diff options
Diffstat (limited to 'docs/reference/plot.mkinfit.html')
| -rw-r--r-- | docs/reference/plot.mkinfit.html | 203 |
1 files changed, 103 insertions, 100 deletions
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index e77b7b54..2126c36d 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — plot.mkinfit • mkin</title> +<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -26,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> <body> @@ -71,6 +72,9 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> <li> @@ -96,21 +100,19 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot the observed data and the fitted model of an mkinfit object</h1> </div> <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 observed data together with the solution of the fitted model.</p> - - <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device, +<p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device, then latex is being used for the formatting of the chi2 error level, if <code>show_errmin = TRUE</code>.</p> - <pre># S3 method for mkinfit + <pre class="usage"># S3 method for mkinfit plot(x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed", @@ -126,100 +128,101 @@ plot(x, fit = x, plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>x</dt> - <dd> - Alias for fit introduced for compatibility with the generic S3 method. - </dd> - <dt>fit</dt> - <dd> - An object of class <code><a href='mkinfit.html'>mkinfit</a></code>. - </dd> - <dt>obs_vars</dt> - <dd> - A character vector of names of the observed variables for which the + <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 which the data and the model should be plotted. Defauls to all observed variables - in the model. - </dd> - <dt>xlab</dt> - <dd> - Label for the x axis. - </dd> - <dt>ylab</dt> - <dd> - Label for the y axis. - </dd> - <dt>xlim</dt> - <dd> - Plot range in x direction. - </dd> - <dt>ylim</dt> - <dd> - Plot range in y direction. - </dd> - <dt>col_obs</dt> - <dd> - 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. - </dd> - <dt>lty_obs</dt> - <dd> - Line types to be used for the model predictions. - </dd> - <dt>add</dt> - <dd> - Should the plot be added to an existing plot? - </dd> - <dt>legend</dt> - <dd> - Should a legend be added to the plot? - </dd> - <dt>show_residuals</dt> - <dd> - Should residuals be shown? If only one plot of the fits is shown, the + 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 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(s) of the legend(s). Passed to <code>legend</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>legend</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>plot</code>. - </dd> - </dl> + "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? 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>lpos</th> + <td><p>Position(s) of the legend(s). Passed to <code>legend</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>legend</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>…</th> + <td><p>Further arguments passed to <code>plot</code>.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |