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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"> @@ -87,8 +31,7 @@ <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> @@ -98,6 +41,9 @@ <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> @@ -112,34 +58,27 @@ <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>Subsetting method for mmkin objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>Extract.mmkin.Rd</code></div> </div> @@ -147,122 +86,116 @@ <p>Subsetting method for mmkin objects</p> </div> - <pre class="usage"># S3 method for mmkin -[(x, i, j, ..., drop = FALSE)</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>x</th> - <td><p>An <code><a href='mmkin.html'>mmkin</a> object</code></p></td> - </tr> - <tr> - <th>i</th> - <td><p>Row index selecting the fits for specific models</p></td> - </tr> - <tr> - <th>j</th> - <td><p>Column index selecting the fits to specific datasets</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used, only there to satisfy the generic method definition</p></td> - </tr> - <tr> - <th>drop</th> - <td><p>If FALSE, the method always returns an mmkin object, otherwise -either a list of mkinfit objects or a single mkinfit object.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre><code># S3 method for mmkin +[(x, i, j, ..., drop = FALSE)</code></pre></div> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd> +<dt>i</dt> +<dd><p>Row index selecting the fits for specific models</p></dd> +<dt>j</dt> +<dd><p>Column index selecting the fits to specific datasets</p></dd> +<dt>...</dt> +<dd><p>Not used, only there to satisfy the generic method definition</p></dd> +<dt>drop</dt> +<dd><p>If FALSE, the method always returns an mmkin object, otherwise +either a list of mkinfit objects or a single mkinfit object.</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> + <p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</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='co'># Only use one core, to pass R CMD check --as-cran</span> - <span class='va'>fits</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, - cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B C -#> FOMC OK OK -#> -#> OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"B"</span><span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B -#> SFO OK -#> FOMC OK -#> -#> OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span><span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B -#> SFO OK -#> -#> OK: No warnings</div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span> - <span class='co'># This extracts an mkinfit object with lots of components</span> - <span class='va'>fits</span><span class='op'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span><span class='op'>]</span><span class='op'>]</span> - <span class='op'>)</span> -</div><div class='output co'>#> $par -#> parent_0 log_alpha log_beta sigma -#> 99.666192 2.549850 5.050586 1.890202 -#> -#> $objective -#> [1] 28.58291 -#> -#> $convergence -#> [1] 0 -#> -#> $iterations -#> [1] 21 -#> -#> $evaluations -#> function gradient -#> 25 78 -#> -#> $message -#> [1] "both X-convergence and relative convergence (5)" -#> </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="co"># Only use one core, to pass R CMD check --as-cran</span></span> +<span class="r-in"> <span class="va">fits</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/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><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>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span> +<span class="r-in"> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B C </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"> <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"> <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"></span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span> +<span class="r-in"> <span class="co"># This extracts an mkinfit object with lots of components</span></span> +<span class="r-in"> <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span> +<span class="r-in"> <span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> $par</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $objective</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $convergence</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $iterations</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 21</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $evaluations</span> +<span class="r-out co"><span class="r-pr">#></span> function gradient </span> +<span class="r-out co"><span class="r-pr">#></span> 25 78 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $message</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "both X-convergence and relative convergence (5)"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs 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