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authorJohannes Ranke <jranke@uni-bremen.de>2019-05-07 08:43:12 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-05-07 08:43:12 +0200
commitc322a8102a399cbb1fe38c4c4ca4485cea8bc4e8 (patch)
tree892ba3d6db12d7f2c6af55beaa12cc8b43d40df3 /docs/articles/FOCUS_D.html
parent8a3475c59f3d91ce5ce7d980d6de09360617e7fe (diff)
Fix hessian calculations
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/articles/FOCUS_D.html')
-rw-r--r--docs/articles/FOCUS_D.html50
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
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+++ 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

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