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nmfs-opensci · Jan 10, 2024 · 02d4753 · 02d4753
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-0ef64de6
+0832a9d4
diff --git a/search.json b/search.json
@@ -1,4 +1,32 @@
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+  {
+    "objectID": "content/customizing.html",
+    "href": "content/customizing.html",
+    "title": "Customization",
+    "section": "",
+    "text": "Quarto allow many bells and whistles to make nice output. Read the documentation here Quarto documentation."
+  },
+  {
+    "objectID": "content/customizing.html#quarto-documentation",
+    "href": "content/customizing.html#quarto-documentation",
+    "title": "Customization",
+    "section": "",
+    "text": "Quarto allow many bells and whistles to make nice output. Read the documentation here Quarto documentation."
+  },
+  {
+    "objectID": "content/customizing.html#examples",
+    "href": "content/customizing.html#examples",
+    "title": "Customization",
+    "section": "Examples",
+    "text": "Examples\nLooking at other people’s Quarto code is a great way to figure out how to do stuff. Most will have a link to a GitHub repo where you can see the raw code. Look for a link to edit page or see source code. This will usually be on the right. Or look for the GitHub icon somewhere.\n\nQuarto gallery\nnmfs-openscapes\nFaye lab manual\nquarto-titlepages Note the link to edit is broken. Go to repo and look in documentation directory."
+  },
+  {
+    "objectID": "content/acknowledgements.html",
+    "href": "content/acknowledgements.html",
+    "title": "Acknowledgments",
+    "section": "",
+    "text": "This repo and GitHub Action was based on the tutorial by Openscapes quarto-website-tutorial by Julia Lowndes and Stefanie Butland."
+  },
   {
     "objectID": "content/publishing.html",
     "href": "content/publishing.html",
@@ -27,48 +55,6 @@
     "section": "Don’t like using gh-pages?",
     "text": "Don’t like using gh-pages?\nIn some cases, you don’t want your website on the gh-pages branch. For example, if you are creating releases and you want the website pages archived in that release, then you won’t want your website pages on the gh-pages branch.\nHere are the changes you need to make if you to avoid gh-pages branch.\n\nAt the top of _quarto.yml add the following:\n\nproject: \n  type: website\n  output-dir: docs\n\nOn GitHub under Settings &gt; Pages set pages to be made from the main branch and the docs directory.\nMake sure docs is not listed in .gitignore\nPublish the site the first time locally using quarto publish from the terminal\nChange the GitHub Action because you can’t use quarto publish gh-pages. You’ll need to push to the main branch yourself (in the GitHub Action)\n\non:\n  push:\n    branches: main\n\nname: Render and Publish\n\njobs:\n  build-deploy:\n    runs-on: ubuntu-latest\n    env:\n      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}\n\n    steps:\n      - name: Check out repository\n        uses: actions/checkout@v2 \n        \n      - name: Set up R (needed for Rmd)\n        uses: r-lib/actions/setup-r@v2\n\n      - name: Install packages (needed for Rmd)\n        run: Rscript -e 'install.packages(c(\"rmarkdown\", \"knitr\", \"jsonlite\"))'\n\n      - name: Set up Quarto\n        uses: quarto-dev/quarto-actions/setup@v2\n        with:\n          # To install LaTeX to build PDF book \n          # tinytex: true \n          # uncomment below and fill to pin a version\n          # version: 0.9.600\n      \n      - name: Render Quarto Project\n        uses: quarto-dev/quarto-actions/render@v2\n        with:\n          to: html\n\n      - name: Set up Git\n        run: |\n          git config --local user.email \"[email protected]\"\n          git config --local user.name \"GitHub Actions\"\n\n      - name: Commit all changes and push\n        run: |\n          git add -A && git commit -m 'Build site' || echo \"No changes to commit\"\n          git push origin || echo \"No changes to commit\""
   },
-  {
-    "objectID": "content/rmarkdown.html",
-    "href": "content/rmarkdown.html",
-    "title": "R Markdown",
-    "section": "",
-    "text": "You can include R Markdown files in your project."
