diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-10-21 18:52:24 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-10-21 18:54:37 +0200 |
| commit | e09f726134ee273b6b191c1ec6465e6f701b082b (patch) | |
| tree | aabc6bec231fb9dd085deef57a030e41ec398bf4 | |
| parent | bea054418c5310103252f5d243b2d18fcbf7b11f (diff) | |
Improve some plotting routines, more tests
Static documentation rebuilt by pkgdown
21 files changed, 792 insertions, 98 deletions
diff --git a/R/mkinresplot.R b/R/mkinresplot.R index 739a80e9..974d0549 100644 --- a/R/mkinresplot.R +++ b/R/mkinresplot.R @@ -1,4 +1,4 @@ -# Copyright (C) 2008-2014 Johannes Ranke
+# Copyright (C) 2008-2014,2019 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -21,7 +21,10 @@ mkinresplot <- function (object, obs_vars = names(object$mkinmod$map),
xlim = c(0, 1.1 * max(object$data$time)),
xlab = "Time", ylab = "Residual",
- maxabs = "auto", legend= TRUE, lpos = "topright", ...)
+ maxabs = "auto", legend= TRUE, lpos = "topright",
+ col_obs = "auto", pch_obs = "auto",
+ frame = TRUE,
+ ...)
{
obs_vars_all <- as.character(unique(object$data$variable))
@@ -33,10 +36,17 @@ mkinresplot <- function (object, if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
- col_obs <- pch_obs <- 1:length(obs_vars)
+ # Set colors and symbols
+ if (col_obs[1] == "auto") {
+ col_obs <- 1:length(obs_vars)
+ }
+
+ if (pch_obs[1] == "auto") {
+ pch_obs <- 1:length(obs_vars)
+ }
names(col_obs) <- names(pch_obs) <- obs_vars
- plot(0, type = "n",
+ plot(0, type = "n", frame = frame,
xlab = xlab, ylab = ylab,
xlim = xlim,
ylim = c(-1.2 * maxabs, 1.2 * maxabs), ...)
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 2a82301f..e39da416 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -30,8 +30,9 @@ plot.mkinfit <- function(x, fit = x, show_errplot = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, + row_layout = FALSE, lpos = "topright", inset = c(0.05, 0.05), - show_errmin = FALSE, errmin_digits = 3, + show_errmin = FALSE, errmin_digits = 3, frame = TRUE, ...) { if (add && show_residuals) stop("If adding to an existing plot we can not show residuals") @@ -80,8 +81,9 @@ plot.mkinfit <- function(x, fit = x, # Layout should be restored afterwards oldpar <- par(no.readonly = TRUE) - # If the observed variables are shown separately, do row layout - if (sep_obs) { + # If the observed variables are shown separately, or if requested, do row layout + if (sep_obs | row_layout) { + row_layout <- TRUE n_plot_cols = if (show_residuals | show_errplot) 2 else 1 n_plots = n_plot_rows * n_plot_cols @@ -114,7 +116,7 @@ plot.mkinfit <- function(x, fit = x, ylim_row = ylim } - if (sep_obs) { + if (row_layout) { # Margins for top row of plots when we have more than one row # Reduce bottom margin by 2.1 - hides x axis legend if (plot_row == 1 & n_plot_rows > 1) { @@ -186,24 +188,14 @@ plot.mkinfit <- function(x, fit = x, mtext(chi2_text, cex = 0.7, line = 0.4) } + if (do_layout & !row_layout) { + par(mar = c(5, 4, 0, 2) + 0.1) + } + # Show residuals if requested if (show_residuals) { - residuals <- subset(fit$data, variable %in% row_obs_vars, residual) - if (maxabs == "auto") { - maxabs_row = max(abs(residuals), na.rm = TRUE) - } else { - maxabs_row = maxabs - } - if (!sep_obs) par(mar = c(5, 4, 0, 2) + 0.1) - plot(0, type="n", - xlim = xlim, - ylim = c(-1.2 * maxabs_row, 1.2 * maxabs_row), - xlab = xlab, ylab = "Residuals", frame = frame) - for(obs_var in row_obs_vars){ - residuals_plot <- subset(fit$data, variable == obs_var, c("time", "residual")) - points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var]) - } - abline(h = 0, lty = 2) + mkinresplot(fit, obs_vars = row_obs_vars, pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], + legend = FALSE, frame = frame) } # Show error model plot if requested @@ -216,7 +208,15 @@ plot.mkinfit <- function(x, fit = x, } # Convenience function for switching on some features of mkinfit # that have not been made the default to keep compatibility -plot_sep <- function(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, ...) { +plot_sep <- function(fit, show_errmin = TRUE, ...) { plot.mkinfit(fit, sep_obs = TRUE, show_residuals = TRUE, - show_errmin = TRUE, ...) + show_errmin = show_errmin, ...) +} +plot_res <- function(fit, sep_obs = FALSE, show_errmin = sep_obs, ...) { + plot.mkinfit(fit, sep_obs = sep_obs, show_errmin = show_errmin, + show_residuals = TRUE, row_layout = TRUE, ...) +} +plot_err <- function(fit, sep_obs = FALSE, show_errmin = sep_obs, ...) { + plot.mkinfit(fit, sep_obs = sep_obs, show_errmin = show_errmin, + show_errplot = TRUE, row_layout = TRUE, ...) } @@ -24,9 +24,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK -* checking top-level files ... NOTE -Non-standard file/directory found at top level: - ‘tests_slow.log’ +* checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK @@ -61,7 +59,7 @@ Non-standard file/directory found at top level: * checking examples ... NOTE Examples with CPU or elapsed time > 5s user system elapsed -synthetic_data_for_UBA_2014 9.778 0.239 10.019 +synthetic_data_for_UBA_2014 9.755 0.273 10.029 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -70,7 +68,7 @@ synthetic_data_for_UBA_2014 9.778 0.239 10.019 * checking PDF version of manual ... OK * DONE -Status: 2 NOTEs +Status: 1 NOTE See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. diff --git a/docs/reference/index.html b/docs/reference/index.html index 08ad3d1a..e74a8ad5 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -175,7 +175,7 @@ <tr> <td> - <p><code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> </p> + <p><code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</a></code> </p> </td> <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> </tr><tr> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index d841909f..eea5b218 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -146,7 +146,10 @@ <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>, - <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='no'>...</span>)</pre> + <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, + <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -184,7 +187,19 @@ <tr> <th>lpos</th> <td><p>Where should the legend be placed? Default is "topright". Will be passed on to - <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td> + <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td> + </tr> + <tr> + <th>col_obs</th> + <td><p>Colors for the observed variables.</p></td> + </tr> + <tr> + <th>pch_obs</th> + <td><p>Symbols to be used for the observed variables.</p></td> + </tr> + <tr> + <th>frame</th> + <td><p>Should a frame be drawn around the plots?</p></td> </tr> <tr> <th>...</th> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 84bec348..6910ae47 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 557046da..8d399598 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex 36fcff6a..20f30221 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 795262f8..df01a00b 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -159,9 +159,12 @@ If the current plot device is a tikz device, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, + <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) -<span class='fu'>plot_sep</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'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> +<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) +<span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>) +<span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -245,6 +248,11 @@ If the current plot device is a tikz device, <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 the first argument. If not length one, this should be of the same length as the obs_var argument.</p></td> @@ -281,7 +289,7 @@ If the current plot device is a tikz device, <span class='co'># parent to sink included</span> <span class='co'># \dontrun{</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</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'>#> <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'><-</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'> + <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'>#> <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'><-</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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.html'>plot</a></span>(<span class='no'>fit</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='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</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> diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 9d8c0931..201ef0fd 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index a639151b..ddc88c21 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -278,12 +278,13 @@ Compare also the code in the example section to see the degradation models." /> <span class='co'># This is just one example of an evaluation using the kinetic model used for</span> <span class='co'># the generation of the data</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 +<span class='co'># \dontrun{</span> + <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Sep 19 12:48:50 2019 -#> Date of summary: Thu Sep 19 12:48:50 2019 +#> Date of fit: Mon Oct 21 18:52:20 2019 +#> Date of summary: Mon Oct 21 18:52:20 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -292,21 +293,20 @@ Compare also the code in the example section to see the degradation models." /> #> #> Model predictions using solution type deSolve #> -#> Fitted using 847 model solutions performed in 2.49 s +#> Fitted using 847 model solutions performed in 2.42 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.350000 state -#> k_parent 0.100000 deparm -#> k_M1 0.100100 deparm -#> k_M2 0.100200 deparm -#> f_parent_to_M1 0.500000 deparm -#> f_M1_to_M2 0.500000 deparm -#> sigma 2.273126 error +#> value type +#> parent_0 101.3500 state +#> k_parent 0.1000 deparm +#> k_M1 0.1001 deparm +#> k_M2 0.1002 deparm +#> f_parent_to_M1 0.5000 deparm +#> f_M1_to_M2 0.5000 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper @@ -316,7 +316,6 @@ Compare also the code in the example section to see the degradation models." /> #> log_k_M2 -2.300587 -Inf Inf #> f_parent_ilr_1 0.000000 -Inf Inf #> f_M1_ilr_1 0.000000 -Inf Inf -#> sigma 2.273126 0 Inf #> #> Fixed parameter values: #> value type @@ -424,7 +423,8 @@ Compare also the code in the example section to see the degradation models." /> #> 90 M2 10.6 1.013e+01 0.47130 #> 90 M2 10.8 1.013e+01 0.67130 #> 120 M2 9.8 5.521e+00 4.27893 -#> 120 M2 3.3 5.521e+00 -2.22107</div></pre> +#> 120 M2 3.3 5.521e+00 -2.22107</div><div class='input'># } +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd index cdcfbd37..e788d836 100644 --- a/man/mkinresplot.Rd +++ b/man/mkinresplot.Rd @@ -14,38 +14,50 @@ obs_vars = names(object$mkinmod$map),
xlim = c(0, 1.1 * max(object$data$time)),
xlab = "Time", ylab = "Residual",
- maxabs = "auto", legend = TRUE, lpos = "topright", ...)
