Fix hessian calculations

Static documentation rebuilt by pkgdown

1 files changed, 29 insertions, 21 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 482e48f2..644a35b5 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -163,17 +163,13 @@
 <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
 <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
 <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div>
-<pre><code>## Warning in summary.mkinfit(object): Could not calculate correlation; no
-## covariance matrix</code></pre>
 <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="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
-<pre><code>## Warning in summary.mkinfit(fit): Could not calculate correlation; no
-## covariance matrix</code></pre>
+<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue May  7 08:09:11 2019 
-## Date of summary: Tue May  7 08:09:11 2019 
+## Date of fit:     Tue May  7 08:37:46 2019 
+## Date of summary: Tue May  7 08:37:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -181,7 +177,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 153 model solutions performed in 0.398 s
+## Fitted using 389 model solutions performed in 1.018 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -207,25 +203,37 @@
 ## m1_0     0 state
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
-##                   Estimate Std. Error Lower Upper
-## parent_0            99.600         NA    NA    NA
-## log_k_parent_sink   -3.038         NA    NA    NA
-## log_k_parent_m1     -2.980         NA    NA    NA
-## log_k_m1_sink       -5.248         NA    NA    NA
-## sigma                3.126         NA    NA    NA
+##                   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
 ## 
 ## Parameter correlation:
-## No covariance matrix
+##                     parent_0 log_k_parent_sink log_k_parent_m1
+## parent_0           1.000e+00         6.067e-01      -6.372e-02
+## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02
+## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00
+## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01
+## sigma              1.164e-09        -8.908e-10       1.652e-08
+##                   log_k_m1_sink      sigma
+## parent_0             -1.688e-01  1.164e-09
+## log_k_parent_sink    -6.252e-01 -8.908e-10
+## log_k_parent_m1       4.731e-01  1.652e-08
+## log_k_m1_sink         1.000e+00 -1.340e-10
+## sigma                -1.340e-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      NA     NA    NA    NA
-## k_parent_sink  0.047920      NA     NA    NA    NA
-## k_parent_m1    0.050780      NA     NA    NA    NA
-## k_m1_sink      0.005261      NA     NA    NA    NA
-## sigma          3.126000      NA     NA    NA    NA
+##                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
 ## 
 ## FOCUS Chi2 error levels in percent:
 ##          err.min n.optim df