Setting up PELMO runs, execution and evaluation

It all works!
author: Johannes Ranke <jranke@uni-bremen.de> 2017-01-29 16:58:53 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2017-01-29 18:52:24 +0100
commit: a6c13f70f6c6669a8088827a602ac475fdf9b624 (patch)
tree: e3bcc3e9ff9e006f3e9d87a1df226752fa4753cc /docs/reference/PELMO_runs.html
parent: c22143d8ec53026cb1e439bdbba1d725a11b4b0c (diff)
1 files changed, 144 insertions, 0 deletions
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
new file mode 100644
index 0000000..e872196
--- /dev/null
+++ b/docs/reference/PELMO_runs.html
@@ -0,0 +1,144 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
+  <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>Set up runs for FOCUS PELMO — PELMO_runs • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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>
+    <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">
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <a class="navbar-brand" href="../index.html">pfm</a>
+    </div>
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+      <div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Set up runs for FOCUS PELMO</h1>
+    </div>
+
+    
+    <p>Per default, the runs are also executed with FOCUS PELMO, and the results are processed
+and returned. Currently, only FOCUS PELMO as installed on Linux (or other Unix systems)
+using the <code>install_PELMO</code> from the <code>PELMO.installeR</code> package
+maintained on github is supported. In such installations, FOCUS PELMO is installed into
+package installation directory of <code>PELMO.installeR</code> and run with <code>wine</code>.</p>
+    
+
+    <pre><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='kw'>execute</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>), <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>run_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>))
+
+<span class='fu'>evaluate_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <dl class="dl-horizontal">
+      <dt>runs</dt>
+      <dd>A list of lists. Each inner lists has an element named &#39;psm&#39;
+that holds the psm string, and elements named using three letter crop acronyms,
+as used in <code><a href='FOCUS_PELMO_crops.html'>FOCUS_PELMO_crops</a></code>,
+that hold character vectors of three letter scenario acronyms
+as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012</a></code>.</dd>
+      <dt>psm_dir</dt>
+      <dd>The directory where the psm files are located</dd>
+      <dt>version</dt>
+      <dd>The FOCUS PELMO version</dd>
+      <dt>PELMO_base</dt>
+      <dd>Where the FOCUS PELMO installation is located</dd>
+      <dt>execute</dt>
+      <dd>Should PELMO be executed directly?</dd>
+      <dt>cores</dt>
+      <dd>The number of cores to execute PELMO runs in parallel</dd>
+      <dt>evaluate</dt>
+      <dd>Should the results be returned?</dd>
+      <dt>overwrite</dt>
+      <dd>Should an existing run directories be overwritten</dd>
+    </dl>
+    
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>PELMO.installeR <a href = 'https://jranke.github.io/PELMO.installeR'>https://jranke.github.io/PELMO.installeR</a></p>
+    <p>Wine <a href = 'https://winehq.org'>https://winehq.org</a></p>
+    
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#references">References</a></li>
+          </ul>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
author	Johannes Ranke <jranke@uni-bremen.de>	2017-01-29 16:58:53 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2017-01-29 18:52:24 +0100
commit	a6c13f70f6c6669a8088827a602ac475fdf9b624 (patch)
tree	e3bcc3e9ff9e006f3e9d87a1df226752fa4753cc /docs/reference/PELMO_runs.html
parent	c22143d8ec53026cb1e439bdbba1d725a11b4b0c (diff)