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authorJohannes Ranke <jranke@uni-bremen.de>2019-10-21 18:52:24 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-10-21 18:54:37 +0200
commite09f726134ee273b6b191c1ec6465e6f701b082b (patch)
treeaabc6bec231fb9dd085deef57a030e41ec398bf4 /docs/reference
parentbea054418c5310103252f5d243b2d18fcbf7b11f (diff)
Improve some plotting routines, more tests
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/mkinresplot.html19
-rw-r--r--docs/reference/plot.mkinfit-2.pngbin52842 -> 57593 bytes
-rw-r--r--docs/reference/plot.mkinfit-3.pngbin51545 -> 61280 bytes
-rw-r--r--docs/reference/plot.mkinfit-5.pngbin59560 -> 59080 bytes
-rw-r--r--docs/reference/plot.mkinfit.html12
-rw-r--r--docs/reference/synthetic_data_for_UBA_2014-1.pngbin62975 -> 62550 bytes
-rw-r--r--docs/reference/synthetic_data_for_UBA_2014.html32
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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>
</div>
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