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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 7b35beeb..4033beba 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -90,7 +90,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -116,8 +116,8 @@ <a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:52:57 2019 -## Date of summary: Thu Sep 19 09:52:57 2019 +## Date of fit: Fri Nov 1 10:10:46 2019 +## Date of summary: Fri Nov 1 10:10:46 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -131,16 +131,14 @@ ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.850000 state -## k_parent_sink 0.100000 deparm -## sigma 2.779827 error +## value type +## parent_0 89.85 state +## k_parent_sink 0.10 deparm ## ## 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 @@ -214,12 +212,12 @@ <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://rdrr.io/r/base/summary.html">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$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:52:59 2019 -## Date of summary: Thu Sep 19 09:52:59 2019 +## Date of fit: Fri Nov 1 10:10:48 2019 +## Date of summary: Fri Nov 1 10:10:48 2019 ## ## ## Warning: Optimisation did not converge: @@ -231,25 +229,23 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 899 model solutions performed in 1.908 s +## Fitted using 899 model solutions performed in 1.91 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.850000 state -## alpha 1.000000 deparm -## beta 10.000000 deparm -## sigma 2.779871 error +## value type +## parent_0 89.85 state +## alpha 1.00 deparm +## beta 10.00 deparm ## ## 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 2.779871 0 Inf ## ## Fixed parameter values: ## None @@ -323,33 +319,31 @@ <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://rdrr.io/r/base/summary.html">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: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:00 2019 -## Date of summary: Thu Sep 19 09:53:00 2019 +## Date of fit: Fri Nov 1 10:10:49 2019 +## Date of summary: Fri Nov 1 10:10:49 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 239 model solutions performed in 0.49 s +## Fitted using 239 model solutions performed in 0.489 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 93.950000 state -## alpha 1.000000 deparm -## beta 10.000000 deparm -## sigma 2.275722 error +## value type +## parent_0 93.95 state +## alpha 1.00 deparm +## beta 10.00 deparm ## ## 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 @@ -399,8 +393,8 @@ <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://rdrr.io/r/base/summary.html">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: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:02 2019 -## Date of summary: Thu Sep 19 09:53:02 2019 +## Date of fit: Fri Nov 1 10:10:51 2019 +## Date of summary: Fri Nov 1 10:10:51 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -409,19 +403,18 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 1.204 s +## Fitted using 572 model solutions performed in 1.218 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 93.950000 state -## k1 0.100000 deparm -## k2 0.010000 deparm -## g 0.500000 deparm -## sigma 1.413899 error +## value type +## parent_0 93.95 state +## k1 0.10 deparm +## k2 0.01 deparm +## g 0.50 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -429,7 +422,6 @@ ## 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 @@ -499,8 +491,8 @@ <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://rdrr.io/r/base/summary.html">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: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:04 2019 -## Date of summary: Thu Sep 19 09:53:04 2019 +## Date of fit: Fri Nov 1 10:10:53 2019 +## Date of summary: Fri Nov 1 10:10:53 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -509,19 +501,18 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.799 s +## Fitted using 373 model solutions performed in 0.784 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 97.800000 state -## k1 0.100000 deparm -## k2 0.010000 deparm -## g 0.500000 deparm -## sigma 1.017292 error +## value type +## parent_0 97.80 state +## k1 0.10 deparm +## k2 0.01 deparm +## g 0.50 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -529,7 +520,6 @@ ## 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 @@ -605,31 +595,29 @@ <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://rdrr.io/r/base/summary.html">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: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:04 2019 -## Date of summary: Thu Sep 19 09:53:05 2019 +## Date of fit: Fri Nov 1 10:10:53 2019 +## Date of summary: Fri Nov 1 10:10:54 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.287 s +## Fitted using 142 model solutions performed in 0.292 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 96.60000 state -## k_parent_sink 0.10000 deparm -## sigma 3.16181 error +## value type +## parent_0 96.6 state +## k_parent_sink 0.1 deparm ## ## 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 @@ -670,33 +658,31 @@ <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://rdrr.io/r/base/summary.html">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: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:05 2019 -## Date of summary: Thu Sep 19 09:53:05 2019 +## Date of fit: Fri Nov 1 10:10:54 2019 +## Date of summary: Fri Nov 1 10:10:54 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.48 s +## Fitted using 224 model solutions performed in 0.455 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 96.600000 state -## alpha 1.000000 deparm -## beta 10.000000 deparm -## sigma 1.830055 error +## value type +## parent_0 96.6 state +## alpha 1.0 deparm +## beta 10.0 deparm ## ## 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 @@ -746,6 +732,7 @@ </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> |