diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-06-28 00:44:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-06-28 01:30:00 +0200 |
| commit | ef7ccf68e086bac3e75858bd4b97e3a2c6872aa1 (patch) | |
| tree | e1b9e55736b0961843e84c60caeb9117e1c35c6d /inst/web/plot.mkinfit.html | |
| parent | 4672c2b3fd6c22e63b00ee5038998dd68a885c25 (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.html | 82 |
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 = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", lpos = "topright", inset = c(0.05, 0.05), ...)</div></pre> + <pre><div>"plot"(x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs, lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE, errmin_digits = 3, ...) +plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = 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 <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), m1 = mkinsub("SFO", full = "Metabolite M1" )) </div> <strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> -<div class='input'>fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +<div class='input'>fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq") 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("topright", "bottomright")) +</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("topright", "bottomright"), + 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("topright", "bottomright")) +</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> --> |