GitLab at IIASA

Skip to content
GitLab
Find file Normal view History Permalink
index.html 10.1 KiB
Newer Older
Hugo Scherer's avatar
Improved FarmDynR package with capacity for FADN data and useful functions for results analysis
Hugo Scherer committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 
<!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>Run FarmDyn from R and create sample farms • FarmDynR</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="Run FarmDyn from R and create sample farms">
Hugo Scherer's avatar
Fixed typos, added imports, updated README and DESCRIPTION  
Hugo Scherer committed
15 
<meta property="og:description" content="This package allows the user to run FarmDyn from R, create sample farms from FADN data for use in FarmDyn, and includes useful functions to work with the results from FarmDyn.">
Hugo Scherer's avatar
Improved FarmDynR package with capacity for FADN data and useful functions for results analysis
Hugo Scherer committed
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 
<!-- 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-home">
      <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">FarmDynR</a>
Hugo Scherer's avatar
Fixed typos, added imports, updated README and DESCRIPTION  
Hugo Scherer committed
36 
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.5.0</span>
Hugo Scherer's avatar
Improved FarmDynR package with capacity for FADN data and useful functions for results analysis
Hugo Scherer committed
37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
<li>
  <a href="reference/index.html">Reference</a>
</li>
<li>
  <a href="news/index.html">Changelog</a>
</li>
      </ul>
<ul class="nav navbar-nav navbar-right"></ul>
</div>
<!--/.nav-collapse -->
  </div>
<!--/.container -->
</div>
<!--/.navbar -->

      

      </header><div class="row">
  <div class="contents col-md-9">
<div class="section level1">
<div class="page-header"><h1 id="farmdynr">FarmDynR<a class="anchor" aria-label="anchor" href="#farmdynr"></a>
</h1></div>
<p>Developed by Hugo Scherer and Marc Müller at Wageningen Economic Research.</p>
<!-- badges: start -->
<!-- badges: end -->
<p>The goal of FarmDynR is to give the user the ability to aggregate FADN data to create representative farms for any grouping available, generate descriptive statistics, and to run FarmDyn from R.</p>
<div class="section level2">
<h2 id="requirements">Requirements<a class="anchor" aria-label="anchor" href="#requirements"></a>
</h2>
Hugo Scherer's avatar
Updated read me  
Hugo Scherer committed
71 72 73 74 75 76 77 78 79 80 81 82 
<p>This package requires that you have GAMS and FarmDyn installed. Additionally, the package imports from:</p>
<ul>
<li><p>gdxrrw (remember to load GAMS with `igdx()` with the path to your version of GAMS)</p></li>
<li><p>readr</p></li>
<li><p>dplyr</p></li>
<li><p>tidyr</p></li>
<li><p>readxl</p></li>
</ul>
<p>It also suggests:</p>
<ul>
<li>stringr</li>
</ul>
Hugo Scherer's avatar
Improved FarmDynR package with capacity for FADN data and useful functions for results analysis
Hugo Scherer committed
83 84 85 86 87 88 89 90 91 92 93 
</div>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<p>You can install the development version of FarmDynR like so:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">'https://gitlab.iiasa.ac.at/mind-step/FarmDynR'</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"></a>
</h2>
Hugo Scherer's avatar
Updated read me  
Hugo Scherer committed
94 95 96 97 98 99 
<p>The workflow for this package is as follows:</p>
<ol style="list-style-type: decimal">
<li><p>Read the FADN data into R</p></li>
<li><p>Run <code><a href="reference/fadn2fd.html">fadn2fd()</a></code> with the FADN data, farmbranch desired, the mapping and the option to save GDX files based on the mapping - Yields will be calculated and the FADN data will be prepared - Outliers are removed</p></li>
<li><p>Write batch file with <code><a href="reference/writeBatch.html">writeBatch()</a></code> and run FarmDyn with <code><a href="reference/runFarmDynfromBatch.html">runFarmDynfromBatch()</a></code> using the created batch file - Optional: Create descriptive statistics for reporting with <code><a href="reference/fd_desc.html">fd_desc()</a></code> with the farmbranch.</p></li>
</ol>
Hugo Scherer's avatar
Improved FarmDynR package with capacity for FADN data and useful functions for results analysis
Hugo Scherer committed
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 
</div>
<div class="section level2">
<h2 id="example">Example<a class="anchor" aria-label="anchor" href="#example"></a>
</h2>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.wur.nl/" class="external-link">FarmDynR</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Read in FADN data</span></span>
<span><span class="va">fadn</span> <span class="op">&lt;-</span> <span class="fu">read_fadn</span><span class="op">(</span><span class="st">"path/to/fadn/data"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Create mapping</span></span>
<span><span class="va">mapping</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</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">"NUTS0"</span>, <span class="st">"misc%OrganicCode"</span><span class="op">)</span>, <span class="st">"NUTS0"</span>, <span class="st">"NUTS2"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Create FarmDyn data</span></span>
<span><span class="va">fd_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/fadn2fd.html">fadn2fd</a></span><span class="op">(</span><span class="va">fadn</span>, <span class="st">"Dairy"</span>, <span class="va">mapping</span>, save_gdx <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Write batch file</span></span>
Hugo Scherer's avatar
Fixed bug with duplicated entries in documentation  
Hugo Scherer committed
117 
<span><span class="fu"><a href="reference/writeBatch.html">writeBatch</a></span><span class="op">(</span><span class="st">"path/to/FarmDyn"</span>, <span class="va">mapping</span>, <span class="va">farmIds</span><span class="op">)</span></span>
Hugo Scherer's avatar
Improved FarmDynR package with capacity for FADN data and useful functions for results analysis
Hugo Scherer committed
118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 
<span></span>
<span><span class="co"># Run FarmDyn</span></span>
<span><span class="fu"><a href="reference/runFarmDynfromBatch.html">runFarmDynfromBatch</a></span><span class="op">(</span><span class="st">"path/to/batch/file"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Create descriptive statistics</span></span>
<span><span class="fu"><a href="reference/fd_desc.html">fd_desc</a></span><span class="op">(</span><span class="va">fd_data</span><span class="op">)</span></span></code></pre></div>
</div>
</div>
  </div>

  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <div class="license">
<h2 data-toc-skip>License</h2>
<ul class="list-unstyled">
<li><a href="LICENSE.html">Full license</a></li>
<li><small>GPL (&gt;= 3)</small></li>
</ul>
</div>


<div class="citation">
<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html#citation">Citing FarmDynR</a></li>
</ul>
</div>

<div class="developers">
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>Hugo Scherer <br><small class="roles"> Author, maintainer </small>  </li>
<li><a href="authors.html">More about authors...</a></li>
</ul>
</div>



  </div>
</div>


      <footer><div class="copyright">
  <p></p>
<p>Developed by Hugo Scherer.</p>
</div>

<div class="pkgdown">
  <p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer>
</div>

  


  

  </body>
</html>

GitLab at IIASA