Better initials for error model parameters

- Also make it possible to specify initial values for error model
parameters.
- Run tests
- Rebuild docs

1 files changed, 9 insertions, 9 deletions

diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 33d0c90f..950e8eab 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
       <h1>Example evaluation of FOCUS dataset Z</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_Z.Rmd</code></div>
@@ -132,11 +132,11 @@
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p>
 <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
 <pre><code>##             Estimate se_notrans    t value     Pr(&gt;t)    Lower    Upper
-## Z0_0      9.7015e+01    3.39373 2.8587e+01 6.4606e-21 91.66556 102.3642
-## k_Z0_sink 4.0181e-10    0.22534 1.7831e-09 5.0000e-01  0.00000      Inf
-## k_Z0_Z1   2.2360e+00    0.15915 1.4050e+01 1.1387e-13  1.95303   2.5600
-## k_Z1_sink 4.8212e-01    0.06547 7.3641e+00 5.1396e-08  0.40341   0.5762
-## sigma     4.8041e+00    0.63763 7.5343e+00 3.4444e-08  3.52677   6.0815</code></pre>
+## Z0_0      9.7015e+01   3.394776 2.8578e+01 6.5093e-21 91.66556 102.3642
+## k_Z0_sink 4.0301e-10   0.225510 1.7871e-09 5.0000e-01  0.00000      Inf
+## k_Z0_Z1   2.2360e+00   0.159161 1.4049e+01 1.1412e-13  1.95303   2.5600
+## k_Z1_sink 4.8212e-01   0.065499 7.3608e+00 5.1791e-08  0.40341   0.5762
+## sigma     4.8041e+00   0.637657 7.5340e+00 3.4468e-08  3.52677   6.0815</code></pre>
 <p>As obvious from the parameter summary (the  component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p>
 <p>A similar result can be obtained when formation fractions are used in the model formulation:</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">Z<span class="fl">.2</span>a.ff &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a>
@@ -335,14 +335,14 @@
 ## 
 ## $SFORB
 ##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 2.4471355 0.0075125 0.0800068 0.0000000 
+## 2.4471329 0.0075123 0.0800074 0.0000000 
 ## 
 ## $distimes
 ##      DT50   DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3043 1.1848    0.28325     92.266         NA         NA
+## Z0 0.3043 1.1848    0.28325     92.268         NA         NA
 ## Z1 1.5148 5.0320         NA         NA         NA         NA
 ## Z2 1.6414 5.4526         NA         NA         NA         NA
-## Z3     NA     NA         NA         NA     8.6636        Inf</code></pre>
+## Z3     NA     NA         NA         NA     8.6635        Inf</code></pre>
 <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p>
 </div>
 <div id="references" class="section level1">