Merge branch 'main' into teaser

nmfs-opensci · Nov 1, 2024 · 5643855 · 5643855
2 parents 47448a8 + 47824a3
commit 5643855
Show file tree

Hide file tree

Showing 6 changed files with 40 additions and 66 deletions.
diff --git a/content/02-jupyterhub-setup-r.qmd b/content/02-jupyterhub-setup-r.qmd
@@ -4,16 +4,17 @@ title: R/RStudio on JupyterHub
 
 Everything you need is installed for you. Note, before you can log in, we will need to add you to the access group.
 
-* <https://nmfs-openscapes.2i2c.cloud>
-* Click Start Server and accept defaults
-* Click the RStudio button. If you don't see it, click the blue button in the top left to open a new 'Launcher' window.
+-   <https://nmfs-openscapes.2i2c.cloud>
+-   Click Start Server and accept defaults
+-   Click the RStudio button. If you don't see it, click the blue button in the top left to open a new 'Launcher' window.
 
 ![](https://nmfs-opensci.github.io/Quarto-Workshop-2024/content/img/jhub-launcher.png)
 
 ## Access to the JupyterHub
 
 ### GitHub username
 
+
 * Log into GitHub.com. Authentication to the JupyterHub uses your username and being a member of the  NMFS Openscapes GitHub org.
 
 ### Get on JupyterHub
@@ -22,9 +23,11 @@ Once you have submitted your GitHub username and have been accepted as a member
 
 <https://nmfs-openscapes.2i2c.cloud>
 
-* **Choose the default Py-R base geospatial image**. [Watch a video](https://youtu.be/o99jZWHqKi8) of the login process and basic JupyterHub orientation.
+-   **Choose the default Py-R base geospatial image**. [Watch a video](https://youtu.be/o99jZWHqKi8) of the login process and basic JupyterHub orientation.
+
 
 * home directory is yours and no one else can see it.
 * To share files, you can connect to a GitHub repository or use the `shared` directory. Everyone can read and write to this directory. Please don't delete content that is not your own.
 
 This is a platform for training. Please do not put confidential info on here.
+
diff --git a/tutorials/tutorial-1.qmd b/tutorials/tutorial-1.qmd
@@ -1,22 +1,27 @@
 ---
-title: Intro to Quarto
+title: Introduction to RStudio and Quarto
 ---
 
 ::: {.callout-note title="Learning Objectives"}
-
-1. objective 1
-2. objective 2
-3. objective 3
+1.  Understand what Quarto is and why we use it
+2.  Get familiar with RStudio
+3.  Create a Quarto file and understand its structure
+4.  Understand how Quarto projects differ from Quarto files
 :::
 
-## Summary
-
+## Logging onto JupyterHub
 
-## Terminology
+For this workshop, we'll be using the [NOAA NMFS JupyterHub](https://dhub.opensci.live/). You're welcome to use your own version of RStudio on your desktop, just make sure R and RStudio are updated to the latest versions. Follow the instructions to set up your JupyterHub access here: [Intro to JupyterHubs](https://nmfs-opensci.github.io/Quarto-Workshop-2024/content/01-intro-to-jupyterhub.html)
 
+## Using the Carpentries Tutorials
 
-## Prerequisites
+Instead of re-inventing the wheel, we will be leveraging open science principles by using the Carpentries Incubator [**Introduction to Reproducible Publications with RStudio**](https://carpentries-incubator.github.io/reproducible-publications-quarto/index.html)tutorial. The tutorial consists of a series of "episodes" that we will be walking through with you. Several of the episodes go a bit further in-depth than we will cover in the workshop, but feel free to explore further on your own time.
 
+For today's session, we will be going through the following episodes:
 
-## Load Required Packages
+1.  [Scientific reproducibility: What is it for?](https://carpentries-incubator.github.io/reproducible-publications-quarto/01-repro-project-org/01-introduction/index.html)
+2.  [Navigating RStudio and Quarto Documents](https://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/01-basic-rstudio/index.html)
+3.  [Working with projects in RStudio](https://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/02-projects-rstudio/index.html)
+4.  [Quarto Files vs Quarto Projects (Section in Working with projects in RStudio)](https://carpentries-incubator.github.io/reproducible-publications-quarto/01-repro-project-org/02-reproducibility/index.html#quarto-projects)
 
+Follow along on your own computer as we walk through the tutorials.
diff --git a/tutorials/tutorial-2.qmd b/tutorials/tutorial-2.qmd
@@ -1,22 +1,9 @@
 ---
-title: Intro to Quarto
+title: Working with Quarto files and the Markdown language
 ---
 
 ::: {.callout-note title="Learning Objectives"}
+1.  Coming Soon!
 
-1. objective 1
-2. objective 2
-3. objective 3
-:::
-
-## Summary
-
-
-## Terminology
-
-
-## Prerequisites
-
-
-## Load Required Packages
-
+## 
+:::
diff --git a/tutorials/tutorial-3.qmd b/tutorials/tutorial-3.qmd
@@ -1,22 +1,9 @@
 ---
-title: Intro to Quarto
+title: Dynamic output in Quarto files: Code, Tables, and Figures
 ---
 
 ::: {.callout-note title="Learning Objectives"}
+1.  Coming Soon!
 
-1. objective 1
-2. objective 2
-3. objective 3
-:::
-
-## Summary
-
-
-## Terminology
-
-
-## Prerequisites
-
-
-## Load Required Packages
-
+## 
+:::
diff --git a/tutorials/tutorial-4.qmd b/tutorials/tutorial-4.qmd
@@ -1,22 +1,7 @@
 ---
-title: Intro to Quarto
+title: Cross-references, bibliography and citations in Quarto files
 ---
 
 ::: {.callout-note title="Learning Objectives"}
-
-1. objective 1
-2. objective 2
-3. objective 3
-:::
-
-## Summary
-
-
-## Terminology
-
-
-## Prerequisites
-
-
-## Load Required Packages
-
+1.  Coming Soon!
+:::
diff --git a/tutorials/tutorial-5.qmd b/tutorials/tutorial-5.qmd
@@ -0,0 +1,7 @@
+---
+title: Introduction to Quarto Projects
+---
+
+::: {.callout-note title="Learning Objectives"}
+1.  Coming Soon!
+:::