deploy: 19bfce3

iobis · Dec 12, 2024 · 684859d · 684859d
1 parent 6dbfafc
commit 684859d
Show file tree

Hide file tree

Showing 43 changed files with 48 additions and 53 deletions.
diff --git a/404.html b/404.html
@@ -376,7 +376,7 @@ <h1>Page not found</h1>
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/FAQ.html b/FAQ.html
@@ -792,7 +792,7 @@ <h4>Accessing data in OBIS<a href="FAQ.html#accessing-data-in-obis" class="ancho
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/access.html b/access.html
@@ -538,7 +538,7 @@ <h2><span class="header-section-number">14.8</span> Interpreting downloaded file
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/checklist.html b/checklist.html
@@ -2431,7 +2431,7 @@ <h2><span class="header-section-number">8.1</span> Darwin Core Term Checklist fo
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/citing.html b/citing.html
@@ -389,7 +389,7 @@ <h2><span class="header-section-number">14.9</span> Citing Data from OBIS<a href
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/common_formatissues.html b/common_formatissues.html
@@ -687,7 +687,7 @@ <h2><span class="header-section-number">10.4</span> Missing required fields<a hr
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/common_qc.html b/common_qc.html
@@ -654,7 +654,7 @@ <h3><span class="header-section-number">12.6.8</span> Non-marine species<a href=
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/contribute.html b/contribute.html
@@ -448,7 +448,7 @@ <h2><span class="header-section-number">2.2</span> How to handle sensitive data<
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/darwin_core.html b/darwin_core.html
@@ -747,9 +747,9 @@ <h5><span class="header-section-number">2.4.1.3.4</span> Location<a href="darwin
 <p><code>locationID</code> is an identifier for the set of location information (e.g. station ID, or MRGID from <a href="http://www.marineregion.org">marineregions</a>), for example the <a href="http://www.marineregions.org/gazetteer.php?p=details&amp;id=3956">Balearic Plain</a> has MRGID: <a href="http://marineregions.org/mrgid/3956">http://marineregions.org/mrgid/3956</a>.</p>
 <p><a href="https://en.wikipedia.org/wiki/Well-known_text">Well-Known Text</a> (WKT) provides a representation of the geoemtry of a location and can be provided in <code>footprintWKT</code>. This is particularly useful for tracks, transects, tows, trawls, habitat extents, or when an exact location is not known. You can use the <a href="https://obis.org/maptool">OBIS Maptool</a> (Figure 2.1) to generate WKT, calculate midpoints of lines and polygons, and determine the radius of a polygon or line. Midpoints can used to populate <code>decimalLongitude</code> and <code>decimalLatitude</code>, while the radius can be used to populate <code>coordinateUncertaintyInMeters</code>. Additionally, an <a href="https://github.com/iobis/obistools#calculate-centroid-and-radius-for-wkt-geometries">obistools R function</a> can calculate centroids and radii. To visualize and share WKT strings, try <a href="https://wktmap.com">wktmap.com</a>.</p>
 <div class="figure"><span style="display:block;" id="fig:fig-wkt"></span>
-<img src="images/wkttool2.png" alt="*A screenshot demonstrating the OBIS Maptool's WKT function. After generating a polygon, pressing the WKT button will open a pop-up where you can copy the string. The Locations table provides the longitude, latitude, and radius to be used in `decimalLongitude`, `decimalLatitude`, and `coordinateUncertaintyInMeters` respectively*." width="90%" />
+<img src="images/wkttool2.png" alt="A screenshot demonstrating the OBIS Maptool's WKT function. After generating a polygon, pressing the WKT button will open a pop-up where you can copy the string. The Locations table provides the longitude, latitude, and radius to be used in `decimalLongitude`, `decimalLatitude`, and `coordinateUncertaintyInMeters` respectively." width="90%" />
 <p class="caption">
-Figure 2.1: <em>A screenshot demonstrating the OBIS Maptool’s WKT function. After generating a polygon, pressing the WKT button will open a pop-up where you can copy the string. The Locations table provides the longitude, latitude, and radius to be used in <code>decimalLongitude</code>, <code>decimalLatitude</code>, and <code>coordinateUncertaintyInMeters</code> respectively</em>.
+Figure 2.1: A screenshot demonstrating the OBIS Maptool’s WKT function. After generating a polygon, pressing the WKT button will open a pop-up where you can copy the string. The Locations table provides the longitude, latitude, and radius to be used in <code>decimalLongitude</code>, <code>decimalLatitude</code>, and <code>coordinateUncertaintyInMeters</code> respectively.
 </p>
 </div>
 <p>Some examples of WKT strings:</p>
@@ -957,7 +957,7 @@ <h5><span class="header-section-number">2.4.1.3.7</span> Sampling<a href="darwin
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/data_format.html b/data_format.html
@@ -438,7 +438,7 @@ <h5><span class="header-section-number">2.4.2.2.4</span> Recommended reading<a h
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/data_map.html b/data_map.html
@@ -513,7 +513,7 @@ <h2><span class="header-section-number">7.1</span> Map data fields to Darwin Cor
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/data_publication.html b/data_publication.html
@@ -395,7 +395,7 @@ <h2><span class="header-section-number">13.1</span> Licenses<a href="data_public
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/data_qc.html b/data_qc.html
@@ -497,7 +497,7 @@ <h3>QC with R package Hmisc<a href="data_qc.html#qc-with-r-package-hmisc" class=
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/data_sharing.html b/data_sharing.html
@@ -626,7 +626,7 @@ <h2><span class="header-section-number">13.6</span> Publish OBIS data to GBIF<a
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/data_standards.html b/data_standards.html
@@ -405,7 +405,7 @@ <h2><span class="header-section-number">2.4</span> Biodiversity data standards<a
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/dataquality.html b/dataquality.html
@@ -467,7 +467,7 @@ <h3>Inspecting QC flags with R<a href="dataquality.html#inspecting-qc-flags-with
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/dataviz.html b/dataviz.html
@@ -403,7 +403,7 @@ <h2><span class="header-section-number">15.2</span> obisindicators: calculating
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/dna_data.html b/dna_data.html
@@ -1228,7 +1228,7 @@ <h3><span class="header-section-number">8.5.4</span> OBIS Bioinformatics Pipelin
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/eml.html b/eml.html
@@ -768,7 +768,7 @@ <h5><span class="header-section-number">2.4.4.2.13</span> Additional Metadata<a
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/examples.html b/examples.html
@@ -371,9 +371,9 @@ <h4>Invertebrates abundance and distribution<a href="examples.html#invertebrates
 <h4>Macroalgae canopy cover and composition<a href="examples.html#macroalgae-canopy-cover-and-composition" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <p>In this section we will encode a fictional macroalgal survey dataset (Figure 9.1) into Darwin Core using the ENV-DATA approach, i.e. using an Event core with an Occurrence extension and an extendedMeasurementOrFact extension.</p>
 <div class="figure"><span style="display:block;" id="fig:fig-macroal"></span>
-<img src="images/dwca_macroalgae_survey.png" alt="*A fictional macroalgae survey with a single site, multiple zones, quadrats, and different types of transects.*." width="95%" />
+<img src="images/dwca_macroalgae_survey.png" alt="A fictional macroalgae survey with a single site, multiple zones, quadrats, and different types of transects." width="95%" />
 <p class="caption">
-Figure 11.1: <em>A fictional macroalgae survey with a single site, multiple zones, quadrats, and different types of transects.</em>.
+Figure 11.1: A fictional macroalgae survey with a single site, multiple zones, quadrats, and different types of transects.
 </p>
 </div>
 <p><strong>Event core:</strong></p>
@@ -912,9 +912,9 @@ <h4>Marine birds abundance and distribution<a href="examples.html#marine-birds-a
 <h4>Marine mammals abundance and distribution<a href="examples.html#marine-mammals-abundance-and-distribution" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <p>In this section we will explore how to encode a marine mammal survey dataset into Darwin Core using the ENV-DATA approach. As an example, sections of the actual dataset <a href="http://ipt.vliz.be/eurobis/resource?r=cetus_cetaceans">CETUS: Cetacean monitoring surveys in the Eastern North Atlantic</a> are used.</p>
 <div class="figure"><span style="display:block;" id="fig:fig-cetus"></span>
-<img src="images/ENV_example_CETUS.png" alt="*A representation of the observation events of [CETUS: Cetacean monitoring surveys in the Eastern North Atlantic](http://ipt.vliz.be/eurobis/resource?r=cetus_cetaceans), presenting the route **Madeira** as a site with three cruises (zones). Each **Cruise** is divided into different **Transects** and each transect contains a number of **Positions***." width="95%" />
+<img src="images/ENV_example_CETUS.png" alt="A representation of cetacean observation events from CETUS: Cetacean monitoring surveys in the Eastern North Atlantic, presenting the route Madeira as a site with three cruises (zones). Each Cruise is divided into different Transects and each transect contains a number of Positions." width="95%" />
 <p class="caption">
-Figure 11.2: <em>A representation of the observation events of <a href="http://ipt.vliz.be/eurobis/resource?r=cetus_cetaceans">CETUS: Cetacean monitoring surveys in the Eastern North Atlantic</a>, presenting the route <strong>Madeira</strong> as a site with three cruises (zones). Each <strong>Cruise</strong> is divided into different <strong>Transects</strong> and each transect contains a number of <strong>Positions</strong></em>.
+Figure 11.2: A representation of cetacean observation events from CETUS: Cetacean monitoring surveys in the Eastern North Atlantic, presenting the route Madeira as a site with three cruises (zones). Each Cruise is divided into different Transects and each transect contains a number of Positions.
 </p>
 </div>
 <a href="https://ipt.vliz.be/eurobis/archive.do?r=cetus_cetaceans&amp;v=1.0">
@@ -2607,7 +2607,7 @@ <h4>Zooplankton biomass and diversity<a href="examples.html#zooplankton-biomass-
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/format_emof.html b/format_emof.html
@@ -462,7 +462,7 @@ <h4><span class="header-section-number">8.4.0.3</span> Stepwise Guidance to Form
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/format_event.html b/format_event.html
@@ -482,7 +482,7 @@ <h3><span class="header-section-number">8.3.1</span> Populating parent and child
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/format_occurrence.html b/format_occurrence.html
@@ -434,7 +434,7 @@ <h4><span class="header-section-number">8.2.0.1</span> Stepwise Guidance to Form
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/formatting.html b/formatting.html
@@ -443,7 +443,7 @@ <h2><span class="header-section-number">5.4</span> Data formatting tools<a href=
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/formatting_intro.html b/formatting_intro.html
@@ -407,7 +407,7 @@ <h1><span class="header-section-number">4</span> Data formatting workflow<a href
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/gethelp.html b/gethelp.html
@@ -383,7 +383,7 @@ <h2><span class="header-section-number">1.4</span> Getting Help in OBIS<a href="
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/identifiers.html b/identifiers.html
@@ -592,7 +592,7 @@ <h3><span class="header-section-number">6.0.2</span> occurrenceID<a href="identi
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/index.html b/index.html
@@ -324,7 +324,7 @@ <h1>
             <section class="normal" id="section-">
 <div id="header">
 <h1 class="title">The OBIS manual</h1>
-<p class="date"><em>09 December, 2024</em></p>
+<p class="date"><em>12 December, 2024</em></p>
 </div>
 <div style="page-break-after: always;"></div>
 <p><img src="images/obis_logo.png" style="width:50.0%" /></p>
@@ -409,7 +409,7 @@ <h2><span class="header-section-number">1.2</span> Acknowledgements<a href="inde
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/ipt.html b/ipt.html
@@ -587,7 +587,7 @@ <h3>Downloading datasets from an IPT<a href="ipt.html#downloading-datasets-from-
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/ipt_admin.html b/ipt_admin.html
@@ -416,7 +416,7 @@ <h3>Maintaining the IPT<a href="ipt_admin.html#maintaining-the-ipt" class="ancho
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/lifewatch_qc.html b/lifewatch_qc.html
@@ -427,7 +427,7 @@ <h4><span class="header-section-number">12.5.0.2</span> OBIS data format validat
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/linklist.html b/linklist.html
@@ -475,7 +475,7 @@ <h4>Publishing Tools &amp; Links<a href="linklist.html#publishing-tools-links" c
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/manual.pdf b/manual.pdf
diff --git a/mofreports.html b/mofreports.html
@@ -407,7 +407,7 @@ <h2><span class="header-section-number">12.4</span> How To Use MoF Report and To
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/name_matching.html b/name_matching.html
@@ -554,7 +554,7 @@ <h3>Taxon Match Tools Overview<a href="name_matching.html#taxon-match-tools-over
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/nodes.html b/nodes.html
@@ -625,7 +625,7 @@ <h2><span class="header-section-number">3.6</span> TOR of OBIS Executive Committ
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/other_data_types.html b/other_data_types.html
@@ -491,7 +491,7 @@ <h2><span class="header-section-number">11.3</span> Tracking data<a href="other_
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/other_resources.html b/other_resources.html
@@ -408,7 +408,7 @@ <h2><span class="header-section-number">16.5</span> Bionomia<a href="other_resou
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/policy.html b/policy.html
@@ -458,7 +458,7 @@ <h4><span class="header-section-number">1.3.0.10</span> Disclaimer<a href="polic
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/relational_db.html b/relational_db.html
@@ -400,7 +400,7 @@ <h4><span class="header-section-number">2.4.3.1</span> How to avoid redundancy<a
 "link": null,
 "text": null
 },
-"download": null,
+"download": ["manual.pdf"],
 "search": {
 "engine": "fuse",
 "options": null

diff --git a/search_index.json b/search_index.json