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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-11 22:12:51 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-11 22:12:51 +0100
commitd185c26e4909efbae9dc4210ed9eac4b2600910e (patch)
tree7ac9660d439a6de997dac800d09c82404027ef9a /docs/reference/mkinfit.html
parenta0bbfd3291aaa1a55438b8746c1e3cfb58ce4172 (diff)
Static docs rebuilt again, with current pkgdown
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html23
1 files changed, 19 insertions, 4 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 10052053..991df1cc 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -27,6 +27,20 @@
<script src="../pkgdown.js"></script>
+<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" />
+
+<meta property="og:description" content="This function uses the Flexible Modelling Environment package
+ FME to create a function calculating the model cost, i.e. the
+ deviation between the kinetic model and the observed data. This model cost is
+ then minimised using the Port algorithm nlminb,
+ using the specified initial or fixed parameters and starting values.
+ Per default, parameters in the kinetic models are internally transformed in order
+ to better satisfy the assumption of a normal distribution of their estimators.
+ In each step of the optimsation, the kinetic model is solved using the
+ function mkinpredict. The variance of the residuals for each
+ observed variable can optionally be iteratively reweighted until convergence
+ using the argument reweight.method = "obs"." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -400,15 +414,15 @@
<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: 3.4.3
-#&gt; Date of fit: Fri Mar 9 23:08:20 2018
-#&gt; Date of summary: Fri Mar 9 23:08:20 2018
+#&gt; Date of fit: Sun Mar 11 22:10:32 2018
+#&gt; Date of summary: Sun Mar 11 22:10:32 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 0.148 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.135 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -477,7 +491,7 @@
<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 elapsed
-#&gt; 0.839 0.000 0.840 </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; 0.829 0.000 0.829 </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
@@ -585,3 +599,4 @@
</body>
</html>
+

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