-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmetadata_EML_pratice.html
1107 lines (1012 loc) · 86.4 KB
/
metadata_EML_pratice.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
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
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="date" content="2024-06-27" />
<title>Construindo metadados em formato EML</title>
<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/navigation-1.1/sourceembed.js"></script>
<script src="site_libs/clipboard-1.7.1/clipboard.min.js"></script>
<link href="site_libs/primer-tooltips-1.4.0/build.css" rel="stylesheet" />
<link href="site_libs/klippy-0.0.0.9500/css/klippy.min.css" rel="stylesheet" />
<script src="site_libs/klippy-0.0.0.9500/js/klippy.min.js"></script>
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">
code {
white-space: pre;
}
.sourceCode {
overflow: visible;
}
</style>
<style type="text/css" data-origin="pandoc">
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 { 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;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ background-color: #f8f8f8; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ef2929; } /* Alert */
code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #204a87; } /* Attribute */
code span.bn { color: #0000cf; } /* BaseN */
code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4e9a06; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #8f5902; font-style: italic; } /* Comment */
code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
code span.dt { color: #204a87; } /* DataType */
code span.dv { color: #0000cf; } /* DecVal */
code span.er { color: #a40000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #0000cf; } /* Float */
code span.fu { color: #204a87; font-weight: bold; } /* Function */
code span.im { } /* Import */
code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
code span.ot { color: #8f5902; } /* Other */
code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
code span.sc { color: #ce5c00; font-weight: bold; } /* SpecialChar */
code span.ss { color: #4e9a06; } /* SpecialString */
code span.st { color: #4e9a06; } /* String */
code span.va { color: #000000; } /* Variable */
code span.vs { color: #4e9a06; } /* VerbatimString */
code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
var sheets = document.styleSheets;
for (var i = 0; i < sheets.length; i++) {
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
var j = 0;
while (j < rules.length) {
var rule = rules[j];
// check if there is a div.sourceCode rule
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
j++;
continue;
}
var style = rule.style.cssText;
// check if color or background-color is set
if (rule.style.color === '' && rule.style.backgroundColor === '') {
j++;
continue;
}
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
}
}
})();
</script>
<style type="text/css">
#rmd-source-code {
display: none;
}
</style>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark the anchor link active (and if it's in a dropdown, also mark that active)
var dropdown = menuAnchor.closest('li.dropdown');
if (window.bootstrap) { // Bootstrap 4+
menuAnchor.addClass('active');
dropdown.find('> .dropdown-toggle').addClass('active');
} else { // Bootstrap 3
menuAnchor.parent().addClass('active');
dropdown.addClass('active');
}
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258";
font-family: 'Glyphicons Halflings';
border: none;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<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-bs-toggle="collapse" data-target="#navbar" data-bs-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">Boas Práticas e Ferramentas da Ciência Aberta na Ecologia - BIE5798</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Início</a>
</li>
<li>
<a href="intro_ciencia_aberta.html">O que é ciência aberta?</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Dados abertos
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="dados_abertos.html">O que são dados abertos?</a>
</li>
<li>
<a href="metadata_EML.html">Metadados</a>
</li>
</ul>
</li>
<li>
<a href="Organizacao_dir_local.html">Organização local</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Versionamento
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="basics_git.html">ABC do versionamento</a>
</li>
<li>
<a href="commits-travel.html">Viajando no tempo</a>
</li>
<li>
<a href="gitgnore.html">Ignorando arquivos</a>
</li>
<li>
<a href="colabs_github.html">Trabalho colaborativo</a>
</li>
<li>
<a href="conflitos.html">Resolvendo conflitos</a>
</li>
<li>
<a href="releasing.html">Release</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Programação letrada
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="rmarkdown-basics.html">Rmarkdown</a>
</li>
<li>
<a href="sites-basics.html">Sites</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Avançado
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="renv-basics.html">Manejo de versões de pacotes</a>
</li>
<li>
<a href="rocker-basics.html">Containers</a>
</li>
<li>
<a href="targets_basics.html">Fluxo de trabalho</a>
</li>
<li>
<a href="metadata_EML_pratice.html">Metadados com EML</a>
</li>
<li>
<a href="git_large_files.html">Manejo de arquivos grandes</a>
</li>
</ul>
</li>
<li>
<a href="publicacoes.html">Acesso aberto</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Outras tendências
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="pre-registro.html">Pré-registro</a>
</li>
<li>
<a href="revisao-codigo.html">Revisão de código</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<div class="btn-group pull-right float-right">
<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
<li><a id="rmd-download-source" href="#">Download Rmd</a></li>
</ul>
</div>
<h1 class="title toc-ignore">Construindo metadados em formato EML</h1>
<h4 class="date">2024-06-27</h4>
</div>
<script>
addClassKlippyTo("pre.r, pre.markdown");
addKlippy('left', 'top', 'auto', '1', 'Copy code', 'Copied!');
</script>
<div id="metadados-na-prática---utilizando-o-pacote-eml"
class="section level1">
<h1>Metadados na prática - utilizando o pacote <code>{EML}</code></h1>
<p>Vamos agora construir um metadado utilizando o pacote EML (Ecological
Metadata Language). O pacote EML foi desenvolvido com o intuito de
oferecer um conjunto de funções que permite a construção de metadados do
tipo XML mas que abrangem as especificidades presentes nos dados
ecológicos. Para relembrar a estrutura dos metadados peço que revejam os
slides dessa aula <a
href="https://gabrielnakamura.github.io/USP_BIE5798_apresentacoes/#33">aqui</a>.</p>
<p>Nesta seção temos duas opções de prática. Aqueles que fizeram os
metadados em palnilhas eletrônicas, podem praticar com seus próprios
dados. Para aqueles que não tem dados próprios iremos utilizar o
conjunto de dados do artigo <a
href="https://www.pnas.org/doi/10.1073/pnas.1221037110">“Organic-matter
loading determines regime shifts and alternative states in an aquatic
ecosystem”</a> para construir um arquivo de metadados. Optamos por usar
este dado pois ele já apresenta um arquivo de metadados associado, assim
podemos reconstruí-lo e verificar como fica. Além disso ele é o mesmo
dado utilizado no tutorial original do pacote EML, sendo conveniente
para fins didáticos. Ao final vamos praticar com um outro conjunto de
dados. Lembrando que se você baixou o repositório do material desta
disciplina, você conseguirá ler os dados sem problemas.</p>
<div id="instalação" class="section level2">
<h2>Instalação</h2>
<p>Para instalar o pacote EML faça o seguinte:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"EML"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">library</span>(EML)</span></code></pre></div>
<p>Vamos utilizar um conjunto de dados contidos no próprio pacote EML
para facilitar a compreensão dos passos necessários para construir um
EML completo</p>
</div>
<div id="construindo-um-eml---harvard-forest-data"
class="section level2">
<h2>Construindo um EML - Harvard Forest Data</h2>
<div id="construindo-os-atributos" class="section level3">
<h3>Construindo os Atributos</h3>
<p>Os atributos são as descrições para as variáveis contidas na nossa
tabela. Aquela aba contendo as informações das variáveis, pois então,
esta seria os atributos da sua tabela de dados. Então, primeiro
precisamos de uma tabela de atributos que define o significado geral de
cada variável em nossa tabela de dados. Esta tabela pode ser gerada aqui
no R direto, como no exemplo abaixo, mas pode ser importada a partir de
uma tabela <code>.csv</code>. A tabela segue o formato a seguir:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>attributes <span class="ot"><-</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>tibble<span class="sc">::</span><span class="fu">tribble</span>(</span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="sc">~</span>attributeName, <span class="sc">~</span>attributeDefinition, <span class="sc">~</span>formatString, <span class="sc">~</span>definition, <span class="sc">~</span>unit, <span class="sc">~</span>numberType,</span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a> <span class="st">"run.num"</span>, <span class="st">"which run number (=block). Range: 1 - 6. (integer)"</span>, <span class="cn">NA</span>, <span class="st">"which run number"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a> <span class="st">"year"</span>, <span class="st">"year, 2012"</span>, <span class="st">"YYYY"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a> <span class="st">"day"</span>, <span class="st">"Julian day. Range: 170 - 209."</span>, <span class="st">"DDD"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a> <span class="st">"hour.min"</span>, <span class="st">"hour and minute of observation. Range 1 - 2400 (integer)"</span>, <span class="st">"hhmm"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a> <span class="st">"i.flag"</span>, <span class="st">"is variable Real, Interpolated or Bad (character/factor)"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a> <span class="st">"variable"</span>, <span class="st">"what variable being measured in what treatment (character/factor)."</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-10"><a href="#cb2-10" tabindex="-1"></a> <span class="st">"value.i"</span>, <span class="st">"value of measured variable for run.num on year/day/hour.min."</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>,</span>
<span id="cb2-11"><a href="#cb2-11" tabindex="-1"></a> <span class="st">"length"</span>, <span class="st">"length of the species in meters (dummy example of numeric data)"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="st">"meter"</span>, <span class="st">"real"</span>)</span></code></pre></div>
<p>Dê uma olhada na tabela de atributos (pode ser feito usano a função
<code>View</code> ou abrindo no Excel). A maioria dos dados seguem este
formato geral.</p>
<p>A seguir precisamos descrever os atributos que apresentam níveis. Por
exemplo o atributo chamado <code>variable</code> apresenta oito níveis.
A estratégia seguida aqui foi criar vetores com os códigos usados para
cada nível dos atributos e uma pequena explicação.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>i.flag <span class="ot"><-</span> <span class="fu">c</span>(<span class="at">R =</span> <span class="st">"real"</span>,</span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a> <span class="at">I =</span> <span class="st">"interpolated"</span>,</span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a> <span class="at">B =</span> <span class="st">"bad"</span>)</span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a>variable <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a> <span class="at">control =</span> <span class="st">"no prey added"</span>,</span>
<span id="cb3-6"><a href="#cb3-6" tabindex="-1"></a> <span class="at">low =</span> <span class="st">"0.125 mg prey added ml-1 d-1"</span>,</span>
<span id="cb3-7"><a href="#cb3-7" tabindex="-1"></a> <span class="at">med.low =</span> <span class="st">"0,25 mg prey added ml-1 d-1"</span>,</span>
<span id="cb3-8"><a href="#cb3-8" tabindex="-1"></a> <span class="at">med.high =</span> <span class="st">"0.5 mg prey added ml-1 d-1"</span>,</span>
<span id="cb3-9"><a href="#cb3-9" tabindex="-1"></a> <span class="at">high =</span> <span class="st">"1.0 mg prey added ml-1 d-1"</span>,</span>
<span id="cb3-10"><a href="#cb3-10" tabindex="-1"></a> <span class="at">air.temp =</span> <span class="st">"air temperature measured just above all plants (1 thermocouple)"</span>,</span>
