diff options
| -rw-r--r-- | docs/404.html | 5 | ||||
| -rw-r--r-- | docs/articles/index.html | 5 | ||||
| -rw-r--r-- | docs/authors.html | 5 | ||||
| -rw-r--r-- | docs/news/index.html | 5 | ||||
| -rw-r--r-- | docs/reference/index.html | 5 | ||||
| -rw-r--r-- | docs/reference/mkinerrplot.html | 17 | ||||
| -rw-r--r-- | docs/reference/synthetic_data_for_UBA_2014.html | 28 |
7 files changed, 38 insertions, 32 deletions
diff --git a/docs/404.html b/docs/404.html index 485641dc..ecb80807 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,11 +8,13 @@ <title>Page not found (404) • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,10 +34,12 @@ + <meta property="og:title" content="Page not found (404)" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -106,7 +110,6 @@ <a href="news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> diff --git a/docs/articles/index.html b/docs/articles/index.html index cc136fdc..babe3137 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -8,11 +8,13 @@ <title>Articles • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,10 +34,12 @@ + <meta property="og:title" content="Articles" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -106,7 +110,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> diff --git a/docs/authors.html b/docs/authors.html index 6e113c82..30c81ddf 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -8,11 +8,13 @@ <title>Authors • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,10 +34,12 @@ + <meta property="og:title" content="Authors" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -106,7 +110,6 @@ <a href="news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> diff --git a/docs/news/index.html b/docs/news/index.html index d3bee7e2..20a71657 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -8,11 +8,13 @@ <title>Changelog • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,10 +34,12 @@ + <meta property="og:title" content="Changelog" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -106,7 +110,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> diff --git a/docs/reference/index.html b/docs/reference/index.html index e74a8ad5..17a879a9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -8,11 +8,13 @@ <title>Function reference • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,10 +34,12 @@ + <meta property="og:title" content="Function reference" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -106,7 +110,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index be2f7614..4386673c 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -8,11 +8,13 @@ <title>Function to plot squared residuals and the error model for an mkin object — mkinerrplot • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Function to plot squared residuals and the error model for an mkin object — mkinerrplot" /> +<meta property="og:title" content="Function to plot squared residuals and the error model for an mkin object — mkinerrplot" /> <meta property="og:description" content="This function plots the squared residuals for the specified subset of the observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. @@ -44,6 +46,7 @@ + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -114,7 +117,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -136,14 +138,12 @@ </div> <div class="ref-description"> - <p>This function plots the squared residuals for the specified subset of the observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model and this error model plot can be obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the argument <code>show_errplot = TRUE</code>.</p> - </div> <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>, @@ -154,7 +154,7 @@ <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"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -210,16 +210,14 @@ <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the mkinfit object.</p></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> @@ -230,11 +228,8 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index ddc88c21..f23b77b0 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -8,11 +8,13 @@ <title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> +<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> <meta property="og:description" content="The 12 datasets were generated using four different models and three different variance components. The four models are either the SFO or the DFOP model with either two sequential or two parallel metabolites. @@ -54,6 +56,7 @@ Compare also the code in the example section to see the degradation models." /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -124,7 +127,6 @@ Compare also the code in the example section to see the degradation models." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -146,7 +148,6 @@ Compare also the code in the example section to see the degradation models." /> </div> <div class="ref-description"> - <p>The 12 datasets were generated using four different models and three different variance components. The four models are either the SFO or the DFOP model with either two sequential or two parallel metabolites.</p> @@ -163,11 +164,11 @@ Compare also the code in the example section to see the degradation models." /> <p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model with two sequential metabolites (linear pathway), with added variance component 'a'.</p> <p>Compare also the code in the example section to see the degradation models.</p> - </div> <pre class="usage"><span class='no'>synthetic_data_for_UBA_2014</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, @@ -177,17 +178,16 @@ Compare also the code in the example section to see the degradation models." /> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># The data have been generated using the following kinetic models</span> + <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> +<span class='co'># The data have been generated using the following kinetic models</span> <span class='no'>m_synth_SFO_lin</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='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</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'> @@ -249,7 +249,7 @@ Compare also the code in the example section to see the degradation models." /> <span class='co'># d_rep = data.frame(lapply(d_long, rep, each = 2))</span> <span class='co'># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span> <span class='co'>#</span> -<span class='co'># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span> +<span class='co'># d_rep[d_rep$time == 0 & d_rep$name </span> <span class='co'># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span> <span class='co'># d_NA$value <- round(d_NA$value, 1)</span> <span class='co'># return(d_NA)</span> @@ -278,13 +278,12 @@ 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='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: Mon Oct 21 18:52:20 2019 -#> Date of summary: Mon Oct 21 18:52:20 2019 +#> Date of fit: Mon Oct 21 22:46:31 2019 +#> Date of summary: Mon Oct 21 22:46:31 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -293,7 +292,7 @@ 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 2.42 s +#> Fitted using 847 model solutions performed in 2.45 s #> #> Error model: Constant variance #> @@ -429,11 +428,8 @@ Compare also the code in the example section to see the degradation models." /> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> |