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@@ -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 &lt;-<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(&gt;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(&gt;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

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