<span id="cb3-11"><a href="#cb3-11" tabindex="-1"></a> <span class="at">water.temp =</span> <span class="st">"water temperature measured within each pitcher"</span>,</span>
<span id="cb3-12"><a href="#cb3-12" tabindex="-1"></a> <span class="at">par =</span> <span class="st">"photosynthetic active radiation (PAR) measured just above all plants (1 sensor)"</span></span>
<span id="cb3-13"><a href="#cb3-13" tabindex="-1"></a>)</span>
<span id="cb3-14"><a href="#cb3-14" tabindex="-1"></a></span>
<span id="cb3-15"><a href="#cb3-15" tabindex="-1"></a>value.i <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb3-16"><a href="#cb3-16" tabindex="-1"></a> <span class="at">control =</span> <span class="st">"% dissolved oxygen"</span>,</span>
<span id="cb3-17"><a href="#cb3-17" tabindex="-1"></a> <span class="at">low =</span> <span class="st">"% dissolved oxygen"</span>,</span>
<span id="cb3-18"><a href="#cb3-18" tabindex="-1"></a> <span class="at">med.low =</span> <span class="st">"% dissolved oxygen"</span>,</span>
<span id="cb3-19"><a href="#cb3-19" tabindex="-1"></a> <span class="at">med.high =</span> <span class="st">"% dissolved oxygen"</span>,</span>
<span id="cb3-20"><a href="#cb3-20" tabindex="-1"></a> <span class="at">high =</span> <span class="st">"% dissolved oxygen"</span>,</span>
<span id="cb3-21"><a href="#cb3-21" tabindex="-1"></a> <span class="at">air.temp =</span> <span class="st">"degrees C"</span>,</span>
<span id="cb3-22"><a href="#cb3-22" tabindex="-1"></a> <span class="at">water.temp =</span> <span class="st">"degrees C"</span>,</span>
<span id="cb3-23"><a href="#cb3-23" tabindex="-1"></a> <span class="at">par =</span> <span class="st">"micromoles m-1 s-1"</span></span>
<span id="cb3-24"><a href="#cb3-24" tabindex="-1"></a>)</span>
<span id="cb3-25"><a href="#cb3-25" tabindex="-1"></a></span>
<span id="cb3-26"><a href="#cb3-26" tabindex="-1"></a><span class="do">## Write these into the data.frame format</span></span>
<span id="cb3-27"><a href="#cb3-27" tabindex="-1"></a>factors <span class="ot"><-</span> <span class="fu">rbind</span>(</span>
<span id="cb3-28"><a href="#cb3-28" tabindex="-1"></a><span class="fu">data.frame</span>(</span>
<span id="cb3-29"><a href="#cb3-29" tabindex="-1"></a> <span class="at">attributeName =</span> <span class="st">"i.flag"</span>,</span>
<span id="cb3-30"><a href="#cb3-30" tabindex="-1"></a> <span class="at">code =</span> <span class="fu">names</span>(i.flag),</span>
<span id="cb3-31"><a href="#cb3-31" tabindex="-1"></a> <span class="at">definition =</span> <span class="fu">unname</span>(i.flag)</span>
<span id="cb3-32"><a href="#cb3-32" tabindex="-1"></a>),</span>
<span id="cb3-33"><a href="#cb3-33" tabindex="-1"></a><span class="fu">data.frame</span>(</span>
<span id="cb3-34"><a href="#cb3-34" tabindex="-1"></a> <span class="at">attributeName =</span> <span class="st">"variable"</span>,</span>
<span id="cb3-35"><a href="#cb3-35" tabindex="-1"></a> <span class="at">code =</span> <span class="fu">names</span>(variable),</span>
<span id="cb3-36"><a href="#cb3-36" tabindex="-1"></a> <span class="at">definition =</span> <span class="fu">unname</span>(variable)</span>
<span id="cb3-37"><a href="#cb3-37" tabindex="-1"></a>),</span>
<span id="cb3-38"><a href="#cb3-38" tabindex="-1"></a><span class="fu">data.frame</span>(</span>
<span id="cb3-39"><a href="#cb3-39" tabindex="-1"></a> <span class="at">attributeName =</span> <span class="st">"value.i"</span>,</span>
<span id="cb3-40"><a href="#cb3-40" tabindex="-1"></a> <span class="at">code =</span> <span class="fu">names</span>(value.i),</span>
<span id="cb3-41"><a href="#cb3-41" tabindex="-1"></a> <span class="at">definition =</span> <span class="fu">unname</span>(value.i)</span>
<span id="cb3-42"><a href="#cb3-42" tabindex="-1"></a>)</span>
<span id="cb3-43"><a href="#cb3-43" tabindex="-1"></a>)</span></code></pre></div>
<p>Após especificadas as características das variáveis categóricas (as
contínuas já estão especificadas na tabela geral de atributos
<code>attributes</code>), usamos a função <code>set_attributes</code>
para criar a lista de atributos geral dos dados, onde devemos
especificar o tipo de atributo que estamos inserindo (se caracter, se
data, se fator etc..)</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a>attributeList <span class="ot"><-</span> <span class="fu">set_attributes</span>(attributes, factors, <span class="at">col_classes =</span> <span class="fu">c</span>(<span class="st">"character"</span>, <span class="st">"Date"</span>, <span class="st">"Date"</span>, <span class="st">"Date"</span>, <span class="st">"factor"</span>, <span class="st">"factor"</span>, <span class="st">"factor"</span>, <span class="st">"numeric"</span>))</span></code></pre></div>
</div>
<div id="construindo-as-características-físicas-do-dado"
class="section level3">
<h3>Construindo as características físicas do dado</h3>
<p>Aqui vamos especificar as características físicas do próprio arquivo
de dados que utilizamos, ou seja, o formato, o tipo de compressão do
arquivo, o separador etc. Resumindo, aqui é especificado a
<strong>característica do arquivo</strong>. Isso é feito facilmente com
a função <code>set_physical</code>. Se estivermos utilizando um arquivo
.csv a função já extrai automaticamente a maior parte das
características relevantes do arquivo de dados.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>physical <span class="ot"><-</span> <span class="fu">set_physical</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"hf205-01-TPexp1-EML-Exemple.csv"</span>))</span></code></pre></div>
</div>
<div id="juntando-atributos-e-características-físicas"
class="section level3">
<h3>Juntando Atributos e Características físicas</h3>
<p>Com o objeto de atributos e o objeto de características físicas temos
o essencial para descrever o nosso conjunto de dados. Agora vamos juntar
ambos com mais algumas informações em uma única lista e denominar isso
como sendo o nosso <code>dataTable</code></p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a>dataTable <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a> <span class="at">entityName =</span> <span class="st">"hf205-01-TPexp1.csv"</span>,</span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a> <span class="at">entityDescription =</span> <span class="st">"tipping point experiment 1"</span>,</span>
