diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/plot.mkinfit.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/plot.mkinfit.html')
| -rw-r--r-- | docs/reference/plot.mkinfit.html | 472 |
1 files changed, 185 insertions, 287 deletions
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index ff6da93e..0ad6ffc0 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script 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initial-scale=1.0"><title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><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." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +observed data together with the solution of the fitted model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,13 +19,12 @@ observed data together with the solution of the fitted model." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -89,8 +33,7 @@ observed data together with the solution of the fitted model." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,6 +43,9 @@ observed data together with the solution of the fitted model." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -114,279 +60,231 @@ observed data together with the solution of the fitted model." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mkinfit.R" class="external-link"><code>R/plot.mkinfit.R</code></a></small> <div class="hidden name"><code>plot.mkinfit.Rd</code></div> </div> <div class="ref-description"> <p>Solves the differential equations with the optimised and fixed parameters -from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the +from a previous successful call to <code><a href="mkinfit.html">mkinfit</a></code> and plots the observed data together with the solution of the fitted model.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> - <span class='va'>x</span>, - fit <span class='op'>=</span> <span class='va'>x</span>, - obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, - xlab <span class='op'>=</span> <span class='st'>"Time"</span>, - ylab <span class='op'>=</span> <span class='st'>"Residue"</span>, - xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>, - ylim <span class='op'>=</span> <span class='st'>"default"</span>, - col_obs <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>obs_vars</span><span class='op'>)</span>, - pch_obs <span class='op'>=</span> <span class='va'>col_obs</span>, - lty_obs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>obs_vars</span><span class='op'>)</span><span class='op'>)</span>, - add <span class='op'>=</span> <span class='cn'>FALSE</span>, - legend <span class='op'>=</span> <span class='op'>!</span><span class='va'>add</span>, - show_residuals <span class='op'>=</span> <span class='cn'>FALSE</span>, - show_errplot <span class='op'>=</span> <span class='cn'>FALSE</span>, - maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, - sep_obs <span class='op'>=</span> <span class='cn'>FALSE</span>, - rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>, - row_layout <span class='op'>=</span> <span class='cn'>FALSE</span>, - lpos <span class='op'>=</span> <span class='st'>"topright"</span>, - inset <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.05</span>, <span class='fl'>0.05</span><span class='op'>)</span>, - show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span>, - errmin_digits <span class='op'>=</span> <span class='fl'>3</span>, - frame <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='fu'>plot_sep</span><span class='op'>(</span> - <span class='va'>fit</span>, - show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>, - show_residuals <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>err_mod</span>, <span class='st'>"const"</span><span class='op'>)</span>, <span class='cn'>TRUE</span>, <span class='st'>"standardized"</span><span class='op'>)</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='fu'>plot_res</span><span class='op'>(</span> - <span class='va'>fit</span>, - sep_obs <span class='op'>=</span> <span class='cn'>FALSE</span>, - show_errmin <span class='op'>=</span> <span class='va'>sep_obs</span>, - standardized <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>err_mod</span>, <span class='st'>"const"</span><span class='op'>)</span>, <span class='cn'>FALSE</span>, <span class='cn'>TRUE</span><span class='op'>)</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='fu'>plot_err</span><span class='op'>(</span><span class='va'>fit</span>, sep_obs <span class='op'>=</span> <span class='cn'>FALSE</span>, show_errmin <span class='op'>=</span> <span class='va'>sep_obs</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span> + <span class="va">x</span>, + fit <span class="op">=</span> <span class="va">x</span>, + obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>, + xlab <span class="op">=</span> <span class="st">"Time"</span>, + ylab <span class="op">=</span> <span class="st">"Residue"</span>, + xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>, + ylim <span class="op">=</span> <span class="st">"default"</span>, + col_obs <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span>, + pch_obs <span class="op">=</span> <span class="va">col_obs</span>, + lty_obs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">obs_vars</span><span class="op">)</span><span class="op">)</span>, + add <span class="op">=</span> <span class="cn">FALSE</span>, + legend <span class="op">=</span> <span class="op">!