+ maxabs = "auto", legend = TRUE, lpos = "topright",
+ col_obs = "auto", pch_obs = "auto",
+ frame = TRUE,
+ ...)
}
\arguments{
\item{object}{
A fit represented in an \code{\link{mkinfit}} object.
-}
+ }
\item{obs_vars}{
A character vector of names of the observed variables for which residuals
should be plotted. Defaults to all observed variables in the model
-}
+ }
\item{xlim}{
plot range in x direction.
}
\item{xlab}{
Label for the x axis. Defaults to "Time [days]".
-}
+ }
\item{ylab}{
Label for the y axis. Defaults to "Residual [\% of applied radioactivity]".
-}
+ }
\item{maxabs}{
Maximum absolute value of the residuals. This is used for the scaling of
the y axis and defaults to "auto".
-}
+ }
\item{legend}{
Should a legend be plotted? Defaults to "TRUE".
-}
+ }
\item{lpos}{
Where should the legend be placed? Default is "topright". Will be passed on to
- \code{\link{legend}}. }
+ \code{\link{legend}}. }
+ \item{col_obs}{
+ Colors for the observed variables.
+ }
+ \item{pch_obs}{
+ Symbols to be used for the observed variables.
+ }
+ \item{frame}{
+ Should a frame be drawn around the plots?
+ }
\item{\dots}{
- further arguments passed to \code{\link{plot}}.
-}
+ further arguments passed to \code{\link{plot}}.
+ }
}
\value{
Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index a4f47073..e7b456a1 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -1,6 +1,8 @@ \name{plot.mkinfit} \alias{plot.mkinfit} \alias{plot_sep} +\alias{plot_res} +\alias{plot_err} \title{ Plot the observed data and the fitted model of an mkinfit object } @@ -26,9 +28,12 @@ show_errplot = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, + row_layout = FALSE, lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE, errmin_digits = 3, frame = TRUE, \dots) -plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) +plot_sep(fit, show_errmin = TRUE, \dots) +plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots) +plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots) } \arguments{ \item{x}{ @@ -92,6 +97,10 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) \item{rel.height.middle}{ The relative height of the middle plot, if more than two rows of plots are shown. } + \item{row_layout}{ + Should we use a row layout where the residual plot or the error model plot is shown + to the right? + } \item{lpos}{ Position(s) of the legend(s). Passed to \code{\link{legend}} as the first argument. If not length one, this should be of the same length as the obs_var argument. @@ -123,8 +132,8 @@ SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), m1 = mkinsub("SFO", full = "Metabolite M1" )) fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc") plot(fit) -plot(fit, show_residuals = TRUE) -plot(fit, show_errplot = TRUE) +plot_res(fit) +plot_err(fit) # Show the observed variables separately plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright")) diff --git a/man/synthetic_data_for_UBA_2014.Rd b/man/synthetic_data_for_UBA_2014.Rd index cfab5622..d68f45d4 100644 --- a/man/synthetic_data_for_UBA_2014.Rd +++ b/man/synthetic_data_for_UBA_2014.Rd @@ -138,9 +138,11 @@ d_synth_err_names = c( # This is just one example of an evaluation using the kinetic model used for
# the generation of the data
-fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
- quiet = TRUE)
-plot_sep(fit)
-summary(fit)
+\dontrun{
+ fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
+ quiet = TRUE)
+ plot_sep(fit)
+ summary(fit)
+}
}
\keyword{datasets}
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(2007) Piacenza paper [5.3 s] ✔ | 4 | Fitting the SFORB model [1.7 s] @@ -23,9 +23,9 @@ Testing mkin ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 84.4 s +Duration: 84.3 s -OK: 106 +OK: 109 Failed: 0 Warnings: 0 Skipped: 0 diff --git a/tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg b/tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg new file mode 100644 index 00000000..88e7aaee --- /dev/null +++ b/tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg @@ -0,0 +1,237 @@ +<?xml version='1.0' encoding='UTF-8' ?> +<svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' viewBox='0 0 720.00 576.00'> +<defs> + <style type='text/css'><![CDATA[ + line, polyline, polygon, path, rect, circle { + fill: none; + stroke: #000000; + stroke-linecap: round; + stroke-linejoin: round; + stroke-miterlimit: 10.00; 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