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Diffstat (limited to 'docs/reference/add_err.html')
| -rw-r--r-- | docs/reference/add_err.html | 20 |
1 files changed, 12 insertions, 8 deletions
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 78574e92..c8024d66 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -193,7 +193,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># The kinetic model</span> <span class='no'>m_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'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='co'># Generate a prediction for a specific set of parameters</span> <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) @@ -203,12 +203,15 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Log'>log</a></span>(<span class='fl'>2</span>)/<span class='fl'>1000</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>), - <span class='no'>sampling_times</span>)</div><div class='output co'>#> <span class='error'>Error in mkinpredict(m_SFO_SFO, c(k_parent = 0.1, f_parent_to_M1 = 0.5, k_M1 = log(2)/1000), c(parent = 100, M1 = 0), sampling_times): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> + <span class='no'>sampling_times</span>) + <span class='co'># Add an error term with a constant (independent of the value) standard deviation</span> <span class='co'># of 10, and generate three datasets</span> -<span class='no'>d_SFO_SFO_err</span> <span class='kw'><-</span> <span class='fu'>add_err</span>(<span class='no'>d_SFO_SFO</span>, <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fl'>10</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456789</span> )</div><div class='output co'>#> <span class='error'>Error in add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789): konnte Funktion "add_err" nicht finden</span></div><div class='input'> +<span class='no'>d_SFO_SFO_err</span> <span class='kw'><-</span> <span class='fu'>add_err</span>(<span class='no'>d_SFO_SFO</span>, <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fl'>10</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456789</span> ) + <span class='co'># Name the datasets for nicer plotting</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in names(d_SFO_SFO_err) <- paste("Dataset", 1:3): Objekt 'd_SFO_SFO_err' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) + <span class='co'># Name the model in the list of models (with only one member in this case)</span> <span class='co'># for nicer plotting later on.</span> <span class='co'># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span> @@ -216,15 +219,16 @@ <span class='co'># checks</span> <span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>), <span class='no'>d_SFO_SFO_err</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)</div><div class='output co'>#> <span class='error'>Error in mmkin(list(`SFO-SFO` = m_SFO_SFO), d_SFO_SFO_err, cores = 1, quiet = TRUE, method.modFit = "Marq"): konnte Funktion "mmkin" nicht finden</span></div><div class='input'> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>)</div><div class='output co'>#> <span class='error'>Error in plot(f_SFO_SFO): Objekt 'f_SFO_SFO' nicht gefunden</span></div><div class='input'> + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) + +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>)</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We would like to inspect the fit for dataset 3 more closely</span> <span class='co'># Using double brackets makes the returned object an mkinfit object</span> <span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in plot(f_SFO_SFO[[3]], show_residuals = TRUE): Objekt 'f_SFO_SFO' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># If we use single brackets, we should give two indices (model and dataset),</span> <span class='co'># and plot.mmkin is used</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='output co'>#> <span class='error'>Error in plot(f_SFO_SFO[1, 3]): Objekt 'f_SFO_SFO' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |