.81e-11 1.31e-04 -## N_parent 3.31e+00 NA 1.69e+00 4.93e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 NA NaN NaN +## k__iore_parent_sink 9.44e-08 NA NaN NaN +## N_parent 3.31e+00 NA NaN NaN +## sigma 1.20e+00 NA 0.796 1.6 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 2.70e-28 NA NA -## k1 9.53e-03 3.39e-01 NA NA -## k2 9.19e-12 5.00e-01 NA NA -## g 3.98e-01 3.92e-01 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 +## k1 9.53e-03 1.20e-01 0.00638 0.0143 +## k2 6.17e-12 5.00e-01 0.00000 Inf +## g 3.98e-01 2.19e-01 0.30481 0.4998 +## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 2.02e+10 1.95e+11 7.54e+10 +## DFOP 3.00e+10 2.91e+11 1.12e+11 ## ## Representative half-life: ## [1] 6697.437</code></pre> @@ -750,14 +789,17 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- +## finite result is doubtful</code></pre> <pre><code>## 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="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -767,22 +809,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 4.98e-16 94.03829 101.8967 -## k_parent_sink 0.00952 5.24e-09 0.00813 0.0112 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 2.00e-15 94.32049 101.615 +## k_parent_sink 0.00952 4.93e-09 0.00824 0.011 +## sigma 4.18778 1.28e-04 2.44588 5.930 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.874 8.30e-16 92.5802 99.167 -## k__iore_parent_sink 0.629 2.39e-01 0.0316 12.519 -## N_parent 0.000 5.00e-01 -0.7219 0.722 +## Estimate Pr(>t) Lower Upper +## parent_0 95.874 2.94e-15 92.937 98.811 +## k__iore_parent_sink 0.629 2.11e-01 0.044 8.982 +## N_parent 0.000 5.00e-01 -0.642 0.642 +## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 NA NA NA -## k1 0.00952 NA NA NA -## k2 0.00952 NA NA NA -## g 0.17247 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 2.85e-13 94.21913 101.7159 +## k1 0.00952 5.68e-02 0.00262 0.0347 +## k2 0.00952 1.52e-04 0.00639 0.0142 +## g 0.22357 NaN NA NA +## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: @@ -793,14 +838,12 @@ ## ## Representative half-life: ## [1] 41.32749</code></pre> -<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" 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 summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" 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>## 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="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -811,21 +854,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 4.99e-18 98.12761 1.04e+02 -## k_parent_sink 4.86e-03 1.76e-10 0.00432 5.46e-03 +## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02 +## k_parent_sink 4.86e-03 2.48e-10 0.00435 5.42e-03 +## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.83 4.49e-17 97.19753 102.5 -## k__iore_parent_sink 0.38 3.41e-01 0.00206 70.0 -## N_parent 0.00 5.00e-01 -1.20105 1.2 +## Estimate Pr(>t) Lower Upper +## parent_0 99.83 1.81e-16 97.51349 102.14 +## k__iore_parent_sink 0.38 3.22e-01 0.00352 41.05 +## N_parent 0.00 5.00e-01 -1.07695 1.08 +## sigma 2.21 2.57e-04 1.23245 3.19 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA NA NA -## k1 4.86e-03 NA NA NA -## k2 4.86e-03 NA NA NA -## g 1.50e-01 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 +## k1 4.86e-03 NA 6.49e-04 3.64e-02 +## k2 4.86e-03 NA 3.36e-03 7.03e-03 +## g 1.50e-01 NA 0.00e+00 1.00e+00 +## sigma 2.76e+00 NA 1.58e+00 3.94e+00 ## ## ## DTx values: @@ -841,14 +887,14 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> <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 representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -858,22 +904,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.953 3.92e-14 61.087 82.819 -## k_parent_sink 0.159 2.27e-06 0.111 0.229 +## Estimate Pr(>t) Lower Upper +## parent_0 71.953 2.33e-13 60.509 83.40 +## k_parent_sink 0.159 4.86e-05 0.102 0.25 +## sigma 11.302 1.25e-08 8.308 14.30 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 8.74e+01 1.74e-16 7.71e+01 97.70701 -## k__iore_parent_sink 4.55e-04 2.28e-01 3.01e-05 0.00688 -## N_parent 2.70e+00 1.87e-08 1.97e+00 3.42611 +## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972 +## k__iore_parent_sink 4.55e-04 2.16e-01 3.48e-05 0.00595 +## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046 +## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.5333 NA 79.3673 97.699 -## k1 18.5562 NA 0.0000 Inf -## k2 0.0776 NA 0.0471 0.128 -## g 0.4733 NA 0.3138 0.639 +## Estimate Pr(>t) Lower Upper +## parent_0 88.5333 7.40e-18 79.9836 97.083 +## k1 18.6317 5.00e-01 0.0000 Inf +## k2 0.0776 1.41e-05 0.0518 0.116 +## g 0.4733 1.41e-09 0.3674 0.582 +## sigma 7.1902 2.11e-08 5.2785 9.102 ## ## ## DTx values: diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png Binary files differindex df60b257..5858c8f1 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png Binary files differindex 02975183..f0077768 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png Binary files differindex 3b39d9fa..0f01d16d 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png Binary files differindex 866f1523..3ef2018d 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png Binary files differindex 7f99d9cd..fe37b65c 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html new file mode 100644 index 00000000..403cb1db --- /dev/null +++ b/docs/articles/web_only/benchmarks.html @@ -0,0 +1,292 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<title>Benchmark timings for mkin on various systems • mkin</title> +<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link 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</header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header toc-ignore"> + <h1>Benchmark timings for mkin on various systems</h1> + <h4 class="author">Johannes Ranke</h4> + + <h4 class="date">2019-04-10</h4> + + + <div class="hidden name"><code>benchmarks.Rmd</code></div> + + </div> + + + +<div id="systems" class="section level2"> +<h2 class="hasAnchor"> +<a href="#systems" class="anchor"></a>Systems</h2> +<p>Each system is characterized by its CPU type, the operating system type and the mkin version.