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authorJohannes Ranke <jranke@uni-bremen.de>2016-06-28 00:44:48 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-06-28 01:30:00 +0200
commitef7ccf68e086bac3e75858bd4b97e3a2c6872aa1 (patch)
treee1b9e55736b0961843e84c60caeb9117e1c35c6d /inst/web/plot.mkinfit.html
parent4672c2b3fd6c22e63b00ee5038998dd68a885c25 (diff)
Avoid multicore fits in vignettes for passing CRAN checks
Also a small fix to the FOCUS Z vignette, and an update of the static documentation generated by staticdocs.
Diffstat (limited to 'inst/web/plot.mkinfit.html')
-rw-r--r--inst/web/plot.mkinfit.html82
1 files changed, 61 insertions, 21 deletions
diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html
index 1da0c8e8..9642b345 100644
--- a/inst/web/plot.mkinfit.html
+++ b/inst/web/plot.mkinfit.html
@@ -2,7 +2,7 @@
<html lang="en">
<head>
<meta charset="utf-8">
-<title>plot.mkinfit. mkin 0.9.42</title>
+<title>plot.mkinfit. mkin 0.9.43</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="
Johannes Ranke
@@ -34,7 +34,7 @@
<div class="navbar">
<div class="navbar-inner">
<div class="container">
- <a class="brand" href="#">mkin 0.9.42</a>
+ <a class="brand" href="#">mkin 0.9.43</a>
<div class="nav">
<ul class="nav">
<li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
@@ -56,7 +56,8 @@
<div class="row">
<div class="span8">
<h2>Usage</h2>
- <pre><div>"plot"(x, fit&nbsp;=&nbsp;x, obs_vars&nbsp;=&nbsp;names(fit$mkinmod$map), xlab&nbsp;=&nbsp;"Time", ylab&nbsp;=&nbsp;"Observed", xlim&nbsp;=&nbsp;range(fit$data$time), ylim&nbsp;=&nbsp;"default", col_obs&nbsp;=&nbsp;1:length(fit$mkinmod$map), pch_obs&nbsp;=&nbsp;col_obs, lty_obs&nbsp;=&nbsp;rep(1, length(fit$mkinmod$map)), add&nbsp;=&nbsp;FALSE, legend&nbsp;=&nbsp;!add, show_residuals&nbsp;=&nbsp;FALSE, maxabs&nbsp;=&nbsp;"auto", lpos&nbsp;=&nbsp;"topright", inset&nbsp;=&nbsp;c(0.05, 0.05), ...)</div></pre>
+ <pre><div>"plot"(x, fit&nbsp;=&nbsp;x, obs_vars&nbsp;=&nbsp;names(fit$mkinmod$map), xlab&nbsp;=&nbsp;"Time", ylab&nbsp;=&nbsp;"Observed", xlim&nbsp;=&nbsp;range(fit$data$time), ylim&nbsp;=&nbsp;"default", col_obs&nbsp;=&nbsp;1:length(obs_vars), pch_obs&nbsp;=&nbsp;col_obs, lty_obs&nbsp;=&nbsp;rep(1, length(obs_vars)), add&nbsp;=&nbsp;FALSE, legend&nbsp;=&nbsp;!add, show_residuals&nbsp;=&nbsp;FALSE, maxabs&nbsp;=&nbsp;"auto", sep_obs&nbsp;=&nbsp;FALSE, rel.height.middle&nbsp;=&nbsp;0.9, lpos&nbsp;=&nbsp;"topright", inset&nbsp;=&nbsp;c(0.05, 0.05), show_errmin&nbsp;=&nbsp;FALSE, errmin_digits&nbsp;=&nbsp;3, ...)
+plot_sep(fit, sep_obs&nbsp;=&nbsp;TRUE, show_residuals&nbsp;=&nbsp;TRUE, show_errmin&nbsp;=&nbsp;TRUE, ...)</div></pre>
<h2>Arguments</h2>
<dl>
@@ -66,7 +67,7 @@
</dd>
<dt>fit</dt>
<dd>
- an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+ An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
</dd>
<dt>obs_vars</dt>
<dd>
@@ -76,60 +77,81 @@
</dd>
<dt>xlab</dt>
<dd>
- label for the x axis.
+ Label for the x axis.
</dd>
<dt>ylab</dt>
<dd>
- label for the y axis.
