Merge pull request #19 from eeholmes/main

add link to source code
oceanhackweek · Sep 19, 2023 · 30ab8e9 · 30ab8e9
2 parents 0634aa1 + f5dd887
commit 30ab8e9
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Showing 20 changed files with 36 additions and 35 deletions.
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,4 @@
 *.Rproj
 _freeze
 /.quarto/
+.DS_Store
diff --git a/_quarto.yml b/_quarto.yml
@@ -28,7 +28,7 @@ website:
   site-url: https://oceanhackweek.org/ohw23_proj_marinesdms
 
   repo-url: https://github.com/oceanhackweek/ohw23_proj_marinesdms
-  repo-actions: [edit, issue]
+  repo-actions: [edit, issue, source]
 
   page-footer: "OceanHackWeek Tutorial" 
 

diff --git a/docs/SDM/Turtle_maxnet.html b/docs/SDM/Turtle_maxnet.html
@@ -314,7 +314,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#visualization" id="toc-visualization" class="nav-link" data-scroll-target="#visualization">Visualization</a></li>
   <li><a href="#discussion" id="toc-discussion" class="nav-link" data-scroll-target="#discussion">Discussion</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/SDM/Turtle_maxnet.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/SDM/Turtle_maxnet.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/SDM/Turtle_maxnet.Rmd" class="toc-action">View source</a></p></div></div></nav>
     </div>
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 <main class="content" id="quarto-document-content">

diff --git a/docs/index.html b/docs/index.html
@@ -251,7 +251,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#who-this-tutorial-is-intended" id="toc-who-this-tutorial-is-intended" class="nav-link" data-scroll-target="#who-this-tutorial-is-intended">Who this tutorial is intended:</a></li>
   <li><a href="#additional-resources" id="toc-additional-resources" class="nav-link" data-scroll-target="#additional-resources">Additional resources</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/index.md" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/index.md" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/index.md" class="toc-action">View source</a></p></div></div></nav>
     </div>
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diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -2,70 +2,70 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/SDM/Turtle_maxnet.html</loc>
-    <lastmod>2023-09-17T18:25:42.762Z</lastmod>
+    <lastmod>2023-09-19T03:45:36.413Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/index.html</loc>
-    <lastmod>2023-09-17T18:25:43.285Z</lastmod>
+    <lastmod>2023-09-19T03:45:37.044Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/**_Extracting_environmental_data.html</loc>
-    <lastmod>2023-09-17T18:25:43.965Z</lastmod>
+    <lastmod>2023-09-19T03:45:37.856Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/00_Region.html</loc>
-    <lastmod>2023-09-17T18:25:44.625Z</lastmod>
+    <lastmod>2023-09-19T03:45:38.641Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/00_Roadmap.html</loc>
-    <lastmod>2023-09-17T18:25:45.013Z</lastmod>
+    <lastmod>2023-09-19T03:45:39.099Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/01_Presence_Data.html</loc>
-    <lastmod>2023-09-17T18:25:45.784Z</lastmod>
+    <lastmod>2023-09-19T03:45:39.973Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/02_Background_Data.html</loc>
-    <lastmod>2023-09-17T18:25:46.560Z</lastmod>
+    <lastmod>2023-09-19T03:45:40.772Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/03_sdmpredictors-variables.html</loc>
-    <lastmod>2023-09-17T18:25:47.471Z</lastmod>
+    <lastmod>2023-09-19T03:45:41.853Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/05_Link_env_to_pts.html</loc>
-    <lastmod>2023-09-17T18:25:47.790Z</lastmod>
+    <lastmod>2023-09-19T03:45:42.208Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/05_fitting.html</loc>
-    <lastmod>2023-09-17T18:25:48.120Z</lastmod>
+    <lastmod>2023-09-19T03:45:42.565Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/05_models.html</loc>
-    <lastmod>2023-09-17T18:25:48.554Z</lastmod>
+    <lastmod>2023-09-19T03:45:43.099Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/Steps_Region.html</loc>
-    <lastmod>2023-09-17T18:25:59.868Z</lastmod>
+    <lastmod>2023-09-19T03:45:43.762Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/Steps_background.html</loc>
-    <lastmod>2023-09-17T18:26:00.433Z</lastmod>
+    <lastmod>2023-09-19T03:45:44.420Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/Steps_occ_env.html</loc>
-    <lastmod>2023-09-17T18:26:01.186Z</lastmod>
+    <lastmod>2023-09-19T03:45:45.229Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/Steps_occurences.html</loc>
-    <lastmod>2023-09-17T18:26:01.814Z</lastmod>
+    <lastmod>2023-09-19T03:45:46.031Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/Steps_sdm_maxnet.html</loc>
-    <lastmod>2023-09-17T18:26:02.474Z</lastmod>
+    <lastmod>2023-09-19T03:45:46.783Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/ohw23_proj_marinesdms/tutorial/Steps_visualization.html</loc>
-    <lastmod>2023-09-17T18:26:03.094Z</lastmod>
+    <lastmod>2023-09-19T03:45:47.482Z</lastmod>
   </url>
 </urlset>
diff --git a/docs/tutorial/**_Extracting_environmental_data.html b/docs/tutorial/**_Extracting_environmental_data.html
@@ -279,7 +279,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#plotting-both-datasets-into-a-single-map" id="toc-plotting-both-datasets-into-a-single-map" class="nav-link" data-scroll-target="#plotting-both-datasets-into-a-single-map">Plotting both datasets into a single map</a></li>
   <li><a href="#extracting-environmental-data" id="toc-extracting-environmental-data" class="nav-link" data-scroll-target="#extracting-environmental-data">Extracting environmental data</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.dev/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/**_Extracting_environmental_data.ipynb" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.dev/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/**_Extracting_environmental_data.ipynb" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/**_Extracting_environmental_data.ipynb" class="toc-action">View source</a></p></div></div></nav>
     </div>
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 <main class="content" id="quarto-document-content">