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a> <span class="at">physical =</span> physical,</span>
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a> <span class="at">attributeList =</span> attributeList)</span></code></pre></div>
</div>
<div
id="características-adicionais---extensão-geográfica-métodos-e-outros"
class="section level3">
<h3>Características adicionais - extensão geográfica, métodos e
outros</h3>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a>geographicDescription <span class="ot"><-</span> <span class="st">"Harvard Forest Greenhouse, Tom Swamp Tract (Harvard Forest)"</span></span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a></span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a>coverage <span class="ot"><-</span> </span>
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a> <span class="fu">set_coverage</span>(<span class="at">begin =</span> <span class="st">'2012-06-01'</span>, <span class="at">end =</span> <span class="st">'2013-12-31'</span>,</span>
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a> <span class="at">sci_names =</span> <span class="st">"Sarracenia purpurea"</span>,</span>
<span id="cb7-7"><a href="#cb7-7" tabindex="-1"></a> <span class="at">geographicDescription =</span> geographicDescription,</span>
<span id="cb7-8"><a href="#cb7-8" tabindex="-1"></a> <span class="at">west =</span> <span class="sc">-</span><span class="fl">122.44</span>, <span class="at">east =</span> <span class="sc">-</span><span class="fl">117.15</span>, </span>
<span id="cb7-9"><a href="#cb7-9" tabindex="-1"></a> <span class="at">north =</span> <span class="fl">37.38</span>, <span class="at">south =</span> <span class="fl">30.00</span>,</span>
<span id="cb7-10"><a href="#cb7-10" tabindex="-1"></a> <span class="at">altitudeMin =</span> <span class="dv">160</span>, <span class="at">altitudeMaximum =</span> <span class="dv">330</span>,</span>
<span id="cb7-11"><a href="#cb7-11" tabindex="-1"></a> <span class="at">altitudeUnits =</span> <span class="st">"meter"</span>)</span></code></pre></div>
<p>Para descrever os métodos em metadados</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>methods_file <span class="ot"><-</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"hf205-methods.docx"</span>)</span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>methods <span class="ot"><-</span> <span class="fu">set_methods</span>(methods_file)</span></code></pre></div>
<p>Identificação dos indivíduos endereço e outras informações sobre
contatos</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>R_person <span class="ot"><-</span> <span class="fu">person</span>(<span class="st">"Aaron"</span>, <span class="st">"Ellison"</span>, ,<span class="st">"fakeaddress@email.com"</span>, <span class="st">"cre"</span>, </span>
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a> <span class="fu">c</span>(<span class="at">ORCID =</span> <span class="st">"0000-0003-4151-6081"</span>))</span>
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a>aaron <span class="ot"><-</span> <span class="fu">as_emld</span>(R_person)</span>
<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a>others <span class="ot"><-</span> <span class="fu">c</span>(<span class="fu">as.person</span>(<span class="st">"Benjamin Baiser"</span>), <span class="fu">as.person</span>(<span class="st">"Jennifer Sirota"</span>))</span>
<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>associatedParty <span class="ot"><-</span> <span class="fu">as_emld</span>(others)</span>
<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a>associatedParty[[<span class="dv">1</span>]]<span class="sc">$</span>role <span class="ot"><-</span> <span class="st">"Researcher"</span></span>
<span id="cb9-7"><a href="#cb9-7" tabindex="-1"></a>associatedParty[[<span class="dv">2</span>]]<span class="sc">$</span>role <span class="ot"><-</span> <span class="st">"Researcher"</span></span>
<span id="cb9-8"><a href="#cb9-8" tabindex="-1"></a></span>
<span id="cb9-9"><a href="#cb9-9" tabindex="-1"></a>HF_address <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb9-10"><a href="#cb9-10" tabindex="-1"></a> <span class="at">deliveryPoint =</span> <span class="st">"324 North Main Street"</span>,</span>
<span id="cb9-11"><a href="#cb9-11" tabindex="-1"></a> <span class="at">city =</span> <span class="st">"Petersham"</span>,</span>
<span id="cb9-12"><a href="#cb9-12" tabindex="-1"></a> <span class="at">administrativeArea =</span> <span class="st">"MA"</span>,</span>
<span id="cb9-13"><a href="#cb9-13" tabindex="-1"></a> <span class="at">postalCode =</span> <span class="st">"01366"</span>,</span>
<span id="cb9-14"><a href="#cb9-14" tabindex="-1"></a> <span class="at">country =</span> <span class="st">"USA"</span>)</span>
<span id="cb9-15"><a href="#cb9-15" tabindex="-1"></a></span>
<span id="cb9-16"><a href="#cb9-16" tabindex="-1"></a>publisher <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb9-17"><a href="#cb9-17" tabindex="-1"></a> <span class="at">organizationName =</span> <span class="st">"Harvard Forest"</span>,</span>
<span id="cb9-18"><a href="#cb9-18" tabindex="-1"></a> <span class="at">address =</span> HF_address)</span>
<span id="cb9-19"><a href="#cb9-19" tabindex="-1"></a></span>
<span id="cb9-20"><a href="#cb9-20" tabindex="-1"></a></span>
<span id="cb9-21"><a href="#cb9-21" tabindex="-1"></a>contact <span class="ot"><-</span> </span>
<span id="cb9-22"><a href="#cb9-22" tabindex="-1"></a> <span class="fu">list</span>(</span>
<span id="cb9-23"><a href="#cb9-23" tabindex="-1"></a> <span class="at">individualName =</span> aaron<span class="sc">$</span>individualName,</span>
<span id="cb9-24"><a href="#cb9-24" tabindex="-1"></a> <span class="at">electronicMailAddress =</span> aaron<span class="sc">$</span>electronicMailAddress,</span>
<span id="cb9-25"><a href="#cb9-25" tabindex="-1"></a> <span class="at">address =</span> HF_address,</span>
<span id="cb9-26"><a href="#cb9-26" tabindex="-1"></a> <span class="at">organizationName =</span> <span class="st">"Harvard Forest"</span>,</span>
<span id="cb9-27"><a href="#cb9-27" tabindex="-1"></a> <span class="at">phone =</span> <span class="st">"000-000-0000"</span>)</span></code></pre></div>
<p>criando keywords para os dados</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>keywordSet <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a> <span class="fu">list</span>(</span>
<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a> <span class="at">keywordThesaurus =</span> <span class="st">"LTER controlled vocabulary"</span>,</span>
<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a> <span class="at">keyword =</span> <span class="fu">list</span>(<span class="st">"bacteria"</span>,</span>
<span id="cb10-5"><a href="#cb10-5" tabindex="-1"></a> <span class="st">"carnivorous plants"</span>,</span>
<span id="cb10-6"><a href="#cb10-6" tabindex="-1"></a> <span class="st">"genetics"</span>,</span>
<span id="cb10-7"><a href="#cb10-7" tabindex="-1"></a> <span class="st">"thresholds"</span>)</span>
<span id="cb10-8"><a href="#cb10-8" tabindex="-1"></a> ),</span>
<span id="cb10-9"><a href="#cb10-9" tabindex="-1"></a> <span class="fu">list</span>(</span>
<span id="cb10-10"><a href="#cb10-10" tabindex="-1"></a> <span class="at">keywordThesaurus =</span> <span class="st">"LTER core area"</span>,</span>
<span id="cb10-11"><a href="#cb10-11" tabindex="-1"></a> <span class="at">keyword =</span> <span class="fu">list</span>(<span class="st">"populations"</span>, <span class="st">"inorganic nutrients"</span>, <span class="st">"disturbance"</span>)</span>
<span id="cb10-12"><a href="#cb10-12" tabindex="-1"></a> ),</span>
<span id="cb10-13"><a href="#cb10-13" tabindex="-1"></a> <span class="fu">list</span>(</span>
<span id="cb10-14"><a href="#cb10-14" tabindex="-1"></a> <span class="at">keywordThesaurus =</span> <span class="st">"HFR default"</span>,</span>
<span id="cb10-15"><a href="#cb10-15" tabindex="-1"></a> <span class="at">keyword =</span> <span class="fu">list</span>(<span class="st">"Harvard Forest"</span>, <span class="st">"HFR"</span>, <span class="st">"LTER"</span>, <span class="st">"USA"</span>)</span>
<span id="cb10-16"><a href="#cb10-16" tabindex="-1"></a> ))</span></code></pre></div>
<p>Outras informações relevantes como abstract etc</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>pubDate <span class="ot"><-</span> <span class="st">"2012"</span> </span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a></span>
<span id="cb11-3"><a href="#cb11-3" tabindex="-1"></a>title <span class="ot"><-</span> <span class="st">"Thresholds and Tipping Points in a Sarracenia </span></span>
<span id="cb11-4"><a href="#cb11-4" tabindex="-1"></a><span class="st">Microecosystem at Harvard Forest since 2012"</span></span>
<span id="cb11-5"><a href="#cb11-5" tabindex="-1"></a></span>
<span id="cb11-6"><a href="#cb11-6" tabindex="-1"></a>abstract <span class="ot"><-</span> <span class="st">"The primary goal of this project is to determine</span></span>
<span id="cb11-7"><a href="#cb11-7" tabindex="-1"></a><span class="st"> experimentally the amount of lead time required to prevent a state</span></span>
<span id="cb11-8"><a href="#cb11-8" tabindex="-1"></a><span class="st">change. To achieve this goal, we will (1) experimentally induce state</span></span>
<span id="cb11-9"><a href="#cb11-9" tabindex="-1"></a><span class="st">changes in a natural aquatic ecosystem - the Sarracenia microecosystem;</span></span>
<span id="cb11-10"><a href="#cb11-10" tabindex="-1"></a><span class="st">(2) use proteomic analysis to identify potential indicators of states</span></span>
<span id="cb11-11"><a href="#cb11-11" tabindex="-1"></a><span class="st">and state changes; and (3) test whether we can forestall state changes</span></span>
<span id="cb11-12"><a href="#cb11-12" tabindex="-1"></a><span class="st">by experimentally intervening in the system. This work uses state-of-the</span></span>
<span id="cb11-13"><a href="#cb11-13" tabindex="-1"></a><span class="st">art molecular tools to identify early warning indicators in the field</span></span>
<span id="cb11-14"><a href="#cb11-14" tabindex="-1"></a><span class="st">of aerobic to anaerobic state changes driven by nutrient enrichment</span></span>
<span id="cb11-15"><a href="#cb11-15" tabindex="-1"></a><span class="st">in an aquatic ecosystem. The study tests two general hypotheses: (1)</span></span>
<span id="cb11-16"><a href="#cb11-16" tabindex="-1"></a><span class="st">proteomic biomarkers can function as reliable indicators of impending</span></span>
<span id="cb11-17"><a href="#cb11-17" tabindex="-1"></a><span class="st">state changes and may give early warning before increasing variances</span></span>
<span id="cb11-18"><a href="#cb11-18" tabindex="-1"></a><span class="st">and statistical flickering of monitored variables; and (2) well-timed</span></span>
<span id="cb11-19"><a href="#cb11-19" tabindex="-1"></a><span class="st">intervention based on proteomic biomarkers can avert future state changes</span></span>
<span id="cb11-20"><a href="#cb11-20" tabindex="-1"></a><span class="st">in ecological systems."</span> </span>
<span id="cb11-21"><a href="#cb11-21" tabindex="-1"></a></span>
<span id="cb11-22"><a href="#cb11-22" tabindex="-1"></a>intellectualRights <span class="ot"><-</span> <span class="st">"This dataset is released to the public and may be freely</span></span>
<span id="cb11-23"><a href="#cb11-23" tabindex="-1"></a><span class="st"> downloaded. Please keep the designated Contact person informed of any</span></span>
<span id="cb11-24"><a href="#cb11-24" tabindex="-1"></a><span class="st">plans to use the dataset. Consultation or collaboration with the original</span></span>
<span id="cb11-25"><a href="#cb11-25" tabindex="-1"></a><span class="st">investigators is strongly encouraged. Publications and data products</span></span>
<span id="cb11-26"><a href="#cb11-26" tabindex="-1"></a><span class="st">that make use of the dataset must include proper acknowledgement. For</span></span>
<span id="cb11-27"><a href="#cb11-27" tabindex="-1"></a><span class="st">more information on LTER Network data access and use policies, please</span></span>
<span id="cb11-28"><a href="#cb11-28" tabindex="-1"></a><span class="st">see: http://www.lternet.edu/data/netpolicy.html."</span></span></code></pre></div>
</div>
<div id="criando-o-arquivo-xml" class="section level3">
<h3>Criando o arquivo XML</h3>
<p>Agora que todas as informações foram criadas (atributos, dados
físicos do arquivo, coverage, dados de contato), precisamos juntar todas
elas em uma única lista.</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a>dataset <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a> <span class="at">title =</span> title,</span>
<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a> <span class="at">creator =</span> aaron,</span>
<span id="cb12-4"><a href="#cb12-4" tabindex="-1"></a> <span class="at">pubDate =</span> pubDate,</span>
<span id="cb12-5"><a href="#cb12-5" tabindex="-1"></a> <span class="at">intellectualRights =</span> intellectualRights,</span>
<span id="cb12-6"><a href="#cb12-6" tabindex="-1"></a> <span class="at">abstract =</span> abstract,</span>
<span id="cb12-7"><a href="#cb12-7" tabindex="-1"></a> <span class="at">associatedParty =</span> associatedParty,</span>
<span id="cb12-8"><a href="#cb12-8" tabindex="-1"></a> <span class="at">keywordSet =</span> keywordSet,</span>
<span id="cb12-9"><a href="#cb12-9" tabindex="-1"></a> <span class="at">coverage =</span> coverage,</span>
<span id="cb12-10"><a href="#cb12-10" tabindex="-1"></a> <span class="at">contact =</span> contact,</span>
<span id="cb12-11"><a href="#cb12-11" tabindex="-1"></a> <span class="at">methods =</span> methods,</span>
<span id="cb12-12"><a href="#cb12-12" tabindex="-1"></a> <span class="at">dataTable =</span> dataTable)</span></code></pre></div>
<p>Antes de criar o arquivo XML é importante criar um uuid para o
arquivo, que nada mais é que um identificador que qualquer um pode
criar, como demonstrado a seguir. Para mais informações sobre o que é um
uuid ver <a
href="https://en.wikipedia.org/wiki/Universally_unique_identifier">esta
explicação no Wikipedia</a></p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a>eml <span class="ot"><-</span> <span class="fu">list</span>(</span>
<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a> <span class="at">packageId =</span> uuid<span class="sc">::</span><span class="fu">UUIDgenerate</span>(),</span>
<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a> <span class="at">system =</span> <span class="st">"uuid"</span>, <span class="co"># type of identifier</span></span>
<span id="cb13-4"><a href="#cb13-4" tabindex="-1"></a> <span class="at">dataset =</span> dataset)</span></code></pre></div>
<p>Finalmente criando o arquivo XML e validando.</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="fu">write_eml</span>(eml, here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"eml_tutorialHF205.xml"</span>))</span>
<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a><span class="fu">eml_validate</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"eml_tutorialHF205.xml"</span>))</span></code></pre></div>
<!-- aqui a seção de metadata para dados de biodiversidade usando DwCore -->
<script>
addClassKlippyTo("pre.r, pre.markdown");
addKlippy('left', 'top', 'auto', '1', 'Copy code', 'Copied!');
</script>
</div>
</div>
</div>
<div id="metadados-para-dados-de-biodiversidade" class="section level1">
<h1>Metadados para dados de biodiversidade</h1>
<p>Se você ainda não passou pela seção de metadados usando o pacote EML,
volte um pouco, por favor. Lá apresento uma introdução geral sobre
metadados em XML e como montá-los usando o pacote EML no R. Aqui
abordarei especificamente como montar arquivos com metadados para dados
de biodiversidade (ocorrência, lista de espécies, pontos etc).</p>
<div id="leituras-sugeridas" class="section level2">
<h2>Leituras sugeridas</h2>
<p>Esta seção é baseada no documento produzido pelo <a
href="https://livingnorway.github.io/LivingNorwayR/articles/LNWorkshopExample_TOV-E.html">Living
Norway Project</a>, que também oferece uma introdução muito interessante
sobre Darwin Core e metadados para biodiversidade.</p>
</div>
<div id="exemplos-de-metadados-de-biodiversidade"
class="section level2">
<h2>Exemplos de metadados de biodiversidade</h2>
<p>O melhor exemplo de esturutura digital que utiliza metadados de
biodiversidade construídos desta maneira que mostrarei é o <a
href="https://www.gbif.org/">GBIF</a>.</p>
</div>
</div>
<div id="metadados-na-prática---utilizando-o-pacote-livingnorwayr"
class="section level1">
<h1>Metadados na prática - utilizando o pacote
<code>{LivingNorwayR}</code></h1>
<div id="instalação-e-dados" class="section level2">
<h2>Instalação e dados</h2>
<p>Primeiro vamos instalar o pacote</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"https://github.com/LivingNorway/LivingNorwayR"</span>)</span>
<span id="cb15-2"><a href="#cb15-2" tabindex="-1"></a><span class="fu">library</span>(LivingNorwayR)</span></code></pre></div>
<p>Aqui os dados que serão utilizados no exemplo. Estes são os mesmos
dados utilizados no tuturial do Living Norway R. Para mais detalhes
visite a <a
href="https://livingnorway.github.io/LivingNorwayR/articles/LNWorkshopExample_TOV-E.html">página
deles</a>.</p>
<p>Vamos utilizar um conjunto de dados que fizemos o download e está
dentro da nossa pasta do curso para criar nosso arquivo Darwin Core.</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a><span class="co"># Lendo o arquivo core</span></span>
<span id="cb16-2"><a href="#cb16-2" tabindex="-1"></a>TOVEEventTableDF <span class="ot"><-</span> <span class="fu">read.table</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"TOVEData"</span>, <span class="st">"event.txt"</span>), <span class="at">sep =</span> <span class="st">"</span><span class="sc">\t</span><span class="st">"</span>, <span class="at">header =</span> <span class="cn">TRUE</span>)</span>
<span id="cb16-3"><a href="#cb16-3" tabindex="-1"></a><span class="fu">head</span>(TOVEEventTableDF)</span></code></pre></div>
<p>Obtendo os arquivos extendidos, neste caso o arquivo de ocorrência de
espécies. Podemos ver que se trata de um simples data frame onde os
nomes das colunas seguem os códigos do Darwin Core</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a>TOVEOccTable <span class="ot"><-</span> <span class="fu">read.table</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"TOVEData"</span>, <span class="st">"occurrence.txt"</span>), <span class="at">sep =</span> <span class="st">"</span><span class="sc">\t</span><span class="st">"</span>, <span class="at">header =</span> <span class="cn">TRUE</span>)</span>
<span id="cb17-2"><a href="#cb17-2" tabindex="-1"></a><span class="fu">head</span>(TOVEOccTable)</span></code></pre></div>
</div>
<div id="construindo-um-xml-baseado-em-darwin-core"
class="section level2">
<h2>Construindo um XML baseado em Darwin Core</h2>
<p>Agora que temos nossos dados podemos construir um arquivo do tipo
Darwin Core</p>
<div id="construindo-o-metadado-para-a-tabela-de-eventos-core"
class="section level3">
<h3>Construindo o metadado para a tabela de eventos
<strong>core</strong></h3>
<p>Primeiro precisamos definir o que será a tabela <strong>core</strong>
e o que serão as suas <strong>extensões</strong>, que por sua vez podem
ser mapeadas a partir de atributos comuns presentes em ambas as tabelas
(neste caso o ID).</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a><span class="co"># 1. Inicializando automaticamente - só funciona caso os nomes já estejam de acordo com o Darwin Core</span></span>
<span id="cb18-2"><a href="#cb18-2" tabindex="-1"></a>newTOVEEventTable <span class="ot"><-</span> <span class="fu">initializeGBIFEvent</span>(TOVEEventTableDF, <span class="st">"id"</span>, <span class="at">nameAutoMap =</span> <span class="cn">TRUE</span>)</span>
<span id="cb18-3"><a href="#cb18-3" tabindex="-1"></a></span>
<span id="cb18-4"><a href="#cb18-4" tabindex="-1"></a><span class="co"># 2. Iniciando manualmente - podemos usar o nome dos atributos que correspondem a cada categoria do Darwin Core. </span></span>
<span id="cb18-5"><a href="#cb18-5" tabindex="-1"></a> <span class="co"># podemos usar o nome ou o número da coluna</span></span>
<span id="cb18-6"><a href="#cb18-6" tabindex="-1"></a>newTOVEEventTable <span class="ot"><-</span> <span class="fu">initializeGBIFEvent</span>(TOVEEventTableDF, <span class="st">"id"</span>,</span>
<span id="cb18-7"><a href="#cb18-7" tabindex="-1"></a> <span class="at">type =</span> <span class="st">"type"</span>,</span>
<span id="cb18-8"><a href="#cb18-8" tabindex="-1"></a> <span class="at">modified =</span> <span class="st">"modified"</span>,</span>
<span id="cb18-9"><a href="#cb18-9" tabindex="-1"></a> <span class="at">datasetName =</span> <span class="st">"datasetName"</span>,</span>
<span id="cb18-10"><a href="#cb18-10" tabindex="-1"></a> <span class="at">ownerInstitutionCode =</span> <span class="st">"ownerInstitutionCode"</span>,</span>
<span id="cb18-11"><a href="#cb18-11" tabindex="-1"></a> <span class="at">informationWithheld =</span> <span class="st">"informationWithheld"</span>,</span>
<span id="cb18-12"><a href="#cb18-12" tabindex="-1"></a> <span class="at">dataGeneralizations =</span> <span class="st">"dataGeneralizations"</span>,</span>
<span id="cb18-13"><a href="#cb18-13" tabindex="-1"></a> <span class="at">eventID =</span> <span class="st">"eventID"</span>,</span>
<span id="cb18-14"><a href="#cb18-14" tabindex="-1"></a> <span class="at">samplingProtocol =</span> <span class="st">"samplingProtocol"</span>,</span>
<span id="cb18-15"><a href="#cb18-15" tabindex="-1"></a> <span class="at">sampleSizeValue =</span> <span class="st">"sampleSizeValue"</span>,</span>
<span id="cb18-16"><a href="#cb18-16" tabindex="-1"></a> <span class="at">sampleSizeUnit =</span> <span class="st">"sampleSizeUnit"</span>,</span>
<span id="cb18-17"><a href="#cb18-17" tabindex="-1"></a> <span class="at">samplingEffort =</span> <span class="st">"samplingEffort"</span>,</span>
<span id="cb18-18"><a href="#cb18-18" tabindex="-1"></a> <span class="at">eventDate =</span> <span class="st">"eventDate"</span>,</span>
<span id="cb18-19"><a href="#cb18-19" tabindex="-1"></a> <span class="at">eventTime =</span> <span class="st">"eventTime"</span>,</span>
<span id="cb18-20"><a href="#cb18-20" tabindex="-1"></a> <span class="at">year =</span> <span class="st">"year"</span>,</span>
<span id="cb18-21"><a href="#cb18-21" tabindex="-1"></a> <span class="at">month =</span> <span class="st">"month"</span>,</span>
<span id="cb18-22"><a href="#cb18-22" tabindex="-1"></a> <span class="at">day =</span> <span class="st">"day"</span>,</span>
<span id="cb18-23"><a href="#cb18-23" tabindex="-1"></a> <span class="at">locationID =</span> <span class="st">"locationID"</span>,</span>
<span id="cb18-24"><a href="#cb18-24" tabindex="-1"></a> <span class="at">country =</span> <span class="st">"country"</span>,</span>
<span id="cb18-25"><a href="#cb18-25" tabindex="-1"></a> <span class="at">countryCode =</span> <span class="st">"countryCode"</span>,</span>
<span id="cb18-26"><a href="#cb18-26" tabindex="-1"></a> <span class="at">stateProvince =</span> <span class="st">"stateProvince"</span>,</span>
<span id="cb18-27"><a href="#cb18-27" tabindex="-1"></a> <span class="at">municipality =</span> <span class="st">"municipality"</span>,</span>
<span id="cb18-28"><a href="#cb18-28" tabindex="-1"></a> <span class="at">locality =</span> <span class="st">"locality"</span>,</span>
<span id="cb18-29"><a href="#cb18-29" tabindex="-1"></a> <span class="at">minimumElevationInMeters =</span> <span class="st">"minimumElevationInMeters"</span>,</span>
<span id="cb18-30"><a href="#cb18-30" tabindex="-1"></a> <span class="at">maximumElevationInMeters =</span> <span class="st">"maximumElevationInMeters"</span>,</span>
<span id="cb18-31"><a href="#cb18-31" tabindex="-1"></a> <span class="at">decimalLatitude =</span> <span class="st">"decimalLatitude"</span>,</span>
<span id="cb18-32"><a href="#cb18-32" tabindex="-1"></a> <span class="at">decimalLongitude =</span> <span class="st">"decimalLongitude"</span>,</span>
<span id="cb18-33"><a href="#cb18-33" tabindex="-1"></a> <span class="at">geodeticDatum =</span> <span class="st">"geodeticDatum"</span>,</span>
<span id="cb18-34"><a href="#cb18-34" tabindex="-1"></a> <span class="at">coordinateUncertaintyInMeters =</span> <span class="st">"coordinateUncertaintyInMeters"</span>)</span>
<span id="cb18-35"><a href="#cb18-35" tabindex="-1"></a></span>
<span id="cb18-36"><a href="#cb18-36" tabindex="-1"></a><span class="co"># Podemos checar se o mapeamento dos termos se deu corretamente</span></span>
<span id="cb18-37"><a href="#cb18-37" tabindex="-1"></a>newTOVEEventTable<span class="sc">$</span><span class="fu">getTermMapping</span>()</span></code></pre></div>
</div>
<div id="construindo-os-metadados-para-as-extensões-da-tabela-core"
class="section level3">
<h3>Construindo os metadados para as extensões da tabela core</h3>
<p>Neste caso a tabela a extensão que temos da tabela chave é a tabela
de ocorrência de espécies. Vamos mapear ela da mesma forma que fizemos
para a tabela core</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a><span class="co"># Função para inicialização da tabela</span></span>
<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a>newTOVEOccTable <span class="ot"><-</span> <span class="fu">initializeGBIFOccurrence</span>(TOVEOccTable, <span class="st">"id"</span>, <span class="at">nameAutoMap =</span> <span class="cn">TRUE</span>)</span>
<span id="cb19-3"><a href="#cb19-3" tabindex="-1"></a></span>
<span id="cb19-4"><a href="#cb19-4" tabindex="-1"></a><span class="co"># Checando quais eventos foram mapeados na tabela, o que aparece com NA não foi mapeado, ou porque não existe ou porque tem o nome incorreto</span></span>
<span id="cb19-5"><a href="#cb19-5" tabindex="-1"></a>newTOVEOccTable<span class="sc">$</span><span class="fu">getTermMapping</span>()</span></code></pre></div>
</div>
<div id="construindo-o-eml" class="section level3">
<h3>Construindo o EML</h3>
<p>O último elemento que precisamos para construir nossos metadados para
os arquivos de biodiversidade que estamos utilizando é o arquivo EML,
que vocês já conhecem. O EML pode ser criado de várias formas. Vimos
anteriormente como criar um EML usando o pacote <code>{EML}</code>. O
pacote <code>{LivingNorwayR}</code> oferece uma maneira simples de criar
um arquivo XML usando um arquivo <code>.Rmd</code>, ou seja, usando o
Rmarkdown. Vamos entender os detalhes de um arquivo do tipo Rmd mais
adiante, por hora precisamos apenas saber que ele é um arquivo que
permite mesclar textos e códigos, além de possibilitar criar tags para
seções (Como os títulos num documento Word). Essas tags são utilizadas
pelas funções do LivingNorwayR para criar o arquivo XML. Vale notar que
isso é mais limitante que criar um XML usando o EML, mas para questões
didáticas vamos usar um arquivo .Rmd pronto, que está na pasta de dados
deste diretório.</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a>createdTOVEMetadata <span class="ot"><-</span> <span class="fu">initializeDwCMetadata</span>(<span class="at">fileLocation =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"TOVEData"</span>, <span class="st">"LNWorkshopExample_Metadata.rmd"</span>), <span class="at">fileType =</span> <span class="st">"rmarkdown"</span>)</span>
<span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a></span>
<span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="co"># Exportando o EML</span></span>
<span id="cb20-4"><a href="#cb20-4" tabindex="-1"></a>createdTOVEMetadata<span class="sc">$</span><span class="fu">exportToEML</span>(<span class="fu">file.path</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"TOVEData"</span>), <span class="st">"newMetadata.xml"</span>))</span></code></pre></div>
<p>Este novo metadado precisa ser lido para o R e assim podemos juntá-lo
com os outros arquivos</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1" tabindex="-1"></a>newTOVEMetadata <span class="ot"><-</span> <span class="fu">initializeDwCMetadata</span>(<span class="fu">file.path</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"TOVEData"</span>), <span class="st">"newMetadata.xml"</span>),</span>
<span id="cb21-2"><a href="#cb21-2" tabindex="-1"></a> <span class="at">fileType =</span> <span class="st">"eml"</span> <span class="co"># This line is not required if the file has the ".xml" file extension</span></span>
<span id="cb21-3"><a href="#cb21-3" tabindex="-1"></a>)</span></code></pre></div>
</div>
</div>
<div id="juntando-todos-os-arquivos" class="section level2">
<h2>Juntando todos os arquivos</h2>
<p>Agora temos os arquivos necessários para juntar em um único arquivo
zipado que pode ser guardado localmente ou submetido em alguma
plataforma de dados, por exemplo, GBIF, como ilustrado abaixo</p>
<p><img src="figs/gibif-upload-zip.png" width="1275" /></p>
<p>Para juntar todos os arquivos criados precisamos usar a seguinte
função</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a><span class="co"># criando um único arquivo com todos os objetos criados anteriormente</span></span>
<span id="cb22-2"><a href="#cb22-2" tabindex="-1"></a>newTOVEArchive <span class="ot"><-</span> <span class="fu">initializeDwCArchive</span>(newTOVEEventTable, <span class="fu">list</span>(newTOVEOccTable), newTOVEMetadata)</span></code></pre></div>
<p>Para salvar o objeto .zip, que agora é nosso Darwin Core Archive,
podemos fazer o seguinte</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" tabindex="-1"></a>newTOVEArchive<span class="sc">$</span><span class="fu">exportAsDwCArchive</span>(<span class="fu">file.path</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"NEWTOVEData"</span>), <span class="st">"newDwCArchive.zip"</span>))</span></code></pre></div>
</div>
<div id="explorando-o-darwin-core-archive" class="section level2">
<h2>Explorando o Darwin Core Archive</h2>
<p>Uma vez criado o arquivo no formato Darwin Core Archive podemos fazer
o caminho inverso e obter as tabelas a partir do arquivo que
criamos.</p>
<p>Para tanto podemos usar as funções do pacote LivingNorwayR para ler o
arquivo zip e extrair as tabelas, incluindo os metadados.</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a>localDataLoc2 <span class="ot"><-</span> <span class="fu">file.path</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"NEWTOVEData"</span>), <span class="st">"newDwCArchive.zip"</span>) </span>
<span id="cb24-2"><a href="#cb24-2" tabindex="-1"></a>NEWTOVEArchive <span class="ot"><-</span> <span class="fu">initializeDwCArchive</span>(localDataLoc2, <span class="st">"UTF-8"</span>)</span></code></pre></div>
<p>Podemos agora explorar os dados dentro do arquivo Darwin Core criado
nos passos anteriores. Ou seja, podemos retomar os dados e importar para
dentro do R para fazer, por exemplo, novas análises</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a><span class="co"># obtendo o dado</span></span>
<span id="cb25-2"><a href="#cb25-2" tabindex="-1"></a>NEWTOVEEventTable <span class="ot"><-</span> NEWTOVEArchive<span class="sc">$</span><span class="fu">getCoreTable</span>()</span>
<span id="cb25-3"><a href="#cb25-3" tabindex="-1"></a><span class="fu">class</span>(NEWTOVEEventTable)</span>
<span id="cb25-4"><a href="#cb25-4" tabindex="-1"></a></span>