-  },
-  {
-    "objectID": "content/rmarkdown.html#r-markdown",
-    "href": "content/rmarkdown.html#r-markdown",
-    "title": "R Markdown",
-    "section": "R Markdown",
-    "text": "R Markdown\nThis is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.\nWhen you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:\n\nsummary(cars)\n\n     speed           dist       \n Min.   : 4.0   Min.   :  2.00  \n 1st Qu.:12.0   1st Qu.: 26.00  \n Median :15.0   Median : 36.00  \n Mean   :15.4   Mean   : 42.98  \n 3rd Qu.:19.0   3rd Qu.: 56.00  \n Max.   :25.0   Max.   :120.00"
-  },
-  {
-    "objectID": "content/rmarkdown.html#including-plots",
-    "href": "content/rmarkdown.html#including-plots",
-    "title": "R Markdown",
-    "section": "Including Plots",
-    "text": "Including Plots\nYou can also embed plots, for example:\n\n\n\n\n\nNote that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot."
-  },
-  {
-    "objectID": "content/customizing.html",
-    "href": "content/customizing.html",
-    "title": "Customization",
-    "section": "",
-    "text": "Quarto allow many bells and whistles to make nice output. Read the documentation here Quarto documentation."
-  },
-  {
-    "objectID": "content/customizing.html#quarto-documentation",
-    "href": "content/customizing.html#quarto-documentation",
-    "title": "Customization",
-    "section": "",
-    "text": "Quarto allow many bells and whistles to make nice output. Read the documentation here Quarto documentation."
-  },
-  {
-    "objectID": "content/customizing.html#examples",
-    "href": "content/customizing.html#examples",
-    "title": "Customization",
-    "section": "Examples",
-    "text": "Examples\nLooking at other people’s Quarto code is a great way to figure out how to do stuff. Most will have a link to a GitHub repo where you can see the raw code. Look for a link to edit page or see source code. This will usually be on the right. Or look for the GitHub icon somewhere.\n\nQuarto gallery\nnmfs-openscapes\nFaye lab manual\nquarto-titlepages Note the link to edit is broken. Go to repo and look in documentation directory."
-  },
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     "objectID": "content/code.html",
     "href": "content/code.html",
@@ -104,27 +90,6 @@
     "section": "GitHub Set-up",
     "text": "GitHub Set-up\n\nClick the green “use template” button to make a repository with this content. Make sure to make your repo public (since GitHub Pages doesn’t work on private repos unless you have a paid account) and check box to include all the branches (so that you get the gh-pages branch). \nTurn on GitHub Pages under Settings &gt; Pages . You will set pages to be made from the gh-pages branch and root directory. \nTurn on GitHub Actions under Settings &gt; Actions &gt; General \nEdit the repo description and Readme to add a link to the webpage. When you edit the description, you will see the link url in the url box or you can click on the Actions tab or the Settings &gt; Pages page to find the url."
   },
-  {
-    "objectID": "content/add-content.html",
-    "href": "content/add-content.html",
-    "title": "Customize",
-    "section": "",
-    "text": "Edit the qmd or md files in the content folder. qmd files can include code (R, Python, Julia) and lots of Quarto markdown bells and whistles (like call-outs, cross-references, auto-citations and much more).\nEach page should start with\n---\ntitle: your title\n---\nand the first header will be the 2nd level, so ##. Note, there are situations where you leave off\n---\ntitle: your title\n---\nand start the qmd file with a level header #, but if using the default title yaml (in the --- fence) is a good habit since it makes it easy for Quarto convert your qmd file to other formats (like into a presentation)."
-  },
-  {
-    "objectID": "content/add-content.html#edit-and-add-your-pages",
-    "href": "content/add-content.html#edit-and-add-your-pages",
-    "title": "Customize",
-    "section": "",
-    "text": "Edit the qmd or md files in the content folder. qmd files can include code (R, Python, Julia) and lots of Quarto markdown bells and whistles (like call-outs, cross-references, auto-citations and much more).\nEach page should start with\n---\ntitle: your title\n---\nand the first header will be the 2nd level, so ##. Note, there are situations where you leave off\n---\ntitle: your title\n---\nand start the qmd file with a level header #, but if using the default title yaml (in the --- fence) is a good habit since it makes it easy for Quarto convert your qmd file to other formats (like into a presentation)."
