-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathgroundwater-basins-import.html
More file actions
704 lines (687 loc) · 39.4 KB
/
groundwater-basins-import.html
File metadata and controls
704 lines (687 loc) · 39.4 KB
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
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.57">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="Andy Lyons">
<meta name="dcterms.date" content="2024-09-13">
<title>How to Import CA Groundwater Basins into R with arcgislayers</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for syntax highlighting */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
}
pre.numberSource { margin-left: 3em; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
</style>
<script src="groundwater-basins-import_files/libs/clipboard/clipboard.min.js"></script>
<script src="groundwater-basins-import_files/libs/quarto-html/quarto.js"></script>
<script src="groundwater-basins-import_files/libs/quarto-html/popper.min.js"></script>
<script src="groundwater-basins-import_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="groundwater-basins-import_files/libs/quarto-html/anchor.min.js"></script>
<link href="groundwater-basins-import_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="groundwater-basins-import_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="groundwater-basins-import_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="groundwater-basins-import_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="groundwater-basins-import_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light"><link href="groundwater-basins-import_files/libs/pagedtable-1.1/css/pagedtable.css" rel="stylesheet">
<script src="groundwater-basins-import_files/libs/pagedtable-1.1/js/pagedtable.js"></script>
</head>
<body>
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active"><h2 id="toc-title">Table of contents</h2>
<ul class="collapse">
<li><a href="#summary" id="toc-summary" class="nav-link active" data-scroll-target="#summary">Summary</a></li>
<li><a href="#locate-the-data" id="toc-locate-the-data" class="nav-link" data-scroll-target="#locate-the-data">Locate the Data</a></li>
<li><a href="#setup" id="toc-setup" class="nav-link" data-scroll-target="#setup">Setup</a></li>
<li><a href="#connect-to-the-mapserver" id="toc-connect-to-the-mapserver" class="nav-link" data-scroll-target="#connect-to-the-mapserver">Connect to the MapServer</a></li>
<li><a href="#import-the-spatial-data" id="toc-import-the-spatial-data" class="nav-link" data-scroll-target="#import-the-spatial-data">Import the Spatial Data</a></li>
<li><a href="#export-one-basin-to-disk" id="toc-export-one-basin-to-disk" class="nav-link" data-scroll-target="#export-one-basin-to-disk">Export One Basin to Disk</a></li>
</ul></nav>
</div>
<main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block default"><div class="quarto-title">
<h1 class="title">How to Import CA Groundwater Basins into R with arcgislayers</h1>
</div>
<div class="quarto-title-meta-author">
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-heading">Affiliation</div>
<div class="quarto-title-meta-contents">
<p class="author">Andy Lyons <a href="https://orcid.org/0000-0002-7505-6709" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a></p>
</div>
<div class="quarto-title-meta-contents">
<p class="affiliation">
<a href="https://igis.ucanr.edu/">
UC Division of Agriculture and Natural Resources
</a>
</p>
</div>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">September 13, 2024</p>
</div>
</div>
</div>
</header><p><br></p>
<section id="summary" class="level2"><h2 class="anchored" data-anchor-id="summary">Summary</h2>
<p>The notebook demonstrates how to import the <a href="https://gis.data.ca.gov/maps/16c6d9866d634c1188913174130133f5">DWR Groundwater Basins 2016</a> layer into R, using the <a href="https://r.esri.com/arcgislayers/"><code>arcgislayers</code></a> package. We will also extract one of the basins and save it to a geojson file.</p>
</section><section id="locate-the-data" class="level2"><h2 class="anchored" data-anchor-id="locate-the-data">Locate the Data</h2>
<p>First, we need to find the data. A Google Search of “CA Groundwater Basins GIS Data” quickly gets us to a list of <a href="https://gis.data.ca.gov/search?q=groundwater">groundwater layers</a> hosted by CA DWR. Select one of the layers and view the full details. The “View Data Source” button gets us to the <a href="https://gispublic.waterboards.ca.gov/portalserver/rest/services/GAMA/DWR_Groundwater_Basins_2016/MapServer">MapServer page</a> for this map.</p>
<p>The layer from this MapServer have been made public, so we should be able to download it fairly easily. If it wasn’t public, but we had an ArcGIS account that gave us permission to view it, we could still get it after authenticating with <code>arcgislayers</code>.</p>
</section><section id="setup" class="level2"><h2 class="anchored" data-anchor-id="setup">Setup</h2>
<p>Next, load the packages we’ll need:</p>
<div class="cell">
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://r.esri.com/arcgislayers/">arcgislayers</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://r-spatial.github.io/sf/">sf</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org">ggplot2</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section><section id="connect-to-the-mapserver" class="level2"><h2 class="anchored" data-anchor-id="connect-to-the-mapserver">Connect to the MapServer</h2>
<p>The general sequence of steps to import data from ArcGIS servers using <code>arcgislayers</code> is</p>
<ol type="1">
<li>authenticate (if needed)<br>
</li>
<li>create a connection to the MapServer or FeatureServer that has the data<br>
</li>
<li>list the FeatureLayers available<br>
</li>
<li>create a connection to the desired FeatureLayer<br>
</li>
<li>view the fields in the FeatureLayer (optional - if you want to construct a WHERE query when you import the data)<br>
</li>
<li>import the data</li>
</ol>
<p><br></p>
<p>First, we open a connection to the <strong>MapServer</strong>.</p>
<div class="cell">
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">grndwtr_basins2016_url</span> <span class="op"><-</span> <span class="st">"https://gispublic.waterboards.ca.gov/portalserver/rest/services/GAMA/DWR_Groundwater_Basins_2016/MapServer"</span></span>
<span><span class="va">grndwtr_basins2016_ms</span> <span class="op"><-</span> <span class="fu"><a href="https://r.esri.com/arcgislayers/reference/arc_open.html">arc_open</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_url</span><span class="op">)</span></span>
<span><span class="va">grndwtr_basins2016_ms</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code><MapServer <1 layer, 0 tables>>
CRS: 3857
Capabilities: Map,Query,Data
0: DWR Groundwater Basins 2016 (esriGeometryPolygon)</code></pre>
</div>
</div>
<p>ArcGIS MapServers and FeatureServers are both set up to share multiple layers. So next, we view which FeatureLayer(s) this MapServer contains:</p>
<div class="cell">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://r.esri.com/arcgislayers/reference/utils.html">list_items</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_ms</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div data-pagedtable="false">
<script data-pagedtable-source="" type="application/json">
{"columns":[{"label":[""],"name":["_rn_"],"type":[""],"align":["left"]},{"label":["id"],"name":[1],"type":["int"],"align":["right"]},{"label":["name"],"name":[2],"type":["chr"],"align":["left"]},{"label":["parentLayerId"],"name":[3],"type":["int"],"align":["right"]},{"label":["defaultVisibility"],"name":[4],"type":["lgl"],"align":["right"]},{"label":["subLayerIds"],"name":[5],"type":["lgl"],"align":["right"]},{"label":["minScale"],"name":[6],"type":["int"],"align":["right"]},{"label":["maxScale"],"name":[7],"type":["int"],"align":["right"]},{"label":["type"],"name":[8],"type":["chr"],"align":["left"]},{"label":["geometryType"],"name":[9],"type":["chr"],"align":["left"]},{"label":["supportsDynamicLegends"],"name":[10],"type":["lgl"],"align":["right"]}],"data":[{"1":"0","2":"DWR Groundwater Basins 2016","3":"-1","4":"TRUE","5":"NA","6":"0","7":"0","8":"Feature Layer","9":"esriGeometryPolygon","10":"TRUE","_rn_":"1"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
</script>
</div>
</div>
</div>
<p>After taking note of the <code>id</code> of the layer we want to import, we can now create a connection to the <strong>FeatureLayer</strong> provided by this MapServer. (Note this still isn’t importing the data, just creating the connection):</p>
<div class="cell">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">grndwtr_basins2016_fl</span> <span class="op"><-</span> <span class="fu"><a href="https://r.esri.com/arcgislayers/reference/get_layer.html">get_layer</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_ms</span>, id <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span>
<span><span class="va">grndwtr_basins2016_fl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code><FeatureLayer>
Name: DWR Groundwater Basins 2016
Geometry Type: esriGeometryPolygon
CRS: 3857
Capabilities: Map,Query,Data</code></pre>
</div>
</div>
<p>Now that we have the FeatureLayer object, we can look at the fields in the attribute table. This could be useful if for example we wanted to create a WHERE expression when we import the data.</p>
<div class="cell">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://r.esri.com/arcgislayers/reference/utils.html">list_fields</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_fl</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div data-pagedtable="false">
<script data-pagedtable-source="" type="application/json">
{"columns":[{"label":[""],"name":["_rn_"],"type":[""],"align":["left"]},{"label":["name"],"name":[1],"type":["chr"],"align":["left"]},{"label":["type"],"name":[2],"type":["chr"],"align":["left"]},{"label":["alias"],"name":[3],"type":["chr"],"align":["left"]},{"label":["domain"],"name":[4],"type":["lgl"],"align":["right"]},{"label":["length"],"name":[5],"type":["int"],"align":["right"]}],"data":[{"1":"FID","2":"esriFieldTypeOID","3":"FID","4":"NA","5":"NA","_rn_":"1"},{"1":"Shape","2":"esriFieldTypeGeometry","3":"Shape","4":"NA","5":"NA","_rn_":"2"},{"1":"basin_id","2":"esriFieldTypeString","3":"basin_id","4":"NA","5":"12","_rn_":"3"},{"1":"basin_subb","2":"esriFieldTypeString","3":"basin_subb","4":"NA","5":"50","_rn_":"4"},{"1":"basin_su_1","2":"esriFieldTypeString","3":"basin_su_1","4":"NA","5":"12","_rn_":"5"},{"1":"basin_name","2":"esriFieldTypeString","3":"basin_name","4":"NA","5":"50","_rn_":"6"},{"1":"subbasin_n","2":"esriFieldTypeString","3":"subbasin_n","4":"NA","5":"50","_rn_":"7"},{"1":"region_off","2":"esriFieldTypeString","3":"region_off","4":"NA","5":"50","_rn_":"8"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
</script>
</div>
</div>
</div>
</section><section id="import-the-spatial-data" class="level2"><h2 class="anchored" data-anchor-id="import-the-spatial-data">Import the Spatial Data</h2>
<p>Up to now, all we’ve done is open connections to the data on DWR’s ArcGIS Server. This is a bit like dialing a phone number and saying hello. We haven’t yet actually imported <strong>any</strong> spatial data into R.</p>
<p>Finally, we have everything we need import the data using <code><a href="https://r.esri.com/arcgislayers/reference/arc_select.html">arc_select()</a></code>. This function imports the layer and returns it as a simple feature (sf) object. It has optional arguments to specify attribute and/or spatial conditions, which can be extremely helpful with large datasets, but we don’t need that here.</p>
<div class="cell">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">grndwtr_basins2016_sf</span> <span class="op"><-</span> <span class="fu"><a href="https://r.esri.com/arcgislayers/reference/arc_select.html">arc_select</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_fl</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Registered S3 method overwritten by 'jsonify':
method from
print.json jsonlite</code></pre>
</div>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">grndwtr_basins2016_sf</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>Simple feature collection with 517 features and 7 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -13843560 ymin: 3833624 xmax: -12715550 ymax: 5161543
Projected CRS: WGS 84 / Pseudo-Mercator
First 10 features:
FID basin_id basin_subb basin_su_1 basin_name subbasin_n region_off
1 0 2-036 2-036 2-36 SAN PEDRO VALLEY NCRO
2 1 2-011 2-011 2-11 SUNOL VALLEY NCRO
3 2 6-014 6-014 6-14 FISH LAKE VALLEY SRO
4 3 2-008 2-008 2-08 CASTRO VALLEY NCRO
5 4 2-032 2-032 2-32 VISITACION VALLEY NCRO
6 5 2-037 2-037 2-37 SOUTH SAN FRANCISCO NCRO
7 6 5-069 5-069 5-69 YOSEMITE VALLEY SCRO
8 7 6-011 6-011 6-11 LONG VALLEY SRO
9 8 2-033 2-033 2-33 ISLAIS VALLEY NCRO
10 9 2-010 2-010 2-10 LIVERMORE VALLEY NCRO
geometry
1 POLYGON ((-13634455 4520706...
2 POLYGON ((-13569437 4528443...
3 POLYGON ((-13111604 4488036...
4 POLYGON ((-13589440 4532332...
5 POLYGON ((-13624018 4538528...
6 POLYGON ((-13620816 4540890...
7 POLYGON ((-13304977 4546014...
8 POLYGON ((-13237363 4546707...
9 POLYGON ((-13623559 4544912...
10 POLYGON ((-13557839 4525079...</code></pre>
</div>
</div>
<p><br></p>
<p>We now have the polygons as a sf object! Let’s create a column of unique colors, and map them:</p>
<div class="cell">
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">grndwtr_basins2016_sf</span><span class="op">$</span><span class="va">color</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/grDevices/palettes.html">rainbow</a></span><span class="op">(</span><span class="fl">255</span>, end<span class="op">=</span><span class="fl">5</span><span class="op">/</span><span class="fl">6</span><span class="op">)</span>, </span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/nrow.html">nrow</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_sf</span><span class="op">)</span>, replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span><span class="op">(</span><span class="va">grndwtr_basins2016_sf</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span><span class="op">(</span>fillColor <span class="op">=</span> <span class="va">color</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> </span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggsf.html">geom_sf</a></span><span class="op">(</span>alpha <span class="op">=</span> <span class="fl">0.3</span>, color <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure"><p><img src="groundwater-basins-import_files/figure-html/unnamed-chunk-7-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section><section id="export-one-basin-to-disk" class="level2"><h2 class="anchored" data-anchor-id="export-one-basin-to-disk">Export One Basin to Disk</h2>
<p>Pull out the groundwater basin for Imperial Valley, and plot it:</p>
<div class="cell">
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">impval_2016_sf</span> <span class="op"><-</span> <span class="va">grndwtr_basins2016_sf</span> <span class="op">|></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">basin_name</span> <span class="op">==</span> <span class="st">"IMPERIAL VALLEY"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggsf.html">geom_sf</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">impval_2016_sf</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure"><p><img src="groundwater-basins-import_files/figure-html/unnamed-chunk-8-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<p>Convert it to geographic coordinates, and save as geojson:</p>
<div class="cell">
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://r-spatial.github.io/sf/reference/st_write.html">st_write</a></span><span class="op">(</span><span class="va">impval_2016_sf</span> <span class="op">|></span> <span class="fu"><a href="https://r-spatial.github.io/sf/reference/st_transform.html">st_transform</a></span><span class="op">(</span><span class="fl">4326</span><span class="op">)</span>, </span>
<span> dsn <span class="op">=</span> <span class="st">"imperial-valley-groundwater-basin-2016.geojson"</span>,</span>
<span> delete_dsn <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>Deleting source `imperial-valley-groundwater-basin-2016.geojson' using driver `GeoJSON'
Writing layer `imperial-valley-groundwater-basin-2016' to data source
`imperial-valley-groundwater-basin-2016.geojson' using driver `GeoJSON'
Writing 1 features with 8 fields and geometry type Polygon.</code></pre>
</div>
</div>
</section></main><!-- /main column --><script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const isCodeAnnotation = (el) => {
for (const clz of el.classList) {
if (clz.startsWith('code-annotation-')) {
return true;
}
}
return false;
}
const onCopySuccess = function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
}
const getTextToCopy = function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
text: getTextToCopy
});
clipboard.on('success', onCopySuccess);
if (window.document.getElementById('quarto-embedded-source-code-modal')) {
// For code content inside modals, clipBoardJS needs to be initialized with a container option
// TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
text: getTextToCopy,
container: window.document.getElementById('quarto-embedded-source-code-modal')
});
clipboardModal.on('success', onCopySuccess);
}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start',
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
const processXRef = (id, note) => {
// Strip column container classes
const stripColumnClz = (el) => {
el.classList.remove("page-full", "page-columns");
if (el.children) {
for (const child of el.children) {
stripColumnClz(child);
}
}
}
stripColumnClz(note)
if (id === null || id.startsWith('sec-')) {
// Special case sections, only their first couple elements
const container = document.createElement("div");
if (note.children && note.children.length > 2) {
container.appendChild(note.children[0].cloneNode(true));
for (let i = 1; i < note.children.length; i++) {
const child = note.children[i];
if (child.tagName === "P" && child.innerText === "") {
continue;
} else {
container.appendChild(child.cloneNode(true));
break;
}
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(container);
}
return container.innerHTML
} else {
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
return note.innerHTML;
}
} else {
// Remove any anchor links if they are present
const anchorLink = note.querySelector('a.anchorjs-link');
if (anchorLink) {
anchorLink.remove();
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
// TODO in 1.5, we should make sure this works without a callout special case
if (note.classList.contains("callout")) {
return note.outerHTML;
} else {
return note.innerHTML;
}
}
}
for (var i=0; i<xrefs.length; i++) {
const xref = xrefs[i];
tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
if (url.startsWith('#')) {
hash = url;
} else {
try { hash = new URL(url).hash; } catch {}
}
if (hash) {
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
} else {
// See if we can fetch a full url (with no hash to target)
// This is a special case and we should probably do some content thinning / targeting
fetch(url)
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.querySelector('main.content');
if (note !== null) {
// This should only happen for chapter cross references
// (since there is no id in the URL)
// remove the first header
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
note.children[0].remove();
}
const html = processXRef(null, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>