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@@ -31,7 +31,7 @@
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -97,7 +97,7 @@
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-07</h4>
+ <h4 class="date">2020-05-11</h4>
<small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -159,10 +159,10 @@
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div>
-<pre><code>## parent
-## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent"
-## m1
-## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre>
+<pre><code>## parent
+## "d_parent = - k_parent * parent"
+## m1
+## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre>
<p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
@@ -175,85 +175,83 @@
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
-<pre><code>## mkin version used for fitting: 0.9.49.11
+<pre><code>## mkin version used for fitting: 0.9.50
## R version used for fitting: 4.0.0
-## Date of fit: Thu May 7 08:59:27 2020
-## Date of summary: Thu May 7 08:59:27 2020
+## Date of fit: Mon May 11 05:14:41 2020
+## Date of summary: Mon May 11 05:14:41 2020
##
## Equations:
-## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-## d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+## d_parent/dt = - k_parent * parent
+## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
##
-## Model predictions using solution type deSolve
+## Model predictions using solution type analytical
##
-## Fitted using 389 model solutions performed in 1.031 s
+## Fitted using 421 model solutions performed in 0.167 s
##
## Error model: Constant variance
##
## Error model algorithm: OLS
##
## Starting values for parameters to be optimised:
-## value type
-## parent_0 100.7500 state
-## k_parent_sink 0.1000 deparm
-## k_parent_m1 0.1001 deparm
-## k_m1_sink 0.1002 deparm
+## value type
+## parent_0 100.7500 state
+## k_parent 0.1000 deparm
+## k_m1 0.1001 deparm
+## f_parent_to_m1 0.5000 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.750000 -Inf Inf
-## log_k_parent_sink -2.302585 -Inf Inf
-## log_k_parent_m1 -2.301586 -Inf Inf
-## log_k_m1_sink -2.300587 -Inf Inf
+## value lower upper
+## parent_0 100.750000 -Inf Inf
+## log_k_parent -2.302585 -Inf Inf
+## log_k_m1 -2.301586 -Inf Inf
+## f_parent_ilr_1 0.000000 -Inf Inf
##
## Fixed parameter values:
## value type
## m1_0 0 state
##
+## Results:
+##
+## AIC BIC logLik
+## 204.4486 212.6365 -97.22429
+##
## Optimised, transformed parameters with symmetric confidence intervals:
-## Estimate Std. Error Lower Upper
-## parent_0 99.600 1.57000 96.400 102.800
-## log_k_parent_sink -3.038 0.07626 -3.193 -2.883
-## log_k_parent_m1 -2.980 0.04033 -3.062 -2.898
-## log_k_m1_sink -5.248 0.13320 -5.518 -4.977
-## sigma 3.126 0.35850 2.396 3.855
+## Estimate Std. Error Lower Upper
+## parent_0 99.60000 1.57000 96.40000 102.8000
+## log_k_parent -2.31600 0.04087 -2.39900 -2.2330
+## log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
+## f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
+## sigma 3.12600 0.35850 2.39600 3.8550
##
## Parameter correlation:
-## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-## parent_0 1.000e+00 6.067e-01 -6.372e-02 -1.688e-01
-## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -6.252e-01
-## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 4.731e-01
-## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 1.000e+00
-## sigma 5.287e-10 3.306e-09 4.421e-08 -3.319e-10
-## sigma
-## parent_0 5.287e-10
-## log_k_parent_sink 3.306e-09
-## log_k_parent_m1 4.421e-08
-## log_k_m1_sink -3.319e-10
-## sigma 1.000e+00
+## parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma
+## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07
+## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07
+## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07
+## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10
+## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00
##
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
## t-test (unrealistically) based on the assumption of normal distribution
## for estimators of untransformed parameters.
-## Estimate t value Pr(&gt;t) Lower Upper
-## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
-## k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02
-## k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02
-## k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03
-## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
+## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
+## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
##
## FOCUS Chi2 error levels in percent:
## err.min n.optim df
## All data 6.398 4 15
-## parent 6.827 3 6
-## m1 4.490 1 9
+## parent 6.459 2 7
+## m1 4.690 2 8
##
## Resulting formation fractions:
## ff
-## parent_sink 0.4855
## parent_m1 0.5145
-## m1_sink 1.0000
+## parent_sink 0.4855
##
## Estimated disappearance times:
## DT50 DT90
@@ -266,10 +264,10 @@
## 0 parent 102.04 99.59848 2.442e+00
## 1 parent 93.50 90.23787 3.262e+00
## 1 parent 92.50 90.23787 2.262e+00
-## 3 parent 63.23 74.07320 -1.084e+01
-## 3 parent 68.99 74.07320 -5.083e+00
-## 7 parent 52.32 49.91207 2.408e+00
-## 7 parent 55.13 49.91207 5.218e+00
+## 3 parent 63.23 74.07319 -1.084e+01
+## 3 parent 68.99 74.07319 -5.083e+00
+## 7 parent 52.32 49.91206 2.408e+00
+## 7 parent 55.13 49.91206 5.218e+00
## 14 parent 27.27 25.01257 2.257e+00
## 14 parent 26.64 25.01257 1.627e+00
## 21 parent 11.50 12.53462 -1.035e+00
@@ -279,7 +277,7 @@
## 50 parent 0.69 0.71624 -2.624e-02
## 50 parent 0.63 0.71624 -8.624e-02
## 75 parent 0.05 0.06074 -1.074e-02
-## 75 parent 0.06 0.06074 -7.382e-04
+## 75 parent 0.06 0.06074 -7.381e-04
## 1 m1 4.84 4.80296 3.704e-02
## 1 m1 5.64 4.80296 8.370e-01
## 3 m1 12.91 13.02400 -1.140e-01

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