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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-03 10:39:34 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-03 10:39:34 +0100
commit5aec8e34680e05671347f7577ae36c9ad8e37063 (patch)
tree2cfc0f696cc202e9c9a7b7951930bfe88c355d23 /docs/reference/plot.mkinfit.html
parent7ceb1dc732ac8674dd8dd70b798fe12378ec10af (diff)
parent8650f26f63a64ac8b72326e2679719744ac99f07 (diff)
Merge branch 'master' of kolab:mkin
Diffstat (limited to 'docs/reference/plot.mkinfit.html')
-rw-r--r--docs/reference/plot.mkinfit.html27
1 files changed, 17 insertions, 10 deletions
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 0af2bbf6..4bdad93f 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -18,12 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
+<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters
+ from a previous successful call to mkinfit and plots
+ the observed data together with the solution of the fitted model.
+If the current plot device is a tikz device,
+ then latex is being used for the formatting of the chi2 error level,
+ if show_errmin = TRUE." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +98,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -237,12 +244,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
<span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
-<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># Show the observed variables separately</span>
-<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># Show the observed variables separately, with residuals</span>
<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
- <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /><div class='input'>
+ <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span>
<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre>
</div>
@@ -269,7 +276,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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