deploy: 744ce03

access.html

@@ -329,7 +329,9 @@ <h1><span class="header-section-number">11</span> Data access<a href="access.htm
 <li><a href="access.html#full-exports">Full data exports</a></li>
 <li><a href="ipt.html">IPT</a></li>
 </ul>
-<p><strong>NOTE</strong> When you download data from the Mapper or full export, the data you will receive is flattened into one table with occurrence plus event data. eMoF data tables are separate upon request. However when you download a dataset from the OBIS homepage or dataset page, all tables (Event, Occurrence, eMoF) are separate files.</p>
+<div class="callbox-blue">
+<p><svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:darkblue;overflow:visible;position:relative;"><path d="M64 32C64 14.3 49.7 0 32 0S0 14.3 0 32V64 368 480c0 17.7 14.3 32 32 32s32-14.3 32-32V352l64.3-16.1c41.1-10.3 84.6-5.5 122.5 13.4c44.2 22.1 95.5 24.8 141.7 7.4l34.7-13c12.5-4.7 20.8-16.6 20.8-30V66.1c0-23-24.2-38-44.8-27.7l-9.6 4.8c-46.3 23.2-100.8 23.2-147.1 0c-35.1-17.6-75.4-22-113.5-12.5L64 48V32z"/></svg> When you download data from the Mapper or full export, the data you will receive is flattened into one table with occurrence plus event data. eMoF data tables are separate upon request. However when you download a dataset from the OBIS homepage or dataset page, all tables (Event, Occurrence, eMoF) are separate files.</p>
+</div>
 <div id="obis-homepage-and-dataset-pages" class="section level2 hasAnchor" number="11.1">
 <h2><span class="header-section-number">11.1</span> OBIS Homepage and dataset pages<a href="access.html#obis-homepage-and-dataset-pages" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>From the OBIS homepage, you can search for data in the search bar in the middle of the page. You can search by particular taxonomic groups, common names, dataset names, OBIS nodes, institute name, areas (e.g., Exclusive Economic Zone (EEZ)), or by the data provider’s country.</p>
@@ -355,7 +357,7 @@ <h2><span class="header-section-number">11.2</span> Mapper<a href="access.html#m
 <ul>
 <li><a href="https://mapper.obis.org" class="uri">https://mapper.obis.org</a></li>
 </ul>
-<p>Watch this video demonstration of how to use the Mapper as well as the OBIS homepage search.</p>
+<p>Watch this video demonstration <svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> of how to use the Mapper as well as the OBIS homepage search.</p>
 <p><iframe width="560" height="315"
 src="https://www.youtube.com/embed/9PSPEtqgjUI"
 frameborder="0"
@@ -380,12 +382,12 @@ <h2><span class="header-section-number">11.3</span> R package<a href="access.htm
 </ul>
 <p>The robis R package has been developed to facilitate connecting to the OBIS API from R. The package can be installed <a href="https://cran.r-project.org/web/packages/robis/index.html">from CRAN</a> or <a href="https://github.com/iobis/robis">from GitHub</a> (latest development version). The package documentation includes a function reference as well as a <a href="https://iobis.github.io/robis/articles/getting-started.html">getting started vignette</a>. As a quick example of what the package can do, you can obtain raw occurrence data by feeding a taxon name or AphiaID to the <code>occurrence</code> function.</p>
 <p>If you’d like to then download this data, you can simply export R objects with the <code>write.csv</code> function. For example, if we wanted to obtain Mollusc data from OBIS:</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="access.html#cb20-1" tabindex="-1"></a><span class="fu">library</span>(robis)</span>
-<span id="cb20-2"><a href="access.html#cb20-2" tabindex="-1"></a>moll<span class="ot">&lt;-</span><span class="fu">occurrence</span>(“Mollusca”)</span>
-<span id="cb20-3"><a href="access.html#cb20-3" tabindex="-1"></a><span class="fu">write.csv</span>(moll, “mollusca<span class="sc">-</span>obis.csv”)</span></code></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="access.html#cb21-1" tabindex="-1"></a><span class="fu">library</span>(robis)</span>
+<span id="cb21-2"><a href="access.html#cb21-2" tabindex="-1"></a>moll<span class="ot">&lt;-</span><span class="fu">occurrence</span>(“Mollusca”)</span>
+<span id="cb21-3"><a href="access.html#cb21-3" tabindex="-1"></a><span class="fu">write.csv</span>(moll, “mollusca<span class="sc">-</span>obis.csv”)</span></code></pre></div>
 <p>This file will be saved to your working directory (if you are not familiar with working directories, read <a href="https://bookdown.org/ndphillips/YaRrr/the-working-directory.html">here</a>). After opening the file, you will notice that the fields in the download do not include every possible field, but instead only those where information has been recorded by data providers, plus the <a href="access.html#interpreting-downloaded-files-from-obis">fields added by OBIS’s quality control pipeline</a>.</p>
 <p>To use <code>robis</code> for visualizing and mapping occurrences, see the <a href="dataviz.html">Visualization</a> section of the manual.</p>
-<p>Watch the video below for a walkthrough of how to use the robis package to obtain OBIS data.</p>
+<p>Watch the video <svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> below for a walkthrough of how to use the robis package to obtain OBIS data.</p>
 <p><iframe width="560" height="315"
 src="https://www.youtube.com/embed/8Ep4fGICQWU"
 frameborder="0"
@@ -422,7 +424,7 @@ <h2><span class="header-section-number">11.4</span> API<a href="access.html#api"
 <li>Institute ID - this should be the Ocean Expert ID (e.g., the ID for <a href="https://oceanexpert.org/institution/7532">NOAA Fisheries Service, Southeast Regional Office St. Petersburg</a> is 7532)</li>
 <li>OBIS node UUID</li>
 </ul>
-<p>A short video demonstrating use of the API is shown below.</p>
+<p>A short video <svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> demonstrating use of the API is shown below.</p>
 <p><iframe width="560" height="315"
 src="https://www.youtube.com/embed/Hocr3N6zpH0"
 frameborder="0"