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href="../index.html">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" 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> + <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> + <a 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href='https://github.com/jranke/mkin/blob/master/R/mixed.mmkin.R'><code>R/mixed.mmkin.R</code></a></small> + <div class="hidden name"><code>mixed.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Create a mixed effects model from an mmkin row object</p> + </div> + + <pre class="usage"><span class='fu'>mixed</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> + +<span class='co'># S3 method for mmkin</span> +<span class='fu'>mixed</span><span class='op'>(</span><span class='va'>object</span>, method <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'>"none"</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span> + +<span class='co'># S3 method for mixed.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</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>object</th> + <td><p>An <a href='mmkin.html'>mmkin</a> row object</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Currently not used</p></td> + </tr> + <tr> + <th>method</th> + <td><p>The method to be used</p></td> + </tr> + <tr> + <th>x</th> + <td><p>A mixed.mmkin object to print</p></td> + </tr> + <tr> + <th>digits</th> + <td><p>Number of digits to use for printing.</p></td> + </tr> + </table> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='va'>sampling_times</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='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> +<span class='va'>n_biphasic</span> <span class='op'><-</span> <span class='fl'>8</span> +<span class='va'>err_1</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>const <span class='op'>=</span> <span class='fl'>1</span>, prop <span class='op'>=</span> <span class='fl'>0.07</span><span class='op'>)</span> + +<span class='va'>DFOP_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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, + quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + +<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456</span><span class='op'>)</span> +<span class='va'>log_sd</span> <span class='op'><-</span> <span class='fl'>0.3</span> +<span class='va'>syn_biphasic_parms</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span> + k1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='va'>n_biphasic</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.05</span><span class='op'>)</span>, <span class='va'>log_sd</span><span class='op'>)</span>, + k2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='va'>n_biphasic</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.01</span><span class='op'>)</span>, <span class='va'>log_sd</span><span class='op'>)</span>, + g <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span><span class='op'>(</span><span class='va'>n_biphasic</span>, <span class='fl'>0</span>, <span class='va'>log_sd</span><span class='op'>)</span><span class='op'>)</span>, + f_parent_to_m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span><span class='op'>(</span><span class='va'>n_biphasic</span>, <span class='fl'>0</span>, <span class='va'>log_sd</span><span class='op'>)</span><span class='op'>)</span>, + k_m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='va'>n_biphasic</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.002</span><span class='op'>)</span>, <span class='va'>log_sd</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> + +<span class='va'>ds_biphasic_mean</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='va'>n_biphasic</span>, + <span class='kw'>function</span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>syn_biphasic_parms</span><span class='op'>[</span><span class='va'>i</span>, <span class='op'>]</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> + <span class='op'>}</span> +<span class='op'>)</span> + +<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span> +<span class='va'>ds_biphasic</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_biphasic_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, + sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='va'>err_1</span><span class='op'>$</span><span class='va'>const</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='va'>err_1</span><span class='op'>$</span><span class='va'>prop</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, + n <span class='op'>=</span> <span class='fl'>1</span>, secondary <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> +<span class='op'>}</span><span class='op'>)</span> + +<span class='co'># \dontrun{</span> +<span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>DFOP_SFO</span><span class='op'>)</span>, <span class='va'>ds_biphasic</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + +<span class='va'>f_mixed</span> <span class='op'><-</span> <span class='fu'>mixed</span><span class='op'>(</span><span class='va'>f_mmkin</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'>f_mixed</span><span class='op'>)</span> +</div><div class='output co'>#> Kinetic model fitted by nonlinear regression to each dataset +#> Structural model: +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) +#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +#> exp(-k2 * time))) * parent - k_m1 * m1 +#> +#> Data: +#> 271 observations of 2 variable(s) grouped in 8 datasets +#> +#> <mmkin> object +#> Status of individual fits: +#> +#> dataset +#> model 1 2 3 4 5 6 7 8 +#> DFOP-SFO OK OK OK OK OK C OK OK +#> +#> OK: No warnings +#> C: Optimisation did not converge: +#> iteration limit reached without convergence (10) +#> +#> Mean fitted parameters: +#> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 +#> 100.606304 -8.759216 -0.002001 -3.350539 -3.989549 +#> g_qlogis +#> -0.090353 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span> +</div><div class='img'><img src='mixed-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +</div></pre> + </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>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> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |