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+<body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-article"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> -<li> - <a href="../reference/index.html">Reference</a> -</li> -<li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> - 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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Introduction to mkin</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Short introduction to mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 15 February 2021 -(rebuilt 2023-04-16)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2023 +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> - <div class="hidden name"><code>mkin.rmd</code></div> - + <div class="d-none name"><code>mkin.rmd</code></div> </div> @@ -222,8 +171,9 @@ was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to -include the output requested by the FOCUS guidance, such as the <span class="math inline">\(\chi^2\)</span> error level as defined in this -guidance.</p> +include the output requested by the FOCUS guidance, such as the +<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msup><mi>χ</mi><mn>2</mn></msup><annotation encoding="application/x-tex">\chi^2</annotation></semantics></math> +error level as defined in this guidance.</p> <p>Also, <code>mkin</code> introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to <code>mkin</code> for the case of @@ -361,13 +311,14 @@ reliability of parameter estimates, based on the FOCUS guidance mentioned above. Therefore, the results of this one-sided t-test are included in the summary output from <code>mkin</code>.</p> <p>As it is not reasonable to test for significant difference of the -transformed parameters (<em>e.g.</em> <span class="math inline">\(log(k)\)</span>) from zero, the t-test is -calculated based on the model definition before parameter -transformation, <em>i.e.</em> in a similar way as in packages that do -not apply such an internal parameter transformation. A note is included -in the <code>mkin</code> output, pointing to the fact that the t-test is -based on the unjustified assumption of normal distribution of the -parameter estimators.</p> +transformed parameters (<em>e.g.</em> +<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>l</mi><mi>o</mi><mi>g</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>k</mi><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">log(k)</annotation></semantics></math>) +from zero, the t-test is calculated based on the model definition before +parameter transformation, <em>i.e.</em> in a similar way as in packages +that do not apply such an internal parameter transformation. A note is +included in the <code>mkin</code> output, pointing to the fact that the +t-test is based on the unjustified assumption of normal distribution of +the parameter estimators.</p> </div> </div> <div class="section level2"> @@ -438,35 +389,26 @@ Sensitivity and Monte Carlo Analysis in <span>R</span> Using Package </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </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="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> |