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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 0060bd69..73ea645a 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">0.9.49.5</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</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">2019-07-04</h4> + <h4 class="date">2019-07-05</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -112,59 +112,54 @@ <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: 0.9.49.5 +<pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.6.0 -## Date of fit: Thu Jul 4 08:04:26 2019 -## Date of summary: Thu Jul 4 08:04:26 2019 +## Date of fit: Fri Jul 5 15:52:52 2019 +## Date of summary: Fri Jul 5 15:52:52 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.278 s +## Fitted with method Port using 37 model solutions performed in 0.084 s ## -## Error model: Constant variance -## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## 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 +## parent_0 92.470 1.36800 89.570 95.370 +## log_k_parent_sink -2.347 0.04057 -2.433 -2.261 ## ## Parameter correlation: -## 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 +## 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 ## ## 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 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 +## 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 ## -## FOCUS Chi2 error levels in percent: +## Chi2 error levels in percent: ## err.min n.optim df ## All data 3.424 2 7 ## parent 3.424 2 7 @@ -205,22 +200,18 @@ <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></code></pre></div> -<pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge: +<pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port 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="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: 0.9.49.5 +<pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.6.0 -## Date of fit: Thu Jul 4 08:04:28 2019 -## Date of summary: Thu Jul 4 08:04:28 2019 +## Date of fit: Fri Jul 5 15:52:54 2019 +## Date of summary: Fri Jul 5 15:52:54 2019 ## ## -## Warning: Optimisation did not converge: +## Warning: Optimisation by method Port did not converge: ## false convergence (8) ## ## @@ -229,54 +220,49 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 899 model solutions performed in 1.876 s +## Fitted with method Port using 741 model solutions performed in 1.637 s ## -## Error model: Constant variance -## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 92.47 1.2800 89.730 95.220 -## log_alpha 10.58 NaN NaN NaN -## log_beta 12.93 NaN NaN NaN -## sigma 2.78 0.4507 1.813 3.747 +## Estimate Std. Error Lower Upper +## parent_0 92.47 1.454 89.37 95.57 +## log_alpha 10.58 1164.000 -2471.00 2492.00 +## log_beta 12.93 1164.000 -2469.00 2495.00 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.00000 NaN NaN 0.01452 -## log_alpha NaN 1 NaN NaN -## log_beta NaN NaN 1 NaN -## sigma 0.01452 NaN NaN 1.00000 +## parent_0 log_alpha log_beta +## parent_0 1.0000 0.2361 0.2361 +## log_alpha 0.2361 1.0000 1.0000 +## log_beta 0.2361 1.0000 1.0000 +## +## Residual standard error: 3.045 on 15 degrees of freedom ## ## 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 72.13000 1.052e-19 89.730 95.220 -## alpha 39440.00 0.02397 4.906e-01 NA NA -## beta 412500.00 0.02397 4.906e-01 NA NA -## sigma 2.78 6.00000 1.628e-05 1.813 3.747 +## Estimate t value Pr(>t) Lower Upper +## parent_0 92.47 65.32000 3.886e-20 89.37 95.57 +## alpha 39440.00 0.01639 4.936e-01 0.00 Inf +## beta 412500.00 0.01639 4.936e-01 0.00 Inf ## -## FOCUS Chi2 error levels in percent: +## Chi2 error levels in percent: ## err.min n.optim df ## All data 3.619 3 6 ## parent 3.619 3 6 @@ -292,19 +278,19 @@ <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="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 class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" 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="cb11-2" 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="cb11-3" 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="cb11-4" 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="cb11-5" 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="cb11-6" 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="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> +<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" 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="cb12-2" 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="cb12-3" 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> @@ -314,69 +300,64 @@ <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="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> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" 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="cb13-2" 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="cb13-3" 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="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: 0.9.49.5 +<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.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: 3.6.0 -## Date of fit: Thu Jul 4 08:04:29 2019 -## Date of summary: Thu Jul 4 08:04:29 2019 +## Date of fit: Fri Jul 5 15:52:55 2019 +## Date of summary: Fri Jul 5 15:52:55 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 0.486 s -## -## Error model: Constant variance +## Fitted with method Port using 81 model solutions performed in 0.178 s ## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 ## ## Optimised, transformed parameters with symmetric confidence intervals: -## 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 +## 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 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.637e-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 -1.387e-07 -## sigma -7.637e-09 -1.617e-07 -1.387e-07 1.000e+00 +## 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 ## ## 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 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 +## 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 ## -## FOCUS Chi2 error levels in percent: +## Chi2 error levels in percent: ## err.min n.optim df ## All data 6.205 3 3 ## parent 6.205 3 3 @@ -390,15 +371,17 @@ <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="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> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" 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="cb16-2" 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="cb16-3" 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="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: 0.9.49.5 +<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.