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For kinetic rate constants and other parameters 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."><!-- 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><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body> +the ilr transformation is used."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">mkin</a> - 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+ </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Functions to transform and backtransform kinetic parameters for fitting</h1> + + <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/transform_odeparms.R" class="external-link"><code>R/transform_odeparms.R</code></a></small> <div class="d-none name"><code>transform_odeparms.Rd</code></div> </div> @@ -111,19 +98,21 @@ the <a href="ilr.html">ilr</a> transformation is used.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>parms</dt> + + +<dl><dt id="arg-parms">parms<a class="anchor" aria-label="anchor" href="#arg-parms"></a></dt> <dd><p>Parameters of kinetic models as used in the differential equations.</p></dd> -<dt>mkinmod</dt> +<dt id="arg-mkinmod">mkinmod<a class="anchor" aria-label="anchor" href="#arg-mkinmod"></a></dt> <dd><p>The kinetic model of class <a href="mkinmod.html">mkinmod</a>, containing the names of the model variables that are needed for grouping the formation fractions before <a href="ilr.html">ilr</a> transformation, the parameter names and the information if the pathway to sink is included in the model.</p></dd> -<dt>transform_rates</dt> +<dt id="arg-transform-rates">transform_rates<a class="anchor" aria-label="anchor" href="#arg-transform-rates"></a></dt> <dd><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 @@ -132,7 +121,7 @@ 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></dd> -<dt>transform_fractions</dt> +<dt id="arg-transform-fractions">transform_fractions<a class="anchor" aria-label="anchor" href="#arg-transform-fractions"></a></dt> <dd><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 @@ -145,16 +134,14 @@ two or more formation fractions need to be transformed whose sum cannot exceed one, the <a href="ilr.html">ilr</a> transformation is used.</p></dd> -<dt>transparms</dt> +<dt id="arg-transparms">transparms<a class="anchor" aria-label="anchor" href="#arg-transparms"></a></dt> <dd><p>Transformed parameters of kinetic models as used in the fitting procedure.</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A vector of transformed or backtransformed parameters</p> + <p>A vector of transformed or backtransformed parameters</p> </div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> @@ -284,23 +271,23 @@ This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</ <span class="r-in"><span></span></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer></div> - - + + </body></html> |