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Quarto GHA Workflow Runner committed Nov 15, 2024
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Expand Down Expand Up @@ -313,86 +313,74 @@ <h1 class="title">Schedule</h1>
<th>Description</th>
<th>Topic</th>
<th>Material</th>
<th>Video</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>Tues 10/29</td>
<td>NMFS R User Group Monthly meeting</td>
<td>Quarto Reports: 5 presenters from across NMFS</td>
<td><a href="https://docs.google.com/presentation/d/1fGmkaCT9NS-iRQq8kvBK6ahoO6wxNTGvbvh8vvgA1Ms/edit#slide=id.g2fefe32098c_0_337">Slides</a> (NOAA only)</td>
<td><a href="https://drive.google.com/file/d/1VwpwKIsiJf8OVtyctByw-qyW3MaJtRc_/view?usp=sharing">Video</a> (NOAA only)</td>
<td>Quarto Reports @ NMFS</td>
<td>5 presenters from across NMFS</td>
</tr>
<tr class="even">
<td>Week of 10/28 to 11/1</td>
<td>Meeting with teams (45 min). Info and Sign-up</td>
<td>Discuss goals and plan.</td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td>Mon &amp; Fri 11/4 &amp; 11/8</td>
<td>Quarto Workshop 1</td>
<td>Getting Started with RStudio and Quarto. Quarto files versus Quarto projects.</td>
<td><a href="https://nmfs-opensci.github.io/Quarto-Workshop-2024/tutorials/tutorial-1.html">Link</a></td>
<td>NA</td>
</tr>
<tr class="even">
<td>Tues &amp; Fri 11/12 &amp; 11/15</td>
<td>Quarto Workshop 2</td>
<td>Working with Quarto files and the Markdown language.</td>
<td><a href="https://nmfs-opensci.github.io/Quarto-Workshop-2024/tutorials/tutorial-2.html">Link</a></td>
<td><a href="https://drive.google.com/file/d/1SSpfljlumfIbEfi2WHgrd8PbavjVoTf0/view?usp=drive_link">Video</a> (NOAA only)</td>
</tr>
<tr class="odd">
<td>Week of 11/11 to 11/15</td>
<td>Seaside chats with teams (60 min)</td>
<td>Review report analysis. Brainstorm first steps.</td>
<td></td>
<td></td>
</tr>
<tr class="even">
<td>Mon &amp; Fri 11/18 &amp; 11/22</td>
<td>Quarto Workshop 3</td>
<td>Dynamic output in Quarto files: code, tables, and figures.</td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td>Mon &amp; Fri 12/2 &amp; 12/6</td>
<td>Quarto Workshop 4</td>
<td>Cross-references, bibliography and citations in Quarto files.</td>
<td></td>
<td></td>
</tr>
<tr class="even">
<td>Week of 12/2 to 12/6</td>
<td>Seaside chats with teams (60-90 min)</td>
<td>Review progress and identify next steps.</td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td>Mon &amp; Wed 12/9 &amp; 12/11</td>
<td>Quarto Workshop 5</td>
<td>Intro to Quarto projects.</td>
<td></td>
<td></td>
</tr>
<tr class="even">
<td>Mon 12/16</td>
<td>Hack Day (3 hours)</td>
<td>Put your skills to work: create a Quarto Book and put online in 3 hours</td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td>Week of 12/16 to 12/19</td>
<td>Seaside chats with teams (60-90 min)</td>
<td>Review progress, get help and identify next steps.</td>
<td></td>
<td></td>
</tr>
</tbody>
</table>
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"section": "",
"text": "Learning Objectives\n\n\n\n\nComing Soon!"
