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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -73,23 +18,21 @@ specified as well." /> </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">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</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"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <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> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,6 +42,9 @@ specified as well." /> <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> @@ -113,34 +59,27 @@ specified as well." /> <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>Export a list of datasets format to a CAKE study file</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/CAKE_export.R'><code>R/CAKE_export.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/CAKE_export.R" class="external-link"><code>R/CAKE_export.R</code></a></small> <div class="hidden name"><code>CAKE_export.Rd</code></div> </div> @@ -149,116 +88,115 @@ specified as well." /> specified as well.</p> </div> - <pre class="usage"><span class='fu'>CAKE_export</span><span class='op'>(</span> - <span class='va'>ds</span>, - map <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='st'>"Parent"</span><span class='op'>)</span>, - links <span class='op'>=</span> <span class='cn'>NA</span>, - filename <span class='op'>=</span> <span class='st'>"CAKE_export.csf"</span>, - path <span class='op'>=</span> <span class='st'>"."</span>, - overwrite <span class='op'>=</span> <span class='cn'>FALSE</span>, - study <span class='op'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>, - description <span class='op'>=</span> <span class='st'>""</span>, - time_unit <span class='op'>=</span> <span class='st'>"days"</span>, - res_unit <span class='op'>=</span> <span class='st'>"% AR"</span>, - comment <span class='op'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>, - date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, - optimiser <span class='op'>=</span> <span class='st'>"IRLS"</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>ds</th> - <td><p>A named list of datasets in long format as compatible with -<code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>map</th> - <td><p>A character vector with CAKE compartment names (Parent, A1, ...), -named with the names used in the list of datasets.</p></td> - </tr> - <tr> - <th>links</th> - <td><p>An optional character vector of target compartments, named with + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">CAKE_export</span><span class="op">(</span></span> +<span> <span class="va">ds</span>,</span> +<span> map <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>parent <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span> +<span> links <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>,</span> +<span> path <span class="op">=</span> <span class="st">"."</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> study <span class="op">=</span> <span class="st">"Degradinol aerobic soil degradation"</span>,</span> +<span> description <span class="op">=</span> <span class="st">""</span>,</span> +<span> time_unit <span class="op">=</span> <span class="st">"days"</span>,</span> +<span> res_unit <span class="op">=</span> <span class="st">"% AR"</span>,</span> +<span> comment <span class="op">=</span> <span class="st">""</span>,</span> +<span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> optimiser <span class="op">=</span> <span class="st">"IRLS"</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>ds</dt> +<dd><p>A named list of datasets in long format as compatible with +<code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + +<dt>map</dt> +<dd><p>A character vector with CAKE compartment names (Parent, A1, ...), +named with the names used in the list of datasets.</p></dd> + + +<dt>links</dt> +<dd><p>An optional character vector of target compartments, named with the names of the source compartments. In order to make this easier, the -names are used as in the datasets supplied.</p></td> - </tr> - <tr> - <th>filename</th> - <td><p>Where to write the result. Should end in .csf in order to be -compatible with CAKE.</p></td> - </tr> - <tr> - <th>path</th> - <td><p>An optional path to the output file.</p></td> - </tr> - <tr> - <th>overwrite</th> - <td><p>If TRUE, existing files are overwritten.</p></td> - </tr> - <tr> - <th>study</th> - <td><p>The name of the study.</p></td> - </tr> - <tr> - <th>description</th> - <td><p>An optional description.</p></td> - </tr> - <tr> - <th>time_unit</th> - <td><p>The time unit for the residue data.</p></td> - </tr> - <tr> - <th>res_unit</th> - <td><p>The unit used for the residues.</p></td> - </tr> - <tr> - <th>comment</th> - <td><p>An optional comment.</p></td> - </tr> - <tr> - <th>date</th> - <td><p>The date of file creation.</p></td> - </tr> - <tr> - <th>optimiser</th> - <td><p>Can be OLS or IRLS.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +names are used as in the datasets supplied.</p></dd> + + +<dt>filename</dt> +<dd><p>Where to write the result. Should end in .csf in order to be +compatible with CAKE.</p></dd> + + +<dt>path</dt> +<dd><p>An optional path to the output file.</p></dd> + + +<dt>overwrite</dt> +<dd><p>If TRUE, existing files are overwritten.</p></dd> + + +<dt>study</dt> +<dd><p>The name of the study.</p></dd> + + +<dt>description</dt> +<dd><p>An optional description.</p></dd> + +<dt>time_unit</dt> +<dd><p>The time unit for the residue data.</p></dd> + + +<dt>res_unit</dt> +<dd><p>The unit used for the residues.</p></dd> + + +<dt>comment</dt> +<dd><p>An optional comment.</p></dd> + + +<dt>date</dt> +<dd><p>The date of file creation.</p></dd> + + +<dt>optimiser</dt> +<dd><p>Can be OLS or IRLS.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function is called for its side effect.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </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> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |