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| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-02-13 16:30:31 +0100 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-02-13 19:20:04 +0100 |
| commit | 6476f5f49b373cd4cf05f2e73389df83e437d597 (patch) | |
| tree | d0ef15c0d2ab42d246f7c8ebaeb4e63f4a928699 /docs/dev/reference/transform_odeparms.html | |
| parent | 786e50724d9d7cc8fe04171d28ed09ea8d698cc3 (diff) | |
Axis legend formatting, update vignettes
Diffstat (limited to 'docs/dev/reference/transform_odeparms.html')
| -rw-r--r-- | docs/dev/reference/transform_odeparms.html | 336 |
1 files changed, 0 insertions, 336 deletions
diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html deleted file mode 100644 index 4cb2e575..00000000 --- a/docs/dev/reference/transform_odeparms.html +++ /dev/null @@ -1,336 +0,0 @@ -<!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><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 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."><meta name="robots" content="noindex"><!-- 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 data-spy="scroll" data-target="#toc"> - - - <div class="container template-reference-topic"> - <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"> - Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"><li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </ul></li> -<li> - <a href="../news/index.html">News</a> -</li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <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="hidden name"><code>transform_odeparms.Rd</code></div> - </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 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 <a href="ilr.html">ilr</a> transformation is used.</p> - </div> - - <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">transform_odeparms</span><span class="op">(</span></span> -<span> <span class="va">parms</span>,</span> -<span> <span class="va">mkinmod</span>,</span> -<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> -<span><span class="op">)</span></span> -<span></span> -<span><span class="fu">backtransform_odeparms</span><span class="op">(</span></span> -<span> <span class="va">transparms</span>,</span> -<span> <span class="va">mkinmod</span>,</span> -<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> -<span><span class="op">)</span></span></code></pre></div> - </div> - - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>parms</dt> -<dd><p>Parameters of kinetic models as used in the differential -equations.</p></dd> - - -<dt>mkinmod</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> -<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 -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></dd> - - -<dt>transform_fractions</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 -of the estimator. The default (TRUE) is to do transformations. -The g parameter of the DFOP model is also seen as a fraction. -If a single fraction is transformed (g parameter of DFOP or only a single -target variable e.g. a single metabolite plus a pathway to sink), a -logistic transformation is used <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">stats::qlogis()</a></code>. In other cases, i.e. if -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> -<dd><p>Transformed parameters of kinetic models as used in the -fitting procedure.</p></dd> - -</dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>A vector of transformed or backtransformed parameters</p> - </div> - <div id="details"> - <h2>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 <a href="mkinfit.html">mkinfit</a>.</p> - </div> - <div id="author"> - <h2>Author</h2> - <p>Johannes Ranke</p> - </div> - - <div id="ref-examples"> - <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span></span> -<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># remove zero values to avoid warning</span></span></span> -<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">fit.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="co"># Transformed and backtransformed parameters</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.60 1.5702 96.40 102.79</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.04 0.0763 -3.19 -2.88</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1_sink -5.25 0.1332 -5.52 -4.98</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.13 0.3585 2.40 3.85</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span><span class="co"># Compare to the version without transforming rate parameters (does not work</span></span></span> -<span class="r-in"><span><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span></span> -<span class="r-in"><span><span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, transform_rates <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> -<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">fit.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 96.40384 1.03e+02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 2.39609 3.85e+00</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</span> -<span class="r-in"><span><span class="co"># }</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">$</span><span class="va">value</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">initials</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 100.750000 -2.302585 -2.301586 -2.300587 </span> -<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent_sink k_parent_m1 k_m1_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 100.7500 0.1000 0.1001 0.1002 </span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span><span class="co"># The case of formation fractions (this is now the default)</span></span></span> -<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">fit.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">fit.ff.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.5985 1.5702 96.404 102.79</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.3157 0.0409 -2.399 -2.23</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.2475 0.1332 -5.518 -4.98</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.0579 0.0893 -0.124 0.24</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.1255 0.3585 2.396 3.85</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> -<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"f_parent_to_m1"</span> <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 </span> -<span class="r-out co"><span class="r-pr">#></span> 0.5 </span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># And without sink</span></span></span> -<span class="r-in"><span><span class="va">SFO_SFO.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">fit.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff.2</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">fit.ff.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff.2</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 84.79 3.012 78.67 90.91</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.76 0.082 -2.92 -2.59</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.21 0.123 -4.46 -3.96</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 8.22 0.943 6.31 10.14</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</span> -<span class="r-in"><span><span class="co"># }</span></span></span> -<span class="r-in"><span></span></span> -</code></pre></div> - </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> - <p></p><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> - - </footer></div> - - - - - - - </body></html> - |