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best_practices.html

@@ -274,8 +274,7 @@ <h1 class="title">Coding Tips</h1>
 
 <section id="welcome" class="level3">
 <h3 class="anchored" data-anchor-id="welcome">Welcome!</h3>
-<p>This page contains the collected best practice tips of the NCEAS Scientific Computing Support Team. More will be added over time and feel free to post <a href="https://github.com/NCEAS/scicomp.github.io/issues">an issue</a> if you have a specific request for a section to add to this document.</p>
-<p>Please feel free to reach out to our team (see <a href="https://nceas.github.io/scicomp.github.io/staff.html">here</a>) if you have any questions about this best practices manual and/or need help implementing some of this content.</p>
+<p>This page contains the collected best practice tips of our team. More will be added over time and feel free to post <a href="https://github.com/lter/scicomp/issues">an issue</a> if you have a specific request for a section to add to this document. Please feel free to reach out to <a href="https://lter.github.io/scicomp/staff.html">our team</a> if you have any questions about this best practices manual and/or need help implementing some of this content.</p>
 <p>Check the headings below or in the table of contents on the right of this page to see which tips and tricks we have included so far and we hope this page is a useful resource to you and your team!</p>
 </section>
 <section id="r-scripts-versus-r-markdowns" class="level2">
@@ -301,7 +300,7 @@ <h3 class="anchored" data-anchor-id="r-markdowns---potential-weaknesses">R Markd
 <h3 class="anchored" data-anchor-id="script-vs.-markdown-summary">Script vs.&nbsp;Markdown Summary</h3>
 <p>Taken together, both R scripts and R markdown files can empower users to write reproducible, transparent code. However, both file types have some key limitations that should be taken into consideration when choosing which to use as you set out to create a new code product.</p>
 <p align="center">
-<img src="images/lter-photos/patches.jpg" width="100%">
+<img src="images/lter-photos/patches.jpg" alt="Photo of people walking sampling insects at a farm where a wildflower strip has been planted between two row-cropped areas" width="100%">
 </p>
 </section>
 </section>
@@ -345,7 +344,7 @@ <h3 class="anchored" data-anchor-id="file-paths-summary">File Paths Summary</h3>
 <p>We strongly recommend following these guidelines so that your scripts work regardless of (1) the operating system, (2) folders “upstream” of the working directory, and (3) folders within the project. This will help your code by flexible and reproducible when others are attempting to re-run your scripts!</p>
 <p>Also, for more information on how to read files in cloud storage locations such as Google Drive, Box, Dropbox, etc., please refer to our <a href="https://nceas.github.io/scicomp.github.io/tutorials.html">Other Tutorials</a>.</p>
 <p align="center">
-<img src="images/lter-photos/penguins.jpg" width="100%">
+<img src="images/lter-photos/penguins.jpg" alt="Photo of two penguins swimming in icy water" width="80%">
 </p>
 </section>
 </section>