</p> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">cpu_model <-<span class="st"> </span>benchmarkme<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/benchmarkme/topics/get_cpu">get_cpu</a></span>()<span class="op">$</span>model_name</a> +<a class="sourceLine" id="cb1-2" title="2">operating_system <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Sys.info">Sys.info</a></span>()[[<span class="st">"sysname"</span>]]</a> +<a class="sourceLine" id="cb1-3" title="3">mkin_version <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/character">as.character</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/packageDescription">packageVersion</a></span>(<span class="st">"mkin"</span>))</a> +<a class="sourceLine" id="cb1-4" title="4">system_string <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(operating_system, <span class="st">", "</span>, cpu_model, <span class="st">", mkin version "</span>, mkin_version)</a> +<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/load">load</a></span>(<span class="st">"~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda"</span>)</a> +<a class="sourceLine" id="cb1-6" title="6">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"CPU"</span>, <span class="st">"OS"</span>, <span class="st">"mkin"</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(cpu_model, operating_system, mkin_version)</a> +<a class="sourceLine" id="cb1-7" title="7"></a> +<a class="sourceLine" id="cb1-8" title="8"><span class="cf">if</span> (mkin_version <span class="op">></span><span class="st"> "0.9.48.1"</span>) {</a> +<a class="sourceLine" id="cb1-9" title="9"> mmkin_bench <-<span class="st"> </span><span class="cf">function</span>(models, datasets, <span class="dt">error_model =</span> <span class="st">"const"</span>) <span class="kw"><a href="../../reference/mmkin.html">mmkin</a></span>(models, datasets, <span class="dt">error_model =</span> error_model, <span class="dt">cores =</span> <span class="dv">1</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-10" title="10">} <span class="cf">else</span> {</a> +<a class="sourceLine" id="cb1-11" title="11"> mmkin_bench <-<span class="st"> </span><span class="cf">function</span>(models, datasets, <span class="dt">error_model =</span> <span class="ot">NULL</span>) <span class="kw"><a href="../../reference/mmkin.html">mmkin</a></span>(models, datasets, <span class="dt">reweight.method =</span> error_model, <span class="dt">cores =</span> <span class="dv">1</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-12" title="12">}</a></code></pre></div> +<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># Parent only</span></a> +<a class="sourceLine" id="cb2-2" title="2">t1 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a> +<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> +<a class="sourceLine" id="cb2-4" title="4"></a> +<a class="sourceLine" id="cb2-5" title="5"><span class="co"># One metabolite</span></a> +<a class="sourceLine" id="cb2-6" title="6">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb2-7" title="7"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb4-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb4-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb6-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb6-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data + +## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data + +## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> +<a class="sourceLine" id="cb10-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data + +## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data + +## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> +<a class="sourceLine" id="cb12-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> +<a class="sourceLine" id="cb12-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> +<a class="sourceLine" id="cb12-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb12-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb12-6" title="6"></a> +<a class="sourceLine" id="cb12-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> +<a class="sourceLine" id="cb12-8" title="8"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb12-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb12-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb12-11" title="11"></a> +<a class="sourceLine" id="cb12-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb12-13" title="13"></a> +<a class="sourceLine" id="cb12-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb12-15" title="15"></a> +<a class="sourceLine" id="cb12-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb12-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb12-18" title="18"></a> +<a class="sourceLine" id="cb12-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb12-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb12-21" title="21"></a> +<a class="sourceLine" id="cb12-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb12-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb12-24" title="24"></a> +<a class="sourceLine" id="cb12-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> +<a class="sourceLine" id="cb12-26" title="26">mkin_benchmarks</a></code></pre></div> +<pre><code>## CPU +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor +## OS +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux +## mkin +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4 +## t1 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 +## 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 6.303 +## 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 21.837 +## 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 4.487 +## 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 14.162 +## 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 6.021 +## 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 2.657 +## 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 4.523 +## 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 4.72 +## 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 8.364 +## 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 3.623 +## 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 5.95</code></pre> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/inst/benchmark_data/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> + <ul class="nav nav-pills nav-stacked"> +<li><a href="#systems">Systems</a></li> + </ul> +</div> + </div> + +</div> + + + <footer><div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> +</div> + </footer> +</div> + + + + </body> +</html> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 269b1098..597b7c55 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-03-04</h4> + <h4 class="date">2019-04-10</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -125,49 +125,103 @@ <a