diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-04-10 10:17:35 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-04-10 10:17:35 +0200 |
| commit | 194659fcaccdd1ee37851725b8c72e99daa3a8cf (patch) | |
| tree | edbbebe8956000b9eb725ca425b91e051571ec02 /docs/articles/FOCUS_D.html | |
| parent | 5814be02f286ce96d6cff8d698aea6844e4025f1 (diff) | |
Adapt tests, vignettes and examples
- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit
Diffstat (limited to 'docs/articles/FOCUS_D.html')
| -rw-r--r-- | docs/articles/FOCUS_D.html | 94 |
1 files changed, 52 insertions, 42 deletions
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 |