-
Notifications
You must be signed in to change notification settings - Fork 22
/
Copy pathFLUXNET2015_processing.html
352 lines (274 loc) · 27.3 KB
/
FLUXNET2015_processing.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
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
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
<!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>FLUXNET2015 processing • FluxnetLSM</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="FLUXNET2015 processing">
<meta property="og:description" content="FluxnetLSM">
<!-- 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-article">
<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">FluxnetLSM</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../reference/index.html">Reference</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/FLUXNET2015_processing.html">FLUXNET2015 processing</a>
</li>
<li>
<a href="../articles/lathuile_processing.html">LaThuile processing</a>
</li>
<li>
<a href="../articles/meta_data.html">Meta-data description</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/aukkola/FluxnetLSM/" 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 toc-ignore">
<h1 data-toc-skip>FLUXNET2015 processing</h1>
<h4 data-toc-skip class="author">Koen
Hufkens</h4>
<h4 data-toc-skip class="date">2022-05-25</h4>
<small class="dont-index">Source: <a href="https://github.com/aukkola/FluxnetLSM/blob/HEAD/vignettes/FLUXNET2015_processing.Rmd" class="external-link"><code>vignettes/FLUXNET2015_processing.Rmd</code></a></small>
<div class="hidden name"><code>FLUXNET2015_processing.Rmd</code></div>
</div>
<div class="section level2">
<h2 id="single-site">Single site<a class="anchor" aria-label="anchor" href="#single-site"></a>
</h2>
<p>Example data conversion for the Howard Springs site using
FLUXNET2015.</p>
<p>See LaThuile/example_conversion_single_site.R for the corresponding
La Thuile example.</p>
<p>Converts useful variables from a FLUXNET2015 “FULLSET” spreatsheet
format into two netcdf files, one for fluxes, and one for met forcings.
For “SUBSET” data, set flx2015_version=“SUBSET” in the main
function.</p>
<p>The user must provide the input directory path, output directory path
and site code. All other settings are optional. This example uses
ERAinterim gapfilling for meteorological variables, all other options
are set to their default values.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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://github.com/aukkola/FluxnetLSM" class="external-link">FluxnetLSM</a></span><span class="op">)</span>
<span class="co">#############################</span>
<span class="co">###--- Required inputs ---###</span>
<span class="co">#############################</span>
<span class="co">#--- User must define these ---#</span>
<span class="co">#Fluxnet site ID (see http://fluxnet.fluxdata.org/sites/site-list-and-pages/)</span>
<span class="va">site_code</span> <span class="op"><-</span> <span class="st">"AU-How"</span>
<span class="co"># This directory should contain appropriate data from </span>
<span class="co"># http://fluxnet.fluxdata.org/data/fluxnet2015-dataset/</span>
<span class="va">in_path</span> <span class="op"><-</span> <span class="st">"./Inputs"</span>
<span class="va">ERA_path</span> <span class="op"><-</span> <span class="st">"./ERA_inputs"</span>
<span class="co">#Outputs will be saved to this directory</span>
<span class="va">out_path</span> <span class="op"><-</span> <span class="st">"./Outputs"</span>
<span class="co">#--- Automatically retrieve all Fluxnet files in input directory ---#</span>
<span class="co"># Input Fluxnet data file (using FULLSET in this example, see R/Helpers.R for details)</span>
<span class="va">infile</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_fluxnet_files.html">get_fluxnet_files</a></span><span class="op">(</span><span class="va">in_path</span>, <span class="va">site_code</span><span class="op">)</span>
<span class="co">#Retrieve dataset version</span>
<span class="va">datasetversion</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_fluxnet_version_no.html">get_fluxnet_version_no</a></span><span class="op">(</span><span class="va">infile</span><span class="op">)</span>
<span class="co">#Retrieve ERAinterim file</span>
<span class="va">era_file</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_fluxnet_erai_files.html">get_fluxnet_erai_files</a></span><span class="op">(</span><span class="va">ERA_path</span>, <span class="va">site_code</span><span class="op">)</span>
<span class="co">###############################</span>
<span class="co">###--- Optional settings ---###</span>
<span class="co">###############################</span>
<span class="co">#Retrieve default processing options</span>
<span class="va">conv_opts</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_default_conversion_options.html">get_default_conversion_options</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># Set gapfilling options to ERAinterim</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">met_gapfill</span> <span class="op"><-</span> <span class="st">"ERAinterim"</span>