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: 3.6.0 -## Date of fit: Thu Jul 4 08:04:30 2019 -## Date of summary: Thu Jul 4 08:04:30 2019 +## Date of fit: Fri Jul 5 15:52:56 2019 +## Date of summary: Fri Jul 5 15:52:56 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -407,19 +390,16 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 1.19 s +## Fitted with method Port using 336 model solutions performed in 0.752 s ## -## Error model: Constant variance -## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 @@ -427,39 +407,32 @@ ## 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 9.998e-01 91.5900 96.3100 -## log_k1 3.1370 2.376e+03 -5616.0000 5622.0000 -## 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 +## 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 ## ## Parameter correlation: -## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 5.155e-07 2.371e-09 2.665e-01 -6.849e-09 -## log_k1 5.155e-07 1.000e+00 8.434e-05 -1.659e-04 -7.791e-06 -## log_k2 2.371e-09 8.434e-05 1.000e+00 -7.903e-01 -1.262e-08 -## g_ilr 2.665e-01 -1.659e-04 -7.903e-01 1.000e+00 3.241e-08 -## sigma -6.849e-09 -7.791e-06 -1.262e-08 3.241e-08 1.000e+00 +## Could not estimate covariance matrix; singular system. +## Residual standard error: 1.732 on 8 degrees of freedom ## ## 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 9.397e+01 2.036e-12 91.5900 96.3100 -## k1 23.0400 4.303e-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 -## -## FOCUS Chi2 error levels in percent: +## 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 +## +## Chi2 error levels in percent: ## err.min n.optim df ## All data 2.53 4 2 ## parent 2.53 4 2 @@ -474,18 +447,18 @@ <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="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 class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" 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="cb20-2" 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="cb20-3" 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="cb20-4" 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="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> +<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> +<a class="sourceLine" id="cb21-2" 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="cb21-3" 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="cb21-4" 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> @@ -494,11 +467,11 @@ <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="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: 0.9.49.5 +<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/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: 3.6.0 -## Date of fit: Thu Jul 4 08:04:32 2019 -## Date of summary: Thu Jul 4 08:04:32 2019 +## Date of fit: Fri Jul 5 15:52:56 2019 +## Date of summary: Fri Jul 5 15:52:57 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -507,19 +480,16 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.773 s +## Fitted with method Port using 137 model solutions performed in 0.305 s ## -## Error model: Constant variance -## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 @@ -527,39 +497,37 @@ ## 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 1.01900 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 +## 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 ## ## 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 -6.872e-07 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 3.200e-07 -## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 7.673e-07 -## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -8.731e-07 -## sigma -6.872e-07 3.200e-07 7.673e-07 -8.731e-07 1.000e+00 +## 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 ## ## 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 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 +## 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 ## -## FOCUS Chi2 error levels in percent: +## Chi2 error levels in percent: ## err.min n.optim df ## All data 2.225 4 4 ## parent 2.225 4 4 @@ -578,7 +546,7 @@ ## 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="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> +<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/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> @@ -588,72 +556,67 @@ <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="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> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" 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="cb25-2" 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="cb25-3" 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="cb25-4" 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="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> +<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> +<a class="sourceLine" id="cb26-2" 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="cb26-3" 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="cb26-4" title="4"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb26-5" 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="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: 0.9.49.5 +<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">"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: 3.6.0 -## Date of fit: Thu Jul 4 08:04:33 2019 -## Date of summary: Thu Jul 4 08:04:33 2019 +## Date of fit: Fri Jul 5 15:52:57 2019 +## Date of summary: Fri Jul 5 15:52:57 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.29 s +## Fitted with method Port using 46 model solutions performed in 0.1 s ## -## Error model: Constant variance -## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## 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 +## parent_0 96.44 1.94900 91.670 101.200 +## log_k_parent_sink -5.03 0.07999 -5.225 -4.834 ## ## Parameter correlation: -## parent_0 log_k_parent_sink sigma -## parent_0 1.000e+00 5.938e-01 3.440e-07 -## log_k_parent_sink 5.938e-01 1.000e+00 5.885e-07 -## sigma 3.440e-07 5.885e-07 1.000e+00 +## 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 ## ## 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 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 +## 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 ## -## FOCUS Chi2 error levels in percent: +## Chi2 error levels in percent: ## err.min n.optim df ## All data 3.287 2 6 ## parent 3.287 2 6 @@ -665,65 +628,60 @@ ## Estimated disappearance times: ## DT50 DT90 ## 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: 0.9.49.5 +<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">"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: 3.6.0 -## Date of fit: Thu Jul 4 08:04:33 2019 -## Date of summary: Thu Jul 4 08:04:33 2019 +## Date of fit: Fri Jul 5 15:52:57 2019 +## Date of summary: Fri Jul 5 15:52:57 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 0.453 s +## Fitted with method Port using 66 model solutions performed in 0.145 s ## -## Error model: Constant variance -## -## Error model algorithm: d_3 +## Weighting: none ## ## 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 ## ## Optimised, transformed parameters with symmetric confidence intervals: -## 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 +## 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 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.563e-07 -## log_alpha -4.696e-01 1.000e+00 9.889e-01 4.066e-08 -## log_beta -5.543e-01 9.889e-01 1.000e+00 6.818e-08 -## sigma -2.563e-07 4.066e-08 6.818e-08 1.000e+00 +## 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 ## ## 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 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 +## 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 ## -## FOCUS Chi2 error levels in percent: +## Chi2 error levels in percent: ## err.min n.optim df ## All data 2.029 3 5 ## parent 2.029 3 5 |