class="sourceLine" id="cb5-12" title="12"> factor_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> <a class="sourceLine" id="cb5-13" title="13">} <span class="cf">else</span> {</a> <a class="sourceLine" id="cb5-14" title="14"> factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span></a> -<a class="sourceLine" id="cb5-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> +<a class="sourceLine" id="cb5-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)</a> <a class="sourceLine" id="cb5-16" title="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> +<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", +## use_compiled = FALSE, : Observations with value of zero were removed from +## the data</code></pre> +<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = +## TRUE): Observations with value of zero were removed from the data</code></pre> +<pre><code>## 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>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", +## use_compiled = FALSE, : Observations with value of zero were removed from +## the data + +## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", +## use_compiled = FALSE, : Observations with value of zero were removed from +## the data + +## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", +## use_compiled = FALSE, : Observations with value of zero were removed from +## the data</code></pre> +<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = +## TRUE): Observations with value of zero were removed from the data + +## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = +## TRUE): Observations with value of zero were removed from the data + +## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = +## TRUE): Observations with value of zero were removed from the data</code></pre> +<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet +## = TRUE): Observations with value of zero were removed from the data + +## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet +## = TRUE): Observations with value of zero were removed from the data + +## 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 2.310 1.000 2.308 0 -## 1 deSolve, not compiled 3 17.509 7.580 17.500 0 -## 2 Eigenvalue based 3 2.859 1.238 2.858 0 +## 3 deSolve, compiled 3 3.215 1.000 3.213 0 +## 1 deSolve, not compiled 3 42.468 13.209 42.445 0 +## 2 Eigenvalue based 3 4.666 1.451 4.663 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 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> +<p>We see that using the compiled model is by a factor of around 13 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"> <a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2> <p>This evaluation is also taken from the example section of mkinfit.</p> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a> -<a class="sourceLine" id="cb8-2" title="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb8-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> -<a class="sourceLine" id="cb8-5" title="5"></a> -<a class="sourceLine" id="cb8-6" title="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> -<a class="sourceLine" id="cb8-7" title="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb8-9" title="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb8-10" title="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> -<a class="sourceLine" id="cb8-11" title="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.2</span>)</a> -<a class="sourceLine" id="cb8-12" title="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> -<a class="sourceLine" id="cb8-13" title="13">} <span class="cf">else</span> {</a> -<a class="sourceLine" id="cb8-14" title="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> -<a class="sourceLine" id="cb8-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> -<a class="sourceLine" id="cb8-16" title="16">}</a></code></pre></div> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a> +<a class="sourceLine" id="cb14-2" title="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb14-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb14-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> +<a class="sourceLine" id="cb14-5" title="5"></a> +<a class="sourceLine" id="cb14-6" title="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> +<a class="sourceLine" id="cb14-7" title="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb14-8" title="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb14-9" title="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb14-10" title="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> +<a class="sourceLine" id="cb14-11" title="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.2</span>)</a> +<a class="sourceLine" id="cb14-12" title="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> +<a class="sourceLine" id="cb14-13" title="13">} <span class="cf">else</span> {</a> +<a class="sourceLine" id="cb14-14" title="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> +<a class="sourceLine" id="cb14-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> +<a class="sourceLine" id="cb14-16" title="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = +## TRUE): Observations with value of zero were removed from the data</code></pre> +<pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with +## value of zero were removed from the data</code></pre> +<pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = +## TRUE): Observations with value of zero were removed from the data + +## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = +## TRUE): Observations with value of zero were removed from the data + +## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = +## TRUE): Observations with value of zero were removed from the data</code></pre> +<pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with +## value of zero were removed from the data + +## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with +## value of zero were removed from the data + +## 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 4.074 1.000 4.072 0 -## 1 deSolve, not compiled 3 37.219 9.136 37.203 0 +## 2 deSolve, compiled 3 4.906 1.000 4.902 0 +## 1 deSolve, not compiled 3 70.459 14.362 70.421 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.48.1 on</p> -<pre><code>## R version 3.5.2 (2018-12-20) +<p>Here we get a performance benefit of a factor of 14 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.49.4 on</p> +<pre><code>## R version 3.5.3 (2019-03-11) ## 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> |
