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authorJohannes Ranke <jranke@uni-bremen.de>2018-07-18 15:18:30 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-07-18 15:58:46 +0200
commit0b98c459c30a0629a728acf6b311de035c55fb64 (patch)
treef146faf4802da38862aa14b0268265f3fad9ba34 /docs/reference/mkinfit.html
parentd3ed95f2a0a43ed74b02ea90e35d043ed4e1e72f (diff)
Correct references to the Rocke and Lorenzato model
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html23
1 files changed, 13 insertions, 10 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index d0b54098..9e59c7e6 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
</span>
</div>
@@ -367,11 +367,14 @@
<code>reweight.tol</code> or up to the maximum number of iterations
specified by <code>reweight.max.iter</code>.
The second reweighting method is called "tc" (two-component error model).
- When using this method, the two components of the error model according
- to Rocke and Lorenzato (1995) are estimated from the fit and the resulting
+ When using this method, the two components an error model similar to
+ Rocke and Lorenzato (1995) are estimated from the fit and the resulting
variances are used for weighting the residuals in each iteration until
convergence of these components or up to the maximum number of iterations
- specified.</p></td>
+ specified. Note that this method deviates from the model by Rocke and
+ Lorenzato, as their model implies that the errors follow a lognormal
+ distribution for large values, not a normal distribution as assumed by this
+ method.</p></td>
</tr>
<tr>
<th>reweight.tol</th>
@@ -427,17 +430,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.1
-#&gt; R version used for fitting: 3.5.0
-#&gt; Date of fit: Wed Jun 6 01:21:36 2018
-#&gt; Date of summary: Wed Jun 6 01:21:36 2018
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Wed Jul 18 15:16:04 2018
+#&gt; Date of summary: Wed Jul 18 15:16:04 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.143 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.134 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -506,7 +509,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.927 0.000 0.929 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.863 0.000 0.864 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000

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