<span class="co">##########################</span>
<span class="co">###--- Run analysis ---###</span>
<span class="co">##########################</span>
<span class="fu"><a href="../reference/convert_fluxnet_to_netcdf.html">convert_fluxnet_to_netcdf</a></span><span class="op">(</span>site_code <span class="op">=</span> <span class="va">site_code</span>, infile <span class="op">=</span> <span class="va">infile</span>,
era_file<span class="op">=</span><span class="va">era_file</span>, out_path <span class="op">=</span> <span class="va">out_path</span>,
conv_opts <span class="op">=</span> <span class="va">conv_opts</span><span class="op">)</span>
<span class="co">#Alternatively you can pass the gapfilling option directly to the main function:</span>
<span class="co"># convert_fluxnet_to_netcdf(site_code = site_code, infile = infile, </span>
<span class="co"># era_file = era_file, out_path = out_path,</span>
<span class="co"># met_gapfill="ERAinterim")</span></code></pre></div>
</div>
<div class="section level2">
<h2 id="multiple-sites">Multiple sites<a class="anchor" aria-label="anchor" href="#multiple-sites"></a>
</h2>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co">#--- Automatically retrieve all Fluxnet files in input directory ---#</span>
<span class="co"># Input Fluxnet data files (using FULLSET in this example, se R/Helpers.R for details)</span>
<span class="va">infiles</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_fluxnet_files.html">get_fluxnet_files</a></span><span class="op">(</span><span class="va">in_path</span><span class="op">)</span>
<span class="co">#Retrieve dataset versions</span>
<span class="va">datasetversions</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">infiles</span>, <span class="va">get_fluxnet_version_no</span><span class="op">)</span>
<span class="co">#Retrieve site codes</span>
<span class="va">site_codes</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">infiles</span>, <span class="va">get_path_site_code</span><span class="op">)</span>
<span class="co">###############################</span>
<span class="co">###--- Optional settings ---###</span>
<span class="co">###############################</span>
<span class="va">conv_opts</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_default_conversion_options.html">get_default_conversion_options</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># ERAinterim meteo file for gap-filling met data (set to NA if not desired)</span>
<span class="co"># Find ERA-files corresponding to site codes</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">met_gapfill</span> <span class="op"><-</span> <span class="st">"ERAinterim"</span>
<span class="va">ERA_files</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">site_codes</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="../reference/get_fluxnet_erai_files.html">get_fluxnet_erai_files</a></span><span class="op">(</span><span class="va">ERA_path</span>, site_code<span class="op">=</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>
<span class="co">#Stop if didn't find ERA files</span>
<span class="kw">if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">ERA_files</span>, <span class="va">length</span><span class="op">)</span><span class="op">==</span><span class="fl">0</span><span class="op">)</span> <span class="op">&</span> <span class="va">conv_opts</span><span class="op">$</span><span class="va">met_gapfill</span><span class="op">==</span><span class="st">"ERAinterim"</span><span class="op">)</span><span class="op">{</span>
<span class="kw"><a href="https://rdrr.io/r/base/stop.html" class="external-link">stop</a></span><span class="op">(</span><span class="st">"No ERA files found, amend input path"</span><span class="op">)</span>
<span class="op">}</span>
<span class="co">##########################</span>
<span class="co">###--- Run analysis ---###</span>
<span class="co">##########################</span>
<span class="co">#Loops through sites</span>
<span class="fu"><a href="https://rdrr.io/r/base/mapply.html" class="external-link">mapply</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">site_code</span>, <span class="va">infile</span>, <span class="va">ERA_file</span>, <span class="va">datasetversion</span><span class="op">)</span> <span class="op">{</span>
<span class="kw"><a href="https://rdrr.io/r/base/try.html" class="external-link">try</a></span><span class="op">(</span>
<span class="fu"><a href="../reference/convert_fluxnet_to_netcdf.html">convert_fluxnet_to_netcdf</a></span><span class="op">(</span>site_code <span class="op">=</span> <span class="va">site_code</span>,
infile <span class="op">=</span> <span class="va">infile</span>,
out_path <span class="op">=</span> <span class="va">out_path</span>,
era_file <span class="op">=</span> <span class="va">ERA_file</span>,
conv_opts <span class="op">=</span> <span class="va">conv_opts</span>,