portfolio.html

@@ -233,7 +233,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#figures-for-publication" id="toc-figures-for-publication" class="nav-link" data-scroll-target="#figures-for-publication">Figures for Publication</a></li>
   <li><a href="#project-websites" id="toc-project-websites" class="nav-link" data-scroll-target="#project-websites">Project Websites</a></li>
   <li><a href="#r-packages" id="toc-r-packages" class="nav-link" data-scroll-target="#r-packages">R Packages</a></li>
-  <li><a href="#r-shiny-apps" id="toc-r-shiny-apps" class="nav-link" data-scroll-target="#r-shiny-apps">R Shiny Apps</a></li>
+  <li><a href="#shiny-apps" id="toc-shiny-apps" class="nav-link" data-scroll-target="#shiny-apps">Shiny Apps</a></li>
   </ul>
 <div class="toc-actions"><ul><li><a href="https://github.com/lter/scicomp/issues/new" class="toc-action"><i class="bi bi-github"></i>Report an issue</a></li></ul></div></nav>
     <div class="quarto-margin-footer"><div class="margin-footer-item">
@@ -294,13 +294,13 @@ <h2 class="anchored" data-anchor-id="project-websites">Project Websites</h2>
 <li>Maintain the website <strong>OR</strong> help <em>you</em> to maintain it
 <ul>
 <li>Quarto is written entirely in “Markdown syntax” which makes it easily maintained by either our team or yours depending on your preference</li>
-<li>We have also created a <a href="https://nceas.github.io/scicomp.github.io/tutorials.html#building-a-website-with-quarto">tutorial on making websites with Quarto</a> that you are welcome to explore!</li>
+<li>We have also created a <a href="https://lter.github.io/scicomp/tutorials.html#building-a-website-with-quarto">tutorial on making websites with Quarto</a> that you are welcome to explore!</li>
 </ul></li>
 </ul>
 </section>
 <section id="r-packages" class="level2">
 <h2 class="anchored" data-anchor-id="r-packages">R Packages</h2>
-<p><img src="images/scicomptools_hex.png" align="right" width="20%"></p>
+<p><img src="images/logos/hex_scicomptools.png" alt="Hex logo for the 'scicomptools' R package" align="right" width="20%"></p>
 <section id="scicomptools" class="level4">
 <h4 class="anchored" data-anchor-id="scicomptools"><code>scicomptools</code></h4>
 <p>While much of the work we do is specific to a given working group or task, sometimes we realize afterwards that our functions have the potential to be useful beyond the scope for which they were initially written. To that end, we have created the R package <a href="https://github.com/NCEAS/scicomptools#readme"><code>scicomptools</code></a>!</p>
@@ -314,7 +314,7 @@ <h5 class="anchored" data-anchor-id="installation-instructions">Installation Ins
 <div class="cell">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"scicomptools"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
-<p><img src="images/HERON_hex.png" align="right" width="17%"></p>
+<p><img src="images/logos/hex_heron.png" align="right" width="17%"></p>
 </section>
 </section>
 <section id="heron" class="level4">
@@ -334,9 +334,9 @@ <h5 class="anchored" data-anchor-id="installation-instructions-1">Installation I
 </section>
 </section>
 </section>
-<section id="r-shiny-apps" class="level2">
-<h2 class="anchored" data-anchor-id="r-shiny-apps">R Shiny Apps</h2>
-<p><img src="images/lterpalettefinder_hex.png" align="right" width="17%"></p>
+<section id="shiny-apps" class="level2">
+<h2 class="anchored" data-anchor-id="shiny-apps">Shiny Apps</h2>
+<p><img src="images/logos/hex_lterpalettefinder.png" alt="Hex logo for the 'lterpalettefinder' R package" align="right" width="17%"></p>
 <p>Our team created another R package–<code>lterpalettefinder</code>–to extract color palettes from user-supplied photos. To help non-R users still explore this package and have fun pulling color palettes from photos, we created <a href="https://cosima.nceas.ucsb.edu/lterpalettefinder-shiny/">this standalone Shiny app</a>. This app lets anyone interact with <code>lterpalettefinder</code> via their browser with no R experience required!</p>
 <p>We have also built apps to help working groups visualize data or present survey results in an interactive, visually-appealing format. Shiny apps can also include useful ‘overview’ portions that serve as an excellent landing page for third parties to your group’s activities!</p>
 

search.json

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-    "text": "R Shiny Apps\n\nOur team created another R package–lterpalettefinder–to extract color palettes from user-supplied photos. To help non-R users still explore this package and have fun pulling color palettes from photos, we created this standalone Shiny app. This app lets anyone interact with lterpalettefinder via their browser with no R experience required!\nWe have also built apps to help working groups visualize data or present survey results in an interactive, visually-appealing format. Shiny apps can also include useful ‘overview’ portions that serve as an excellent landing page for third parties to your group’s activities!"
+    "section": "Shiny Apps",
+    "text": "Shiny Apps\n\nOur team created another R package–lterpalettefinder–to extract color palettes from user-supplied photos. To help non-R users still explore this package and have fun pulling color palettes from photos, we created this standalone Shiny app. This app lets anyone interact with lterpalettefinder via their browser with no R experience required!\nWe have also built apps to help working groups visualize data or present survey results in an interactive, visually-appealing format. Shiny apps can also include useful ‘overview’ portions that serve as an excellent landing page for third parties to your group’s activities!"
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+    "text": "This page contains the collected best practice tips of our team. More will be added over time and feel free to post an issue if you have a specific request for a section to add to this document. Please feel free to reach out to our team if you have any questions about this best practices manual and/or need help implementing some of this content.\nCheck the headings below or in the table of contents on the right of this page to see which tips and tricks we have included so far and we hope this page is a useful resource to you and your team!"
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