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diff --git a/docs/dev/reference/read_spreadsheet.html b/docs/dev/reference/read_spreadsheet.html new file mode 100644 index 00000000..d9c6ca2d --- /dev/null +++ b/docs/dev/reference/read_spreadsheet.html @@ -0,0 +1,155 @@ +<!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, shrink-to-fit=no"><title>Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet"><meta name="description" content="This function imports one dataset from each sheet of a spreadsheet file. +These sheets are selected based on the contents of a sheet 'Datasets', with +a column called 'Dataset Number', containing numbers identifying the dataset +sheets to be read in. In the second column there must be a grouping +variable, which will often be named 'Soil'. Optionally, time normalization +factors can be given in columns named 'Temperature' and 'Moisture'."><meta property="og:description" content="This function imports one dataset from each sheet of a spreadsheet file. +These sheets are selected based on the contents of a sheet 'Datasets', with +a column called 'Dataset Number', containing numbers identifying the dataset +sheets to be read in. In the second column there must be a grouping +variable, which will often be named 'Soil'. Optionally, time normalization +factors can be given in columns named 'Temperature' and 'Moisture'."><meta name="robots" content="noindex"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> 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class="external-link"><code>R/read_spreadsheet.R</code></a></small> + <div class="d-none name"><code>read_spreadsheet.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>This function imports one dataset from each sheet of a spreadsheet file. +These sheets are selected based on the contents of a sheet 'Datasets', with +a column called 'Dataset Number', containing numbers identifying the dataset +sheets to be read in. In the second column there must be a grouping +variable, which will often be named 'Soil'. Optionally, time normalization +factors can be given in columns named 'Temperature' and 'Moisture'.</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_spreadsheet</span><span class="op">(</span></span> +<span> <span class="va">path</span>,</span> +<span> valid_datasets <span class="op">=</span> <span class="st">"all"</span>,</span> +<span> parent_only <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> normalize <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-path">path<a class="anchor" aria-label="anchor" href="#arg-path"></a></dt> +<dd><p>Absolute or relative path to the spreadsheet file</p></dd> + + +<dt id="arg-valid-datasets">valid_datasets<a class="anchor" aria-label="anchor" href="#arg-valid-datasets"></a></dt> +<dd><p>Optional numeric index of the valid datasets, default is +to use all datasets</p></dd> + + +<dt id="arg-parent-only">parent_only<a class="anchor" aria-label="anchor" href="#arg-parent-only"></a></dt> +<dd><p>Should only the parent data be used?</p></dd> + + +<dt id="arg-normalize">normalize<a class="anchor" aria-label="anchor" href="#arg-normalize"></a></dt> +<dd><p>Should the time scale be normalized using temperature +and moisture normalisation factors in the sheet 'Datasets'?</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> + <p>There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'. +The first row read after the header read in from this sheet is assumed +to contain name and acronym of the parent compound.</p> +<p>The dataset sheets should be named using the dataset numbers read in from +the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, the name +of the observed variable (e.g. the acronym of the parent compound or +one of its transformation products) should be in the first column, +the time values should be in the second colum, and the observed value +in the third column.</p> +<p>In case relevant covariate data are available, they should be given +in a sheet 'Covariates', containing one line for each value of the grouping +variable specified in 'Datasets'. These values should be in the first +column and the column must have the same name as the second column in +'Datasets'. Covariates will be read in from columns four and higher. +Their names should preferably not contain special characters like spaces, +so they can be easily used for specifying covariate models.</p> +<p>A similar data structure is defined as the R6 class <a href="mkindsg.html">mkindsg</a>, but +is probably more complicated to use.</p> + </div> + + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> +</div> + + </footer></div> + + + + + + </body></html> + |