datasetversion <span class="op">=</span> <span class="va">datasetversion</span>
<span class="op">)</span>
<span class="op">)</span><span class="op">}</span>,
site_code <span class="op">=</span> <span class="va">site_codes</span>,
infile <span class="op">=</span> <span class="va">infiles</span>,
ERA_file <span class="op">=</span> <span class="va">ERA_files</span>,
datasetversion <span class="op">=</span> <span class="va">datasetversions</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level2">
<h2 id="multiple-sites-parallel">Multiple sites (parallel)<a class="anchor" aria-label="anchor" href="#multiple-sites-parallel"></a>
</h2>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># Get default conversion options. See help(get_default_conversion_options)</span>
<span class="va">conv_opts</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_default_conversion_options.html">get_default_conversion_options</a></span><span class="op">(</span><span class="op">)</span>
<span class="co">#--- Automatically retrieve all Fluxnet files in input directory ---#</span>
<span class="co"># Input Fluxnet data files (using FULLSET in this example, se R/Helpers.R for details)</span>
<span class="va">infiles</span> <span class="op"><-</span> <span class="fu"><a href="../reference/get_fluxnet_files.html">get_fluxnet_files</a></span><span class="op">(</span><span class="va">in_path</span>,
datasetname <span class="op">=</span> <span class="va">conv_opts</span><span class="op">$</span><span class="va">datasetname</span>,
subset <span class="op">=</span> <span class="va">conv_opts</span><span class="op">$</span><span class="va">flx2015_version</span><span class="op">)</span>
<span class="co">#Retrieve dataset versions</span>
<span class="va">datasetversions</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">infiles</span>, <span class="va">get_fluxnet_version_no</span><span class="op">)</span>
<span class="co">#Retrieve site codes</span>
<span class="va">site_codes</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">infiles</span>, <span class="va">get_path_site_code</span><span class="op">)</span>
<span class="co">###############################</span>
<span class="co">###--- Optional settings ---###</span>
<span class="co">###############################</span>
<span class="co"># ERAinterim meteo file for gap-filling met data (set to FALSE if not desired)</span>
<span class="co"># Find ERA-files corresponding to site codes</span>
<span class="va">ERA_gapfill</span> <span class="op"><-</span> <span class="cn">TRUE</span>
<span class="va">ERA_files</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">site_codes</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span>
<span class="fu"><a href="../reference/get_fluxnet_erai_files.html">get_fluxnet_erai_files</a></span><span class="op">(</span><span class="va">ERA_path</span>, site_code <span class="op">=</span> <span class="va">x</span>,
datasetname <span class="op">=</span> <span class="va">conv_opts</span><span class="op">$</span><span class="va">datasetname</span><span class="op">)</span>
<span class="op">}</span><span class="op">)</span>
<span class="co">#Stop if didn't find ERA files</span>
<span class="kw">if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">ERA_files</span>, <span class="va">length</span><span class="op">)</span><span class="op">==</span><span class="fl">0</span><span class="op">)</span> <span class="op">&</span> <span class="va">ERA_gapfill</span><span class="op">==</span><span class="cn">TRUE</span><span class="op">)</span><span class="op">{</span>
<span class="kw"><a href="https://rdrr.io/r/base/stop.html" class="external-link">stop</a></span><span class="op">(</span><span class="st">"No ERA files found, amend input path"</span><span class="op">)</span>
<span class="op">}</span>
<span class="co">#Thresholds for missing and gap-filled time steps</span>
<span class="co">#Note: Always checks for missing values. If no gapfilling </span>
<span class="co">#thresholds set, will not check for gap-filling.</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">missing</span> <span class="op"><-</span> <span class="fl">15</span> <span class="co">#max. percent missing (must be set)</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">gapfill_all</span> <span class="op"><-</span> <span class="fl">20</span> <span class="co">#max. percent gapfilled (optional)</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">gapfill_good</span> <span class="op"><-</span> <span class="cn">NA</span> <span class="co">#max. percent good-quality gapfilled (optional, ignored if gapfill_all set)</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">gapfill_med</span> <span class="op"><-</span> <span class="cn">NA</span> <span class="co">#max. percent medium-quality gapfilled (optional, ignored if gapfill_all set)</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">gapfill_poor</span> <span class="op"><-</span> <span class="cn">NA</span> <span class="co">#max. percent poor-quality gapfilled (optional, ignored if gapfill_all set)</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">min_yrs</span> <span class="op"><-</span> <span class="fl">2</span> <span class="co">#min. number of consecutive years</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">met_gapfill</span> <span class="op"><-</span> <span class="st">"ERAinterim"</span> <span class="co">#min. number of consecutive years</span>
<span class="co">#Should code produce plots to visualise outputs? Set to NA if not desired.</span>
<span class="co">#(annual: average monthly cycle; diurnal: average diurnal cycle by season;</span>
<span class="co">#timeseries: 14-day running mean time series)</span>
<span class="va">plot</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"annual"</span>, <span class="st">"diurnal"</span>,<span class="st">"timeseries"</span><span class="op">)</span>
<span class="co">#Should all evaluation variables be included regardless of data gaps?</span>
<span class="co">#If FALSE, removes evaluation variables with gaps in excess of thresholds</span>
<span class="va">conv_opts</span><span class="op">$</span><span class="va">include_all_eval</span> <span class="op"><-</span> <span class="cn">TRUE</span>
<span class="co">##########################</span>
<span class="co">###--- Run analysis ---###</span>
<span class="co">##########################</span>
<span class="co">#Initialise clusters (using 2 cores here)</span>
<span class="va">cl</span> <span class="op"><-</span> <span class="fu">makeCluster</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">'cl.cores'</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
<span class="co">#Import variables to cluster</span>
<span class="fu">clusterExport</span><span class="op">(</span><span class="va">cl</span>, <span class="st">"out_path"</span><span class="op">)</span>
<span class="kw">if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">exists</a></span><span class="op">(</span><span class="st">"conv_opts"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span><span class="fu">clusterExport</span><span class="op">(</span><span class="va">cl</span>, <span class="st">"conv_opts"</span><span class="op">)</span><span class="op">}</span>
<span class="kw">if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">exists</a></span><span class="op">(</span><span class="st">"datasetversion"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span><span class="fu">clusterExport</span><span class="op">(</span><span class="va">cl</span>, <span class="st">"datasetversion"</span><span class="op">)</span><span class="op">}</span>
<span class="kw">if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">exists</a></span><span class="op">(</span><span class="st">"plot"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span><span class="fu">clusterExport</span><span class="op">(</span><span class="va">cl</span>, <span class="st">"plot"</span><span class="op">)</span><span class="op">}</span>
<span class="co">#Loops through sites</span>
<span class="fu">clusterMap</span><span class="op">(</span>cl <span class="op">=</span> <span class="va">cl</span>, <span class="kw">function</span><span class="op">(</span><span class="va">site_code</span>, <span class="va">infile</span>, <span class="va">ERA_file</span>, <span class="va">datasetversion</span><span class="op">)</span> <span class="op">{</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://github.com/aukkola/FluxnetLSM" class="external-link">FluxnetLSM</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/conditions.html" class="external-link">tryCatch</a></span><span class="op">(</span>
<span class="fu"><a href="../reference/convert_fluxnet_to_netcdf.html">convert_fluxnet_to_netcdf</a></span><span class="op">(</span>
site_code <span class="op">=</span> <span class="va">site_code</span>,
infile <span class="op">=</span> <span class="va">infile</span>,
era_file <span class="op">=</span> <span class="va">ERA_file</span>,
out_path<span class="op">=</span><span class="va">out_path</span>,
conv_opts <span class="op">=</span> <span class="va">conv_opts</span>,
plot <span class="op">=</span> <span class="va">plot</span>,
datasetversion <span class="op">=</span> <span class="va">datasetversion</span> <span class="co"># overrides conv_opts</span>
<span class="op">)</span>,
error <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">e</span><span class="op">)</span> <span class="cn">NULL</span><span class="op">)</span>
<span class="op">}</span>,
site_code <span class="op">=</span> <span class="va">site_codes</span>,
infile <span class="op">=</span> <span class="va">infiles</span>,
datasetversion <span class="op">=</span> <span class="va">datasetversions</span>,
ERA_file <span class="op">=</span> <span class="va">ERA_files</span><span class="op">)</span>
<span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer><div class="copyright">
<p></p>
<p>Developed by Ukkola Anna.</p>
</div>
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
</div>
</footer>
</div>
</body>
</html>