diff options
Diffstat (limited to 'docs/reference/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 432 |
1 files changed, 188 insertions, 244 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index bbaad91e..25d0e76b 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -1,72 +1,17 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <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 +<!-- 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." /> - - - - -<!-- 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]> +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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -77,13 +22,12 @@ the ilr transformation is used." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -92,8 +36,7 @@ the ilr transformation is used." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -103,6 +46,9 @@ the ilr transformation is used." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -117,34 +63,27 @@ the ilr transformation is used." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </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/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small> + <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> @@ -154,205 +93,210 @@ 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> +the <a href="ilr.html">ilr</a> transformation is used.</p> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span><span class='op'>(</span> - <span class='va'>parms</span>, - <span class='va'>mkinmod</span>, - transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, - transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span> - -<span class='fu'>backtransform_odeparms</span><span class='op'>(</span> - <span class='va'>transparms</span>, - <span class='va'>mkinmod</span>, - transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, - transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">transform_odeparms</span><span class="op">(</span> + <span class="va">parms</span>, + <span class="va">mkinmod</span>, + transform_rates <span class="op">=</span> <span class="cn">TRUE</span>, + transform_fractions <span class="op">=</span> <span class="cn">TRUE</span> +<span class="op">)</span> + +<span class="fu">backtransform_odeparms</span><span class="op">(</span> + <span class="va">transparms</span>, + <span class="va">mkinmod</span>, + transform_rates <span class="op">=</span> <span class="cn">TRUE</span>, + transform_fractions <span class="op">=</span> <span class="cn">TRUE</span> +<span class="op">)</span></code></pre></div> + </div> - <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>mkinmod</th> - <td><p>The kinetic model of class <a href='mkinmod.html'>mkinmod</a>, containing + <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></td> - </tr> - <tr> - <th>transform_rates</th> - <td><p>Boolean specifying if kinetic rate constants should +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></td> - </tr> - <tr> - <th>transform_fractions</th> - <td><p>Boolean specifying if formation fractions +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'>stats::qlogis()</a></code>. In other cases, i.e. if +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></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> - +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> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </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> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - +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> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='va'>FOCUS_D</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>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 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 class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -<span class='co'># Transformed and backtransformed parameters</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='co'># Compare to the version without transforming rate parameters (does not work</span> -<span class='co'># with analytical solution, we get NA values for m1 in predictions)</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>, - 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 class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.57022 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</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 class='fu'><a href='https://rdrr.io/r/base/names.html'>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'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span> -<span class='va'>transformed</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span> -<span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><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> -</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink -#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='co'># The case of formation fractions (this is now the default)</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> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<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 class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.5985 1.5702 96.404 102.79 -#> log_k_parent -2.3157 0.0409 -2.399 -2.23 -#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 -#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 -#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 -#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 -#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='va'>initials</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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 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 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> -</div><div class='output co'>#> f_parent_to_m1 -#> 0.5 </div><div class='input'> -<span class='co'># And without sink</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> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - -<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 class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 84.79 3.012 78.67 90.91 -#> log_k_parent -2.76 0.082 -2.92 -2.59 -#> log_k_m1 -4.21 0.123 -4.46 -3.96 -#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 -#> 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'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> +<span class="r-in"><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 class="r-in"> 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 class="r-in"> 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 class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span> +<span class="r-in"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/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 class="r-in"><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 class="r-in"><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 class="r-in"><span class="co"># Transformed and backtransformed parameters</span></span> +<span class="r-in"><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">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.60 1.5702 96.40 102.79</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.04 0.0763 -3.19 -2.88</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1_sink -5.25 0.1332 -5.52 -4.98</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.13 0.3585 2.40 3.85</span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span 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 class="r-in"><span class="co"># \dontrun{</span></span> +<span class="r-in"><span class="co"># Compare to the version without transforming rate parameters (does not work</span></span> +<span class="r-in"><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span> +<span class="r-in"><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 class="r-in"> 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 class="r-in"><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 class="r-in"><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">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 96.40384 1.03e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 2.39609 3.85e+00</span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span 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 class="co"># }</span></span> +<span class="r-in"></span> +<span class="r-in"><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 class="r-in"><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">$</span><span class="va">start</span><span class="op">)</span></span> +<span class="r-in"><span class="va">transformed</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span> +<span class="r-in"><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 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 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 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 class="r-in"><span class="co"># \dontrun{</span></span> +<span class="r-in"><span class="co"># The case of formation fractions (this is now the default)</span></span> +<span class="r-in"><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 class="r-in"> 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 class="r-in"> 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 class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</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 class="r-in"><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 class="r-in"><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 class="r-in"><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">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.5985 1.5702 96.404 102.79</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.3157 0.0409 -2.399 -2.23</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.2475 0.1332 -5.518 -4.98</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.0579 0.0893 -0.124 0.24</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.1255 0.3585 2.396 3.85</span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span 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 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 class="r-in"><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 class="r-in"><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 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 class="r-in"><span class="co"># And without sink</span></span> +<span class="r-in"><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 class="r-in"> 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 class="r-in"> 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 class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</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 class="r-in"></span> +<span class="r-in"><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 class="r-in"><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 class="r-in"><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">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 84.79 3.012 78.67 90.91</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.76 0.082 -2.92 -2.59</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.21 0.123 -4.46 -3.96</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.22 0.943 6.31 10.14</span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span> +<span 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 class="co"># }</span></span> +<span class="r-in"></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |