Improve some plotting routines, more tests

Static documentation rebuilt by pkgdown

8 files changed, 44 insertions, 21 deletions

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>&lt;mkinfit&gt;</i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> </p>
+          <p><code><a href="plot.mkinfit.html">plot(<i>&lt;mkinfit&gt;</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
index 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
index 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
index 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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>#&gt; <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'>&lt;-</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'>#&gt; <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
index 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'>&lt;-</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>]]$<span class='no'>data</span>,
-               <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.6 
+<span class='co'># \dontrun{</span>
+  <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<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'>#&gt; mkin version used for fitting:    0.9.49.6 
 #&gt; R version used for fitting:       3.6.1 
-#&gt; Date of fit:     Thu Sep 19 12:48:50 2019 
-#&gt; Date of summary: Thu Sep 19 12:48:50 2019 
+#&gt; Date of fit:     Mon Oct 21 18:52:20 2019 
+#&gt; Date of summary: Mon Oct 21 18:52:20 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -292,21 +293,20 @@ Compare also the code in the example section to see the degradation models." />
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 847 model solutions performed in 2.49 s
+#&gt; Fitted using 847 model solutions performed in 2.42 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
 #&gt; Error model algorithm: OLS 
 #&gt; 
 #&gt; Starting values for parameters to be optimised:
-#&gt;                     value   type
-#&gt; parent_0       101.350000  state
-#&gt; k_parent         0.100000 deparm
-#&gt; k_M1             0.100100 deparm
-#&gt; k_M2             0.100200 deparm
-#&gt; f_parent_to_M1   0.500000 deparm
-#&gt; f_M1_to_M2       0.500000 deparm
-#&gt; sigma            2.273126  error
+#&gt;                   value   type
+#&gt; parent_0       101.3500  state
+#&gt; k_parent         0.1000 deparm
+#&gt; k_M1             0.1001 deparm
+#&gt; k_M2             0.1002 deparm
+#&gt; f_parent_to_M1   0.5000 deparm
+#&gt; f_M1_to_M2       0.5000 deparm
 #&gt; 
 #&gt; Starting values for the transformed parameters actually optimised:
 #&gt;                     value lower upper
@@ -316,7 +316,6 @@ Compare also the code in the example section to see the degradation models." />
 #&gt; log_k_M2        -2.300587  -Inf   Inf
 #&gt; f_parent_ilr_1   0.000000  -Inf   Inf
 #&gt; f_M1_ilr_1       0.000000  -Inf   Inf
-#&gt; sigma            2.273126     0   Inf
 #&gt; 
 #&gt; Fixed parameter values:
 #&gt;      value  type
@@ -424,7 +423,8 @@ Compare also the code in the example section to see the degradation models." />
 #&gt;    90       M2     10.6  1.013e+01  0.47130
 #&gt;    90       M2     10.8  1.013e+01  0.67130
 #&gt;   120       M2      9.8  5.521e+00  4.27893
-#&gt;   120       M2      3.3  5.521e+00 -2.22107</div></pre>
+#&gt;   120       M2      3.3  5.521e+00 -2.22107</div><div class='input'># }
+</div></pre>
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     <h2>Contents</h2>