diff options
Diffstat (limited to 'docs/reference/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 119 |
1 files changed, 64 insertions, 55 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index b1a952d9..4d88a03e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -8,11 +8,13 @@ <title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • 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 --> @@ -32,21 +34,19 @@ -<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> -<meta property="og:description" content="The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - constants and other paramters that can only take on positive values, a - simple log transformation is used. For compositional parameters, such as - the formations fractions that should always sum up to 1 and can not be - negative, the ilr transformation is used. -The transformation of sets of formation fractions is fragile, as it supposes - the same ordering of the components in forward and backward transformation. - This is no problem for the internal use in mkinfit." /> +<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> +<meta property="og:description" content="The transformations are intended to map parameters that should only take on +restricted values to the full scale of real numbers. For kinetic rate +constants and other paramters that can only take on positive values, a +simple log transformation is used. For compositional parameters, such as the +formations fractions that should always sum up to 1 and can not be negative, +the ilr transformation is used." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -117,7 +117,6 @@ The transformation of sets of formation fractions is fragile, as it supposes <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -139,71 +138,80 @@ The transformation of sets of formation fractions is fragile, as it supposes </div> <div class="ref-description"> - - <p>The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - constants and other paramters that can only take on positive values, a - simple log transformation is used. For compositional parameters, such as - the formations fractions that should always sum up to 1 and can not be - negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> -<p>The transformation of sets of formation fractions is fragile, as it supposes - the same ordering of the components in forward and backward transformation. - This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - + <p>The transformations are intended to map parameters that should only take on +restricted values to the full scale of real numbers. For kinetic rate +constants and other paramters that can only take on positive values, a +simple log transformation is used. For compositional parameters, such as the +formations fractions that should always sum up to 1 and can not be negative, +the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - + <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</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> <tr> <th>parms</th> - <td><p>Parameters of kinetic models as used in the differential equations.</p></td> - </tr> - <tr> - <th>transparms</th> - <td><p>Transformed parameters of kinetic models as used in the fitting procedure.</p></td> + <td><p>Parameters of kinetic models as used in the differential +equations.</p></td> </tr> <tr> <th>mkinmod</th> - <td><p>The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of - the model variables that are needed for grouping the formation fractions - before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and - the information if the pathway to sink is included in the model.</p></td> + <td><p>The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing +the names of the model variables that are needed for grouping the +formation fractions before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter +names and the information if the pathway to sink is included in the model.</p></td> </tr> <tr> <th>transform_rates</th> - <td><p>Boolean specifying if kinetic rate constants should be transformed in the - model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. If TRUE, also - alpha and beta parameters of the FOMC model are log-transformed, as well - as k1 and k2 rate constants for the DFOP and HS models and the break point tb - of the HS model.</p></td> + <td><p>Boolean specifying if kinetic rate constants should +be transformed in the model specification used in the fitting for better +compliance with the assumption of normal distribution of the estimator. If +TRUE, also alpha and beta parameters of the FOMC model are +log-transformed, as well as k1 and k2 rate constants for the DFOP and HS +models and the break point tb of the HS model.</p></td> </tr> <tr> <th>transform_fractions</th> - <td><p>Boolean specifying if formation fractions constants should be transformed in the - model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. The default (TRUE) is - to do transformations. The g parameter of the DFOP and HS models are also - transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> - transformation.</p></td> + <td><p>Boolean specifying if formation fractions +constants should be transformed in the model specification used in the +fitting for better compliance with the assumption of normal distribution +of the estimator. The default (TRUE) is to do transformations. The g +parameter of the DFOP and HS models are also transformed, as they can also +be seen as compositional data. The transformation used for these +transformations is the <code><a href='ilr.html'>ilr</a></code> transformation.</p></td> + </tr> + <tr> + <th>transparms</th> + <td><p>Transformed parameters of kinetic models as used in the +fitting procedure.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A vector of transformed or backtransformed parameters with the same names - as the original parameters.</p> + <p>A vector of transformed or backtransformed parameters with the same + names as the original parameters.</p> + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>The transformation of sets of formation fractions is fragile, as it supposes +the same ordering of the components in forward and backward transformation. +This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2> + +<ul> +<li><p><code>backtransform_odeparms</code>: Backtransform the set of transformed parameters</p></li> +</ul> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <pre class="examples"><div class='input'> +<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='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'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>))</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'># Fit the model to the FOCUS example dataset D using defaults</span> <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>)</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='no'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>) @@ -278,15 +286,16 @@ The transformation of sets of formation fractions is fragile, as it supposes #> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 #> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 #> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <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="#details">Details</a></li> + <li><a href="#functions">Functions</a></li> <li><a href="#examples">Examples</a></li> </ul> |