},
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"section": "Today’s Carpentries Tutorials",
"text": "Today’s Carpentries Tutorials\nDuring these workshops, we will be using the Carpentries Incubator Reproducible Publications with RStudio set of tutorials from UCSB (https://carpentries-incubator.github.io/reproducible-publications-quarto/) for most of our content. While we will be walking everyone through the tutorials, it may be helpful for you to look through the tutorials prior to attending. This will give you a feel for what we will be covering during each session, and will highlight some areas where you may need some additional work or assistance.\nFor this session, we will be covering the following topics:\n\nhttps://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/05-code-qmd/index.html\nhttps://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/06-rendering-code-yaml/index.html\n\nFor this week’s tutorials, we will be relying on the forked repository from the previous week. If you have not yet set up your forked repository in RStudio, follow the instructions here: https://nmfs-opensci.github.io/Quarto-Workshop-2024/tutorials/tutorial-2.html#instructions-for-forking-the-carpentries-example-repository"
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"section": "More practice with Code Chunks",
"text": "More practice with Code Chunks\nThe Carpentries tutorials provide a good introduction to code chunks, but you may want some more practice. The Quarto workshop from posit::conf(2024) slide deck includes some extra examples for integrating dynamic code into Quarto documents: https://posit-conf-2024.github.io/quarto-intro/materials/1-single-docs/1-welcome-to-quarto/slides.html#/code-cells\nWe will walk through some of the features discussed in this slide deck, but feel free to click through on your own for some additional practice.\nCode chunk options let you control the output of a code chunk in a YAML-like header at the beginning of the chunk. We will go over a few of these options in this week’s sessions, but there are many more options available than what we will cover. Use this reference guide for the options available in an R code chunk."
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"text": "All times Pacific.\n\n\n\nDate\nDescription\nTopic\nMaterial\nVideo\n\n\n\n\nTues 10/29\nNMFS R User Group Monthly meeting\nQuarto Reports: 5 presenters from across NMFS\nSlides (NOAA only)\nVideo (NOAA only)\n\n\nWeek of 10/28 to 11/1\nMeeting with teams (45 min). Info and Sign-up\nDiscuss goals and plan.\n\n\n\n\nMon & Fri 11/4 & 11/8\nQuarto Workshop 1\nGetting Started with RStudio and Quarto. Quarto files versus Quarto projects.\nLink\nNA\n\n\nTues & Fri 11/12 & 11/15\nQuarto Workshop 2\nWorking with Quarto files and the Markdown language.\nLink\nVideo (NOAA only)\n\n\nWeek of 11/11 to 11/15\nSeaside chats with teams (60 min)\nReview report analysis. Brainstorm first steps.\n\n\n\n\nMon & Fri 11/18 & 11/22\nQuarto Workshop 3\nDynamic output in Quarto files: code, tables, and figures.\n\n\n\n\nMon & Fri 12/2 & 12/6\nQuarto Workshop 4\nCross-references, bibliography and citations in Quarto files.\n\n\n\n\nWeek of 12/2 to 12/6\nSeaside chats with teams (60-90 min)\nReview progress and identify next steps.\n\n\n\n\nMon & Wed 12/9 & 12/11\nQuarto Workshop 5\nIntro to Quarto projects.\n\n\n\n\nMon 12/16\nHack Day (3 hours)\nPut your skills to work: create a Quarto Book and put online in 3 hours\n\n\n\n\nWeek of 12/16 to 12/19\nSeaside chats with teams (60-90 min)\nReview progress, get help and identify next steps.",
"text": "All times Pacific.\n\n\n\nDate\nDescription\nTopic\nMaterial\n\n\n\n\nTues 10/29\nNMFS R User Group Monthly meeting\nQuarto Reports @ NMFS\n5 presenters from across NMFS\n\n\nWeek of 10/28 to 11/1\nMeeting with teams (45 min). Info and Sign-up\nDiscuss goals and plan.\n\n\n\nMon & Fri 11/4 & 11/8\nQuarto Workshop 1\nGetting Started with RStudio and Quarto. Quarto files versus Quarto projects.\nLink\n\n\nTues & Fri 11/12 & 11/15\nQuarto Workshop 2\nWorking with Quarto files and the Markdown language.\nLink\n\n\nWeek of 11/11 to 11/15\nSeaside chats with teams (60 min)\nReview report analysis. Brainstorm first steps.\n\n\n\nMon & Fri 11/18 & 11/22\nQuarto Workshop 3\nDynamic output in Quarto files: code, tables, and figures.\n\n\n\nMon & Fri 12/2 & 12/6\nQuarto Workshop 4\nCross-references, bibliography and citations in Quarto files.\n\n\n\nWeek of 12/2 to 12/6\nSeaside chats with teams (60-90 min)\nReview progress and identify next steps.\n\n\n\nMon & Wed 12/9 & 12/11\nQuarto Workshop 5\nIntro to Quarto projects.\n\n\n\nMon 12/16\nHack Day (3 hours)\nPut your skills to work: create a Quarto Book and put online in 3 hours\n\n\n\nWeek of 12/16 to 12/19\nSeaside chats with teams (60-90 min)\nReview progress, get help and identify next steps.",
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"href": "tutorials/tutorial-2.html#instructions-for-forking-the-carpentries-example-repository",
"title": "Working with Quarto Files and the Markdown Language",
"section": "Instructions for Forking the Carpentries Example Repository",
"text": "Instructions for Forking the Carpentries Example Repository\nThe Carpentries tutorials we are using will require you to “fork” the GitHub repository that contains the course material for future sessions. This will put a copy of the repository in your GitHub that will allow you to make commits without changing the original repository. To make things go smoothly in future sessions, make sure you set up your forked repository in RStudio. Instructions below and here a video showing Eli forking the repository.\n\nTo fork the repository, go to the following link: https://github.com/UCSBCarpentry/Quarto-Project-Example/fork\nThis should take you to a screen that looks something like the attached screenshot. Keep everything the way it is and click the “Create Fork” button in the bottom right-hand corner of the page. Once https://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/03-quarto-documents/index.htmlthe repository finishes setting up, it will open with the forked copy on your GitHub.\n\nAfter forking the repository, click the green Code button in the center-right of the repository window. This will bring down a dropdown menu with the link to the forked repository. Copy the link using the icon with the two squares on the right.\n\nIn RStudio (either in JupyterHub or desktop), go to the File menu and click New Project. In the dialogue box that pops up, click Version Control, then Git. Paste your copied repository URL from GitHub into the URL box (the Project directory name will auto-populate). RStudio will create a folder as a subdirectory that includes all of the files from the forked repository. If you are working on your own desktop version of RStudio, you may want to change the project directory; otherwise, leave this as a default. Click Create Project, and RStudio will download the repository and create the project for you.",
"text": "Instructions for Forking the Carpentries Example Repository\nThe Carpentries tutorials we are using will require you to “fork” the GitHub repository that contains the course material for future sessions. This will put a copy of the repository in your GitHub that will allow you to make commits without changing the original repository. To make things go smoothly in future sessions, make sure you set up your forked repository in RStudio. Instructions below and here a video showing Eli forking the repository.\n\nTo fork the repository, go to the following link: https://github.com/UCSBCarpentry/Quarto-Project-Example/fork\nThis should take you to a screen that looks something like the attached screenshot. Keep everything the way it is and click the “Create Fork” button in the bottom right-hand corner of the page. Once the repository finishes setting up, it will open with the forked copy on your GitHub.\n\nAfter forking the repository, click the green Code button in the center-right of the repository window. This will bring down a dropdown menu with the link to the forked repository. Copy the link using the icon with the two squares on the right.\n\nIn RStudio (either in JupyterHub or desktop), go to the File menu and click New Project. In the dialogue box that pops up, click Version Control, then Git. Paste your copied repository URL from GitHub into the URL box (the Project directory name will auto-populate). RStudio will create a folder as a subdirectory that includes all of the files from the forked repository. If you are working on your own desktop version of RStudio, you may want to change the project directory; otherwise, leave this as a default. Click Create Project, and RStudio will download the repository and create the project for you.",
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