-  },
-  {
-    "objectID": "content/add-content.html#add-your-pages-the-project",
-    "href": "content/add-content.html#add-your-pages-the-project",
-    "title": "Customize",
-    "section": "Add your pages the project",
-    "text": "Add your pages the project\n\nAdd the files to _quarto.yml"
-  },
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     "objectID": "content/rendering.html",
     "href": "content/rendering.html",
@@ -154,10 +119,45 @@
     "text": "Step 3. Render within RStudio\nRStudio will recognize that this is a Quarto project by the presence of the _quarto.yml file and will see the “Build” tab. Click the “Render website” button to render to the _site folder.\nPreviewing: You can either click index.html in the _site folder and specify “preview in browser” or set up RStudio to preview to the viewer panel. To do the latter, go to Tools &gt; Global Options &gt; R Markdown. Then select “Show output preview in: Viewer panel”."
   },
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-    "objectID": "content/acknowledgements.html",
-    "href": "content/acknowledgements.html",
-    "title": "Acknowledgments",
+    "objectID": "content/add-content.html",
+    "href": "content/add-content.html",
+    "title": "Customize",
     "section": "",
-    "text": "This repo and GitHub Action was based on the tutorial by Openscapes quarto-website-tutorial by Julia Lowndes and Stefanie Butland."
+    "text": "Edit the qmd or md files in the content folder. qmd files can include code (R, Python, Julia) and lots of Quarto markdown bells and whistles (like call-outs, cross-references, auto-citations and much more).\nEach page should start with\n---\ntitle: your title\n---\nand the first header will be the 2nd level, so ##. Note, there are situations where you leave off\n---\ntitle: your title\n---\nand start the qmd file with a level header #, but if using the default title yaml (in the --- fence) is a good habit since it makes it easy for Quarto convert your qmd file to other formats (like into a presentation)."
+  },
+  {
+    "objectID": "content/add-content.html#edit-and-add-your-pages",
+    "href": "content/add-content.html#edit-and-add-your-pages",
+    "title": "Customize",
+    "section": "",
+    "text": "Edit the qmd or md files in the content folder. qmd files can include code (R, Python, Julia) and lots of Quarto markdown bells and whistles (like call-outs, cross-references, auto-citations and much more).\nEach page should start with\n---\ntitle: your title\n---\nand the first header will be the 2nd level, so ##. Note, there are situations where you leave off\n---\ntitle: your title\n---\nand start the qmd file with a level header #, but if using the default title yaml (in the --- fence) is a good habit since it makes it easy for Quarto convert your qmd file to other formats (like into a presentation)."
+  },
+  {
+    "objectID": "content/add-content.html#add-your-pages-the-project",
+    "href": "content/add-content.html#add-your-pages-the-project",
+    "title": "Customize",
+    "section": "Add your pages the project",
+    "text": "Add your pages the project\n\nAdd the files to _quarto.yml"
+  },
+  {
+    "objectID": "content/rmarkdown.html",
+    "href": "content/rmarkdown.html",
+    "title": "R Markdown",
+    "section": "",
+    "text": "You can include R Markdown files in your project."
+  },
+  {
+    "objectID": "content/rmarkdown.html#r-markdown",
+    "href": "content/rmarkdown.html#r-markdown",
+    "title": "R Markdown",
+    "section": "R Markdown",
+    "text": "R Markdown\nThis is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.\nWhen you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:\n\nsummary(cars)\n\n     speed           dist       \n Min.   : 4.0   Min.   :  2.00  \n 1st Qu.:12.0   1st Qu.: 26.00  \n Median :15.0   Median : 36.00  \n Mean   :15.4   Mean   : 42.98  \n 3rd Qu.:19.0   3rd Qu.: 56.00  \n Max.   :25.0   Max.   :120.00"
+  },
+  {
+    "objectID": "content/rmarkdown.html#including-plots",
+    "href": "content/rmarkdown.html#including-plots",
+    "title": "R Markdown",
+    "section": "Including Plots",
+    "text": "Including Plots\nYou can also embed plots, for example:\n\n\n\n\n\nNote that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot."
   }
 ]
diff --git a/sitemap.xml b/sitemap.xml
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