+ Label for the y axis.
</dd>
<dt>xlim</dt>
<dd>
- plot range in x direction.
+ Plot range in x direction.
</dd>
<dt>ylim</dt>
<dd>
- plot range in y direction.
+ Plot range in y direction.
</dd>
<dt>col_obs</dt>
<dd>
- colors used for plotting the observed data and the corresponding model prediction lines.
+ Colors used for plotting the observed data and the corresponding model prediction lines.
</dd>
<dt>pch_obs</dt>
<dd>
- symbols to be used for plotting the data.
+ Symbols to be used for plotting the data.
</dd>
<dt>lty_obs</dt>
<dd>
- line types to be used for the model predictions.
+ Line types to be used for the model predictions.
</dd>
<dt>add</dt>
<dd>
- should the plot be added to an existing plot?
+ Should the plot be added to an existing plot?
</dd>
<dt>legend</dt>
<dd>
- should a legend be added to the plot?
+ Should a legend be added to the plot?
</dd>
<dt>show_residuals</dt>
<dd>
- should residuals be shown in the lower third of the plot?
+ Should residuals be shown? If only one plot of the fits is shown, the
+ residual plot is in the lower third of the plot? Otherwise, i.e. if
+ "sep_obs" is given, the residual plots will be located to the right of
+ the plots of the fitted curves.
</dd>
<dt>maxabs</dt>
<dd>
Maximum absolute value of the residuals. This is used for the scaling of
the y axis and defaults to "auto".
</dd>
+ <dt>sep_obs</dt>
+ <dd>
+ Should the observed variables be shown in separate subplots? If yes, residual plots
+ requested by "show_residuals" will be shown next to, not below the plot of the fits.
+ </dd>
+ <dt>rel.height.middle</dt>
+ <dd>
+ The relative height of the middle plot, if more than two rows of plots are shown.
+ </dd>
<dt>lpos</dt>
<dd>
- position of the legend. Passed to <code><a href='http://www.inside-r.org/r-doc/graphics/legend'>legend</a></code> as the first argument.
+ Position(s) of the legend(s). Passed to <code><a href='http://www.inside-r.org/r-doc/graphics/legend'>legend</a></code> as the first argument.
+ If not length one, this should be of the same length as the obs_var argument.
</dd>
<dt>inset</dt>
<dd>
Passed to <code><a href='http://www.inside-r.org/r-doc/graphics/legend'>legend</a></code> if applicable.
</dd>
+ <dt>show_errmin</dt>
+ <dd>
+ Should the FOCUS chi2 error value be shown in the upper margin of the plot?
+ </dd>
+ <dt>errmin_digits</dt>
+ <dd>
+ The number of significant digits for rounding the FOCUS chi2 error percentage.
+ </dd>
<dt>...</dt>
<dd>
- further arguments passed to <code><a href='http://www.inside-r.org/r-doc/graphics/plot'>plot</a></code>.
+ Further arguments passed to <code><a href='http://www.inside-r.org/r-doc/graphics/plot'>plot</a></code>.
</dd>
</dl>
@@ -153,22 +175,40 @@
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'># One parent compound, one metabolite, both single first order, path from
-# parent to sink included
+# parent to sink included, use Levenberg-Marquardt for speed
SFO_SFO &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;, full = &quot;Parent&quot;),
m1 = mkinsub(&quot;SFO&quot;, full = &quot;Metabolite M1&quot; ))
</div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'>fit &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+<div class='input'>fit &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = &quot;Marq&quot;)
plot(fit)
</div>
-<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p></pre>
+<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p>
+<div class='input'>plot(fit, show_residuals = TRUE)
+</div>
+<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p>
+<div class='input'>
+# Show the observed variables separately
+plot(fit, sep_obs = TRUE, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;))
+</div>
+<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p>
+<div class='input'>
+# Show the observed variables separately, with residuals
+plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;),
+ show_errmin = TRUE)
+</div>
+<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p>
+<div class='input'>
+# The same can be obtained with less typing, using the convenience function plot_sep
+plot_sep(fit, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;))
+</div></pre>
</div>
<div class="span4">
<!-- <ul>
- <li>plot.mkinfit</li>
+ <li>plot.mkinfit</li><li>plot_sep</li>
</ul>
<ul>
- <li> hplot </li>
+
</ul> -->

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