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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 8af99f6c..b05963ae 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -113,19 +113,19 @@ <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: 0.9.49.4 -## 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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:31 2019 +## Date of summary: Thu May 2 12:40:31 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 133 model solutions performed in 0.344 s +## Fitted using 133 model solutions performed in 0.289 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -163,7 +163,7 @@ ## 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: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.424 2 7 ## parent 3.424 2 7 @@ -214,9 +214,9 @@ <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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:33 2019 +## Date of summary: Thu May 2 12:40:33 2019 ## ## ## Warning: Optimisation did not converge: @@ -228,24 +228,24 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method using 344 model solutions performed in 0.778 s +## Fitted using 599 model solutions performed in 1.277 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.85000 state -## alpha 1.00000 deparm -## beta 10.00000 deparm -## sigma 2.77987 error +## value type +## parent_0 89.850000 state +## alpha 1.000000 deparm +## beta 10.000000 deparm +## sigma 2.779868 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 +## sigma 2.779868 0 Inf ## ## Fixed parameter values: ## None @@ -253,16 +253,16 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## 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 +## log_alpha 10.66 NaN NaN NaN +## log_beta 13.01 NaN NaN NaN +## sigma 2.78 0.4599 1.794 3.766 ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000000 NaN NaN 0.008714 +## parent_0 1.000000 NaN NaN 0.003475 ## log_alpha NaN 1 NaN NaN ## log_beta NaN NaN 1 NaN -## sigma 0.008714 NaN NaN 1.000000 +## sigma 0.003475 NaN NaN 1.000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -270,11 +270,11 @@ ## for estimators of untransformed parameters. ## 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 +## alpha 42700.00 0.02298 4.910e-01 NA NA +## beta 446600.00 0.02298 4.910e-01 NA NA +## sigma 2.78 6.00000 1.628e-05 1.794 3.766 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.619 3 6 ## parent 3.619 3 6 @@ -318,19 +318,19 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></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.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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:34 2019 +## Date of summary: Thu May 2 12:40:34 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 240 model solutions performed in 0.564 s +## Fitted using 240 model solutions performed in 0.506 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -373,7 +373,7 @@ ## 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: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 6.205 3 3 ## parent 6.205 3 3 @@ -393,9 +393,9 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></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>(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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:35 2019 +## Date of summary: Thu May 2 12:40:35 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -404,10 +404,10 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method using 585 model solutions performed in 1.296 s +## Fitted using 587 model solutions performed in 1.273 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -431,18 +431,18 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## 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_k1 3.1330 2.265e+03 -5354.0000 5360.0000 ## 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: ## 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 +## parent_0 1.000e+00 5.434e-07 -9.989e-11 2.665e-01 -3.978e-10 +## log_k1 5.434e-07 1.000e+00 8.888e-05 -1.748e-04 -8.207e-06 +## log_k2 -9.989e-11 8.888e-05 1.000e+00 -7.903e-01 5.751e-10 +## g_ilr 2.665e-01 -1.748e-04 -7.903e-01 1.000e+00 -7.109e-10 +## sigma -3.978e-10 -8.207e-06 5.751e-10 -7.109e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -450,19 +450,19 @@ ## 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 23.0000 4.377e-04 4.998e-01 0.0000 Inf +## k1 22.9300 4.514e-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: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.53 4 2 ## parent 2.53 4 2 ## ## Estimated disappearance times: ## DT50 DT90 DT50_k1 DT50_k2 -## parent 0.5335 5.311 0.03014 2.058</code></pre> +## parent 0.5335 5.311 0.03023 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> @@ -492,9 +492,9 @@ <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="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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:37 2019 +## Date of summary: Thu May 2 12:40:37 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -503,10 +503,10 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method using 372 model solutions performed in 0.809 s +## Fitted using 372 model solutions performed in 0.777 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -537,11 +537,11 @@ ## ## Parameter correlation: ## 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 +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 1.660e-07 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 6.635e-08 +## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 3.880e-07 +## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -3.822e-07 +## sigma 1.660e-07 6.635e-08 3.880e-07 -3.822e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -554,7 +554,7 @@ ## 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: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.225 4 4 ## parent 2.225 4 4 @@ -597,19 +597,19 @@ <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="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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:38 2019 +## Date of summary: Thu May 2 12:40:38 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 146 model solutions performed in 0.306 s +## Fitted using 146 model solutions performed in 0.298 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -634,9 +634,9 @@ ## ## Parameter correlation: ## 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 +## parent_0 1.000e+00 5.938e-01 4.256e-10 +## log_k_parent_sink 5.938e-01 1.000e+00 -7.280e-10 +## sigma 4.256e-10 -7.280e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -647,7 +647,7 @@ ## 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: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.287 2 6 ## parent 3.287 2 6 @@ -661,19 +661,19 @@ ## parent 106 352</code></pre> <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 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:38 2019 +## Date of summary: Thu May 2 12:40:38 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 224 model solutions performed in 0.478 s +## Fitted using 224 model solutions performed in 0.458 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -701,10 +701,10 @@ ## ## Parameter correlation: ## 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 +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.473e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.429e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 5.183e-08 +## sigma -2.473e-07 2.429e-08 5.183e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -716,7 +716,7 @@ ## 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: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.029 3 5 ## parent 2.029 3 5 |