aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/read_spreadsheet.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2022-11-17 14:54:20 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-17 14:56:25 +0100
commite5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 (patch)
tree18740ef050a68d1a6fe91f1bd2fdfdd97ac6448b /docs/reference/read_spreadsheet.html
parent90354f5cd9e095f9ef98424689a2716770b248d4 (diff)
Complete update of online docs for v1.2.0
Diffstat (limited to 'docs/reference/read_spreadsheet.html')
-rw-r--r--docs/reference/read_spreadsheet.html179
1 files changed, 179 insertions, 0 deletions
diff --git a/docs/reference/read_spreadsheet.html b/docs/reference/read_spreadsheet.html
new file mode 100644
index 00000000..d2873cee
--- /dev/null
+++ b/docs/reference/read_spreadsheet.html
@@ -0,0 +1,179 @@
+<!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=1.0"><title>Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet • 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="Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet"><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'."><!-- 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><body data-spy="scroll" data-target="#toc">
+
+
+ <div class="container template-reference-topic">
+ <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">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </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">1.2.0</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" data-bs-toggle="dropdown" 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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
+ </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/" class="external-link">
+ <span class="fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Read datasets and relevant meta information from a spreadsheet file</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/read_spreadsheet.R" class="external-link"><code>R/read_spreadsheet.R</code></a></small>
+ <div class="hidden name"><code>read_spreadsheet.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <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 id="ref-usage">
+ <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 id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>path</dt>
+<dd><p>Absolute or relative path to the spreadsheet file</p></dd>
+
+
+<dt>valid_datasets</dt>
+<dd><p>Optional numeric index of the valid datasets, default is
+to use all datasets</p></dd>
+
+
+<dt>parent_only</dt>
+<dd><p>Should only the parent data be used?</p></dd>
+
+
+<dt>normalize</dt>
+<dd><p>Should the time scale be normalized using temperature
+and moisture normalisation factors in the sheet 'Datasets'?</p></dd>
+
+</dl></div>
+ <div id="details">
+ <h2>Details</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, 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>An similar data structure is defined as the R6 class <a href="mkindsg.html">mkindsg</a>, but
+is probably more complicated to use.</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>
+</div>
+
+
+ <footer><div class="copyright">
+ <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <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>
+
+
+
+
+
+
+ </body></html>
+

Contact - Imprint