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| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 17:36:12 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 17:36:12 +0100 |
| commit | b9be19af5e3085216d0cd5af439332f631fa8b92 (patch) | |
| tree | e10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs/dev/articles/FOCUS_L.html | |
| parent | 11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff) | |
Fully rebuild docs, rerun tests and check
Diffstat (limited to 'docs/dev/articles/FOCUS_L.html')
| -rw-r--r-- | docs/dev/articles/FOCUS_L.html | 129 |
1 files changed, 64 insertions, 65 deletions
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html index 2695db5e..547ec630 100644 --- a/docs/dev/articles/FOCUS_L.html +++ b/docs/dev/articles/FOCUS_L.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> </span> </div> @@ -81,7 +81,7 @@ <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -95,14 +95,13 @@ - </header><link href="FOCUS_L_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> -<script src="FOCUS_L_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> + </header><script src="FOCUS_L_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-30</h4> + <h4 class="date">Last change 17 November 2016 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -128,10 +127,10 @@ <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:52 2020 -## Date of summary: Mon Nov 30 16:01:52 2020 +## Date of fit: Mon Feb 15 17:13:39 2021 +## Date of summary: Mon Feb 15 17:13:39 2021 ## ## Equations: ## d_parent/dt = - k_parent * parent @@ -234,17 +233,17 @@ <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:53 2020 -## Date of summary: Mon Nov 30 16:01:53 2020 +## Date of fit: Mon Feb 15 17:13:40 2021 +## Date of summary: Mon Feb 15 17:13:40 2021 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 380 model solutions performed in 0.087 s +## Fitted using 369 model solutions performed in 0.084 s ## ## Error model: Constant variance ## @@ -272,22 +271,22 @@ ## ## Results: ## -## AIC BIC logLik -## 95.88778 99.44927 -43.94389 +## AIC BIC logLik +## 95.88781 99.44929 -43.9439 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 92.47 1.2820 89.720 95.220 -## log_alpha 16.92 NaN NaN NaN -## log_beta 19.26 NaN NaN NaN -## sigma 2.78 0.4501 1.814 3.745 +## log_alpha 13.78 NaN NaN NaN +## log_beta 16.13 NaN NaN NaN +## sigma 2.78 0.4598 1.794 3.766 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.000000 NaN NaN 0.002218 -## log_alpha NaN 1 NaN NaN -## log_beta NaN NaN 1 NaN -## sigma 0.002218 NaN NaN 1.000000 +## parent_0 log_alpha log_beta sigma +## parent_0 1.0000000 NaN NaN 0.0001671 +## log_alpha NaN 1 NaN NaN +## log_beta NaN NaN 1 NaN +## sigma 0.0001671 NaN NaN 1.0000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -295,9 +294,9 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 9.247e+01 NA NA 89.720 95.220 -## alpha 2.223e+07 NA NA NA NA -## beta 2.325e+08 NA NA NA NA -## sigma 2.780e+00 NA NA 1.814 3.745 +## alpha 9.658e+05 NA NA NA NA +## beta 1.010e+07 NA NA NA NA +## sigma 2.780e+00 NA NA 1.794 3.766 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df @@ -346,10 +345,10 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:54 2020 -## Date of summary: Mon Nov 30 16:01:54 2020 +## Date of fit: Mon Feb 15 17:13:40 2021 +## Date of summary: Mon Feb 15 17:13:40 2021 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -391,10 +390,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09 -## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07 -## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.386e-07 -## sigma -7.436e-09 -1.617e-07 -1.386e-07 1.000e+00 +## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09 +## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.602e-07 +## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.372e-07 +## sigma -7.828e-09 -1.602e-07 -1.372e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -427,10 +426,10 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:54 2020 -## Date of summary: Mon Nov 30 16:01:54 2020 +## Date of fit: Mon Feb 15 17:13:41 2021 +## Date of summary: Mon Feb 15 17:13:41 2021 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -439,7 +438,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 581 model solutions performed in 0.136 s +## Fitted using 581 model solutions performed in 0.134 s ## ## Error model: Constant variance ## @@ -470,18 +469,18 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.950 9.998e-01 91.5900 96.3100 -## log_k1 3.117 1.929e+03 -4558.0000 4564.0000 +## log_k1 3.112 1.842e+03 -4353.0000 4359.0000 ## log_k2 -1.088 6.285e-02 -1.2370 -0.9394 ## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638 ## sigma 1.414 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: -## parent_0 log_k1 log_k2 g_qlogis sigma -## parent_0 1.000e+00 6.459e-07 9.147e-11 2.665e-01 8.413e-11 -## log_k1 6.459e-07 1.000e+00 1.061e-04 -2.087e-04 -9.802e-06 -## log_k2 9.147e-11 1.061e-04 1.000e+00 -7.903e-01 -2.429e-09 -## g_qlogis 2.665e-01 -2.087e-04 -7.903e-01 1.000e+00 4.049e-09 -## sigma 8.413e-11 -9.802e-06 -2.429e-09 4.049e-09 1.000e+00 +## parent_0 log_k1 log_k2 g_qlogis sigma +## parent_0 1.000e+00 6.783e-07 -3.390e-10 2.665e-01 -2.967e-10 +## log_k1 6.783e-07 1.000e+00 1.116e-04 -2.196e-04 -1.031e-05 +## log_k2 -3.390e-10 1.116e-04 1.000e+00 -7.903e-01 2.917e-09 +## g_qlogis 2.665e-01 -2.196e-04 -7.903e-01 1.000e+00 -4.408e-09 +## sigma -2.967e-10 -1.031e-05 2.917e-09 -4.408e-09 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -489,7 +488,7 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 -## k1 22.5800 5.303e-04 4.998e-01 0.0000 Inf +## k1 22.4800 5.553e-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 @@ -501,7 +500,7 @@ ## ## Estimated disappearance times: ## DT50 DT90 DT50back DT50_k1 DT50_k2 -## parent 0.5335 5.311 1.599 0.0307 2.058</code></pre> +## parent 0.5335 5.311 1.599 0.03084 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> @@ -533,10 +532,10 @@ <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="cb24"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:55 2020 -## Date of summary: Mon Nov 30 16:01:55 2020 +## Date of fit: Mon Feb 15 17:13:41 2021 +## Date of summary: Mon Feb 15 17:13:42 2021 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -545,7 +544,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 376 model solutions performed in 0.081 s +## Fitted using 376 model solutions performed in 0.082 s ## ## Error model: Constant variance ## @@ -583,11 +582,11 @@ ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_qlogis sigma -## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.671e-08 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.148e-07 +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.664e-08 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.147e-07 ## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06 -## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.929e-07 -## sigma -9.671e-08 7.148e-07 1.022e-06 -7.929e-07 1.000e+00 +## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.926e-07 +## sigma -9.664e-08 7.147e-07 1.022e-06 -7.926e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -646,10 +645,10 @@ <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="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:55 2020 -## Date of summary: Mon Nov 30 16:01:55 2020 +## Date of fit: Mon Feb 15 17:13:42 2021 +## Date of summary: Mon Feb 15 17:13:42 2021 ## ## Equations: ## d_parent/dt = - k_parent * parent @@ -711,17 +710,17 @@ ## parent 106 352</code></pre> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.50.4 +<pre><code>## mkin version used for fitting: 1.0.3.9000 ## R version used for fitting: 4.0.3 -## Date of fit: Mon Nov 30 16:01:55 2020 -## Date of summary: Mon Nov 30 16:01:56 2020 +## Date of fit: Mon Feb 15 17:13:42 2021 +## Date of summary: Mon Feb 15 17:13:42 2021 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.045 s +## Fitted using 224 model solutions performed in 0.046 s ## ## Error model: Constant variance ## @@ -756,10 +755,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07 -## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.169e-08 -## log_beta -5.543e-01 9.889e-01 1.000e+00 4.910e-08 -## sigma -2.456e-07 2.169e-08 4.910e-08 1.000e+00 +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.478e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 5.211e-08 +## sigma -2.468e-07 2.478e-08 5.211e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -783,7 +782,7 @@ <div id="references" class="section level1 unnumbered"> <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-ranke2014"> <p>Ranke, Johannes. 2014. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.</p> </div> |