</span><span class="va">add</span>, + show_residuals <span class="op">=</span> <span class="cn">FALSE</span>, + show_errplot <span class="op">=</span> <span class="cn">FALSE</span>, + maxabs <span class="op">=</span> <span class="st">"auto"</span>, + sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, + rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>, + row_layout <span class="op">=</span> <span class="cn">FALSE</span>, + lpos <span class="op">=</span> <span class="st">"topright"</span>, + inset <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.05</span>, <span class="fl">0.05</span><span class="op">)</span>, + show_errmin <span class="op">=</span> <span class="cn">FALSE</span>, + errmin_digits <span class="op">=</span> <span class="fl">3</span>, + frame <span class="op">=</span> <span class="cn">TRUE</span>, + <span class="va">...</span> +<span class="op">)</span> + +<span class="fu">plot_sep</span><span class="op">(</span> + <span class="va">fit</span>, + show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, + show_residuals <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">TRUE</span>, <span class="st">"standardized"</span><span class="op">)</span>, + <span class="va">...</span> +<span class="op">)</span> + +<span class="fu">plot_res</span><span class="op">(</span> + <span class="va">fit</span>, + sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, + show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, + standardized <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">err_mod</span>, <span class="st">"const"</span><span class="op">)</span>, <span class="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>, + <span class="va">...</span> +<span class="op">)</span> + +<span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>Alias for fit introduced for compatibility with the generic S3 -method.</p></td> - </tr> - <tr> - <th>fit</th> - <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>obs_vars</th> - <td><p>A character vector of names of the observed variables for + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>Alias for fit introduced for compatibility with the generic S3 +method.</p></dd> +<dt>fit</dt> +<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> +<dt>obs_vars</dt> +<dd><p>A character vector of names of the observed variables for which the data and the model should be plotted. Defauls to all observed -variables in the model.</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>Plot range in x direction.</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>Plot range in y direction.</p></td> - </tr> - <tr> - <th>col_obs</th> - <td><p>Colors used for plotting the observed data and the -corresponding model prediction lines.</p></td> - </tr> - <tr> - <th>pch_obs</th> - <td><p>Symbols to be used for plotting the data.</p></td> - </tr> - <tr> - <th>lty_obs</th> - <td><p>Line types to be used for the model predictions.</p></td> - </tr> - <tr> - <th>add</th> - <td><p>Should the plot be added to an existing plot?</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be added to the plot?</p></td> - </tr> - <tr> - <th>show_residuals</th> - <td><p>Should residuals be shown? If only one plot of the +variables in the model.</p></dd> +<dt>xlab</dt> +<dd><p>Label for the x axis.</p></dd> +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> +<dt>xlim</dt> +<dd><p>Plot range in x direction.</p></dd> +<dt>ylim</dt> +<dd><p>Plot range in y direction.</p></dd> +<dt>col_obs</dt> +<dd><p>Colors used for plotting the observed data and the +corresponding model prediction lines.</p></dd> +<dt>pch_obs</dt> +<dd><p>Symbols to be used for plotting the data.</p></dd> +<dt>lty_obs</dt> +<dd><p>Line types to be used for the model predictions.</p></dd> +<dt>add</dt> +<dd><p>Should the plot be added to an existing plot?</p></dd> +<dt>legend</dt> +<dd><p>Should a legend be added to the plot?</p></dd> +<dt>show_residuals</dt> +<dd><p>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. If this is set to 'standardized', a plot of the residuals divided by the standard deviation -given by the fitted error model will be shown.</p></td> - </tr> - <tr> - <th>show_errplot</th> - <td><p>Should squared residuals and the error model be shown? +given by the fitted error model will be shown.</p></dd> +<dt>show_errplot</dt> +<dd><p>Should squared residuals and the error model be shown? If only one plot of the fits is shown, this 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.</p></td> - </tr> - <tr> - <th>maxabs</th> - <td><p>Maximum absolute value of the residuals. This is used for the -scaling of the y axis and defaults to "auto".</p></td> - </tr> - <tr> - <th>sep_obs</th> - <td><p>Should the observed variables be shown in separate subplots? +be located to the right of the plots of the fitted curves.</p></dd> +<dt>maxabs</dt> +<dd><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></dd> +<dt>sep_obs</dt> +<dd><p>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.</p></td> - </tr> - <tr> - <th>rel.height.middle</th> - <td><p>The relative height of the middle plot, if more -than two rows of plots are shown.</p></td> - </tr> - <tr> - <th>row_layout</th> - <td><p>Should we use a row layout where the residual plot or the -error model plot is shown to the right?</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as +to, not below the plot of the fits.</p></dd> +<dt>rel.height.middle</dt> +<dd><p>The relative height of the middle plot, if more +than two rows of plots are shown.</p></dd> +<dt>row_layout</dt> +<dd><p>Should we use a row layout where the residual plot or the +error model plot is shown to the right?</p></dd> +<dt>lpos</dt> +<dd><p>Position(s) of the legend(s). Passed to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code> as the first argument. If not length one, this should be of the same length -as the obs_var argument.</p></td> - </tr> - <tr> - <th>inset</th> - <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td> - </tr> - <tr> - <th>show_errmin</th> - <td><p>Should the FOCUS chi2 error value be shown in the upper -margin of the plot?</p></td> - </tr> - <tr> - <th>errmin_digits</th> - <td><p>The number of significant digits for rounding the FOCUS -chi2 error percentage.</p></td> - </tr> - <tr> - <th>frame</th> - <td><p>Should a frame be drawn around the plots?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>When calling 'plot_res', should the residuals be -standardized in the residual plot?</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - +as the obs_var argument.</p></dd> +<dt>inset</dt> +<dd><p>Passed to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code> if applicable.</p></dd> +<dt>show_errmin</dt> +<dd><p>Should the FOCUS chi2 error value be shown in the upper +margin of the plot?</p></dd> +<dt>errmin_digits</dt> +<dd><p>The number of significant digits for rounding the FOCUS +chi2 error percentage.</p></dd> +<dt>frame</dt> +<dd><p>Should a frame be drawn around the plots?</p></dd> +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> +<dt>standardized</dt> +<dd><p>When calling 'plot_res', should the residuals be +standardized in the residual plot?</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then + </div> + <div id="details"> + <h2>Details</h2> + <p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then latex is being used for the formatting of the chi2 error level, if <code>show_errmin = TRUE</code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># One parent compound, one metabolite, both single first order, path from</span> -<span class='co'># parent to sink included</span> -<span class='co'># \dontrun{</span> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full <span class='op'>=</span> <span class='st'>"Parent"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, full <span class='op'>=</span> <span class='st'>"Metabolite M1"</span> <span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span><span class='op'>(</span><span class='va'>fit</span>, standardized <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Show the observed variables separately, with residuals</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span>, - show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></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='op'>(</span><span class='va'>fit</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Show the observed variables separately, with the error model</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_errplot <span class='op'>=</span> <span class='cn'>TRUE</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span>, - show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mkinfit-7.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> +<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order, path from</span></span> +<span class="r-in"><span class="co"># parent to sink included</span></span> +<span class="r-in"><span class="co"># \dontrun{</span></span> +<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span> +<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-4.png" alt="" width="700" height="433"></span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># Show the observed variables separately, with residuals</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span> +<span class="r-in"> show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-5.png" alt="" width="700" height="433"></span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># The same can be obtained with less typing, using the convenience function plot_sep</span></span> +<span class="r-in"><span class="fu">plot_sep</span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-6.png" alt="" width="700" height="433"></span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># Show the observed variables separately, with the error model</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_errplot <span class="op">=</span> <span class="cn">TRUE</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span>,</span> +<span class="r-in"> show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-plt img"><img src="plot.mkinfit-7.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |