Fix bug in yesterdays release, add methods for BIC

1 files changed, 52 insertions, 65 deletions

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>