diff --git a/docs/tutorial/00_Region.html b/docs/tutorial/00_Region.html
@@ -276,7 +276,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#create-a-world-map" id="toc-create-a-world-map" class="nav-link" data-scroll-target="#create-a-world-map">Create a world map</a></li>
   <li><a href="#create-a-region-map" id="toc-create-a-region-map" class="nav-link" data-scroll-target="#create-a-region-map">Create a region map</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/00_Region.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/00_Region.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/00_Region.Rmd" class="toc-action">View source</a></p></div></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">

diff --git a/docs/tutorial/00_Roadmap.html b/docs/tutorial/00_Roadmap.html
@@ -240,7 +240,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#sdm-workflow" id="toc-sdm-workflow" class="nav-link active" data-scroll-target="#sdm-workflow">SDM Workflow</a></li>
   <li><a href="#references" id="toc-references" class="nav-link" data-scroll-target="#references">References</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/00_Roadmap.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/00_Roadmap.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/00_Roadmap.Rmd" class="toc-action">View source</a></p></div></div></nav>
     </div>
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 <main class="content" id="quarto-document-content">

diff --git a/docs/tutorial/01_Presence_Data.html b/docs/tutorial/01_Presence_Data.html
@@ -279,7 +279,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#problematic-observations" id="toc-problematic-observations" class="nav-link" data-scroll-target="#problematic-observations">Problematic observations</a></li>
   <li><a href="#saving-clean-data" id="toc-saving-clean-data" class="nav-link" data-scroll-target="#saving-clean-data">Saving clean data</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/01_Presence_Data.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/01_Presence_Data.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/01_Presence_Data.Rmd" class="toc-action">View source</a></p></div></div></nav>
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diff --git a/docs/tutorial/02_Background_Data.html b/docs/tutorial/02_Background_Data.html
@@ -312,7 +312,7 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   <li><a href="#approach-3.-random-points-a-convex-hull" id="toc-approach-3.-random-points-a-convex-hull" class="nav-link" data-scroll-target="#approach-3.-random-points-a-convex-hull">Approach 3. Random points a convex hull</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/02_Background_Data.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/02_Background_Data.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/02_Background_Data.Rmd" class="toc-action">View source</a></p></div></div></nav>
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diff --git a/docs/tutorial/03_sdmpredictors-variables.html b/docs/tutorial/03_sdmpredictors-variables.html
@@ -285,7 +285,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#view-the-sdmpredictors-variables" id="toc-view-the-sdmpredictors-variables" class="nav-link" data-scroll-target="#view-the-sdmpredictors-variables">View the sdmpredictors variables</a></li>
   <li><a href="#extract-these-variables" id="toc-extract-these-variables" class="nav-link" data-scroll-target="#extract-these-variables">Extract these variables</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/03_sdmpredictors-variables.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/03_sdmpredictors-variables.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/03_sdmpredictors-variables.Rmd" class="toc-action">View source</a></p></div></div></nav>
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diff --git a/docs/tutorial/05_Link_env_to_pts.html b/docs/tutorial/05_Link_env_to_pts.html
@@ -626,7 +626,7 @@ <h1 class="title">Link environmental layer to points</h1>
     <div class="nav-footer-left">
       &nbsp;
     </div>   
-    <div class="nav-footer-center">OceanHackWeek Tutorial<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/05_Link_env_to_pts.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></div>
+    <div class="nav-footer-center">OceanHackWeek Tutorial<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/05_Link_env_to_pts.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/05_Link_env_to_pts.Rmd" class="toc-action">View source</a></p></div></div></div>
     <div class="nav-footer-right">
       &nbsp;
     </div>

diff --git a/docs/tutorial/05_fitting.html b/docs/tutorial/05_fitting.html
@@ -240,7 +240,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#data-frame" id="toc-data-frame" class="nav-link active" data-scroll-target="#data-frame">Data frame</a></li>
   <li><a href="#fitting" id="toc-fitting" class="nav-link" data-scroll-target="#fitting">Fitting</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/05_fitting.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/05_fitting.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/05_fitting.Rmd" class="toc-action">View source</a></p></div></div></nav>
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diff --git a/docs/tutorial/05_models.html b/docs/tutorial/05_models.html
@@ -243,7 +243,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#models" id="toc-models" class="nav-link active" data-scroll-target="#models">Models</a></li>
   <li><a href="#maxent" id="toc-maxent" class="nav-link" data-scroll-target="#maxent">Maxent</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/05_models.md" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/05_models.md" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/05_models.md" class="toc-action">View source</a></p></div></div></nav>
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diff --git a/docs/tutorial/Steps_Region.html b/docs/tutorial/Steps_Region.html
@@ -283,7 +283,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#create-a-region-map" id="toc-create-a-region-map" class="nav-link" data-scroll-target="#create-a-region-map">Create a region map</a></li>
   <li><a href="#loading-in-the-save-files" id="toc-loading-in-the-save-files" class="nav-link" data-scroll-target="#loading-in-the-save-files">Loading in the save files</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/Steps_Region.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/edit/main/tutorial/Steps_Region.Rmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/oceanhackweek/ohw23_proj_marinesdms/blob/main/tutorial/Steps_Region.Rmd" class="toc-action">View source</a></p></div></div></nav>
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