Setting up book structure according to course schedule

NCEAS · Apr 30, 2024 · 361c7f0 · 361c7f0
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diff --git a/materials/_quarto.yml b/materials/_quarto.yml
@@ -3,8 +3,8 @@ project:
   output-dir: _book
 
 book: 
-  title: "UCSB Faculty Seminar Series: Grow Your Data & Team Science Skills"
-  # date: "January 22-26, 2024"
+  title: "NCEAS coreR for Delta Science Program"
+  subtitle: "June 10 - 13, 2024"
   reader-mode: false
 
   # NoteHD: cover image is not working
@@ -23,26 +23,26 @@ book:
       - icon: twitter
         href: https://twitter.com/ucsb_nceas
       - icon: github
-        href: https://github.com/NCEAS/nceas-training/tree/2024-03-ucsb-faculty
+        href: https://github.com/NCEAS/nceas-training/tree/2024-06-delta
 
   chapters:
     - index.qmd # preface 
-    - session_01.qmd # Intro and Lego
-    - session_02.qmd # Data Visualization
-    - session_03.qmd # Text Analysis (Casey)
-    - session_04.qmd # Survey data
-    - session_05.qmd # Visualizing spatial data (Rachel)
-    - session_06.qmd # GitHub for project management 
-    - session_07.qmd # Publishing to Web
-    - session_08.qmd # GitHub Workflows
-    - session_09.qmd # Message Box
-    - session_10.qmd # Quarto Dashboards
-    - session_11.qmd # Practice Session
-    - session_12.qmd # reproducibility and provenance
-    - session_13.qmd # check PAT
-    # - session_14.qmd # Social Aspects of collab
-    # - session_15.qmd # Functions
-    # - session_16.qmd # Packages
+    - session_01.qmd # Introduction
+    - session_02.qmd # R Setup
+    - session_03.qmd # Git and GitHub set up
+    - session_04.qmd # Literate Analysis
+    - session_05.qmd # Intro to Git and GitHub
+    - session_06.qmd # Data Management
+    - session_07.qmd # Collaborating with Git
+    - session_08.qmd # Data Modeling Essentials
+    - session_09.qmd # Cleaning and Wrangling
+    - session_10.qmd # Practice Session
+    - session_11.qmd # Publishing to the Web
+    - session_12.qmd # Intro to Data Viz
+    - session_13.qmd # Spatial Data
+    - session_14.qmd # Shiny
+    - session_15.qmd # Reproducibility and Provenence
+    # - session_16.qmd # Appendix: Set up in personla comp
     # - session_17.qmd # Practice Session II
     # - session_18.qmd # Data Portals
     # - session_19.qmd # Spatial Data

diff --git a/materials/index.qmd b/materials/index.qmd
@@ -4,32 +4,32 @@
 
 ![](cover.png){width="80%" fig-align="center"}
 
-![](images/logo-ucsb-office-research.png){width="80%" fig-align="center"}
+![](images/delta/delta-logo.png){width="80%" fig-align="center"}
 
 :::
 
 ## About the course {.unnumbered}
 
-Hosted by the [National Center for Ecological Anlysis and Synthesis (NCEAS)](https://www.nceas.ucsb.edu/) and in partnership with [UCSB's Office of Research](https://www.research.ucsb.edu/), this seminar series is a training program where participants engage in synthesis research in a small cohort. It will equip participants with data science and team science tools, and provide them with a platform to conduct collaborative synthesis research. The overall aim is to grow cross-departmental relationships and interdisciplinary research outputs.
+[ADD]
 
 ## NCEAS Expertise
 
-NCEAS, a research affiliate of UCSB, is a leading expert on interdisciplinary data science and works collaboratively to answer the world's largest and most complex questions. The NCEAS approach leverages existing data and employs a team science philosophy to squeeze out all potential insights and solutions efficiently - this is called [synthesis science](https://www.nceas.ucsb.edu/our-approach). NCEAS has over 25 years of success with this model among working groups and environmental professionals.
+The [National Center for Ecological Analysis and Synthesis (NCEAS)](https://www.nceas.ucsb.edu/), a research affiliate of UCSB, is a leading expert on interdisciplinary data science and works collaboratively to answer the world's largest and most complex questions. The NCEAS approach leverages existing data and employs a team science philosophy to squeeze out all potential insights and solutions efficiently - this is called [synthesis science](https://www.nceas.ucsb.edu/our-approach).
 
-## Week Three: Communicating your Science and Reproducible Workflows
+NCEAS has over 25 years of success with this model among working groups and environmental professionals. Together with the Delta Science Program and the Delta Stewardship Council we are excited to pass along skills, workflows, mindsets learn throughout the years.
 
-*March 25 - 27, 2024*
+
+<!-- *June 10 - 13, 2024* -->
 
 ### Learning Objectives
 
--   Explore visualization tools such as `ggplot2`, Quarto Dashboards and different packages to plot spatial data.
--   Broaden the tool kit of data science analytical tools by exploring text analysis methods and reproducible workflows to access survey data.
--   Recap and wrap up the concept of reproducibility and how to apply it into the everyday workflow.
+[ADD]
 
 ### Week's Schedule
+[UPDATE]
 
 :::{.column-body-outset}
-![](images/schedule.png)
+<!-- ![](images/schedule.png) -->
 :::
 
 
@@ -43,7 +43,7 @@ These written materials are the result of a continuous and collaborative effort
 
 This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
 
-**Citation:** Camila Vargas Poulsen, Rachel King, Casey O'Hara (2024), UCSB Faculty Seminar Series: Grow Your Data & Team Science Skills, March 25-27, NCEAS Learning Hub. URL <https://learning.nceas.ucsb.edu/2024-03-ucsb-faculty>.
+**Citation:** Camila Vargas Poulsen & Angel Chen (2024), NCEAS coreR for Delta Science Program, June 2024, NCEAS Learning Hub. URL <https://learning.nceas.ucsb.edu/2024-06-delta>.
 
 **Additional contributors:** Ben Bolker, Amber E. Budden, Julien Brun, Samantha Csik, Halina Do-Linh, Natasha Haycock-Chavez, S. Jeanette Clark, Julie Lowndes, Stephanie Hampton, Matt Jone, Samanta Katz, Erin McLean, Bryce Mecum, Deanna Pennington, Karthik Ram, Jim Regetz, Tracy Teal, Daphne Virlar-Knight, Leah Wasser.
 

diff --git a/materials/sections/git-setup.qmd b/materials/sections/git-setup.qmd
@@ -1,11 +1,9 @@
-## Git and GitHub Setup
-
 ## Learning Objectives {.unnumbered}
 
 -   Set global options in your `.gitconfig` file
 -   Practice how to set up GitHub Authentication using a Personal Access Token (PAT)
 
-### Set up global options in Git
+## Set up global options in Git
 
 Before using Git, you need to tell it who you are, also known as setting the **global options**. To do this, we will be setting the global options in the Terminal. 
 
@@ -69,7 +67,7 @@ Finally, check to make sure everything looks correct by entering this command, w
 git config --global --list
 ```
 
-### GitHub Authentication
+## GitHub Authentication
 
 GitHub recently deprecated password authentication for accessing repositories, so we need to set up a secure way to authenticate. 
 

diff --git a/materials/sections/rstudio-server-setup.qmd b/materials/sections/rstudio-server-setup.qmd
@@ -1,12 +1,11 @@
-## RStudio Setup
 
 ## Learning Objectives {.unnumbered}
 
 - Practice creating an R Project
 - Organize an R Project for effective project management
 - Understand how to move in an R Project using paths and working directories
 
-### Logon to the RStudio Server
+## Logon to the RStudio Server
 
 To prevent us from spending most of this lesson troubleshooting the myriad of issues that can arise when setting up the R, RStudio, and git environments, we have chosen to have everyone work on a remote server with all of the software you need installed. We will be using a special kind of RStudio just for servers called RStudio Server. If you have never worked on a remote server before, you can think of it like working on a different computer via the internet. Note that the server has no knowledge of the files on your local filesystem, but it is easy to transfer files from the server to your local computer, and vice-versa, using the RStudio server interface.
 
@@ -19,7 +18,7 @@ After you have successfully changed your password log in at: [https://included-c
 [![](images/included-crab-login.png)](https://included-crab.nceas.ucsb.edu/)
 :::
 
-### Create an R Project
+## Create an R Project
 
 In this course, we are going to be using an R project to organize our work. An R project is tied to a directory on your local computer, and makes organizing your work and collaborating with others easier.
 
@@ -38,23 +37,23 @@ In this course, we are going to be using an R project to organize our work. An R
 RStudio should open your new project automatically after creating it. One way to check this is by looking at the top right corner and checking for the project name.
 :::
 
-::: {.callout-tip icon=false}
-## Sharing your project
-To share your project with the instructor team, locate the “project switcher” dropdown menu in the upper right of your RStudio window. This dropdown has the name of your project (eg: training_vargas), and a dropdown arrow. Click the dropdown menu, then “Share Project.” When the dialog box pops up, add the following usernames to your project:
+<!-- ::: {.callout-tip icon=false} -->
+<!-- ## Sharing your project -->
+<!-- To share your project with the instructor team, locate the “project switcher” dropdown menu in the upper right of your RStudio window. This dropdown has the name of your project (eg: training_vargas), and a dropdown arrow. Click the dropdown menu, then “Share Project.” When the dialog box pops up, add the following usernames to your project: -->
 
--   jclark
--   mmklope
--   achen
--   jeakadi
--   agarcia
--   vargas-pouslen
+<!-- -   jclark -->
+<!-- -   mmklope -->
+<!-- -   achen -->
+<!-- -   jeakadi -->
+<!-- -   agarcia -->
+<!-- -   vargas-pouslen -->
 
 
-Once those names show up in the list, click “OK”.
+<!-- Once those names show up in the list, click “OK”. -->
 
-:::
+<!-- ::: -->
 
-### Organizing an R Project
+## Organizing an R Project
 
 
 When starting a new research project, one of the first things I do is create an R Project for it (just like we have here!). The next step is to then populate that project with relevant directories. There are many tools out there that can do this automatically. Some examples are `rrtools` or `usethis::create_package()`. The goal is to organize your project so that it is a compendium of your research. This means that the project has all of the digital parts needed to replicate your analysis, like code, figures, the manuscript, and data access.
@@ -79,7 +78,7 @@ Directory organization will vary from project to project, but the ultimate goal
 
 
 
-### Moving in an R Project using Paths & Working Directories
+## Moving in an R Project using Paths & Working Directories
 
 ![](images/allison-horst-pathways.png){fig-alt="Artwork by Allison Horst. A cartoon of a cracked glass cube looking frustrated with casts on its arm and leg, with bandaids on it, containing “setwd,” looks on at a metal riveted cube labeled “R Proj” holding a skateboard looking sympathetic, and a smaller cube with a helmet on labeled “here” doing a trick on a skateboard."}
 

diff --git a/materials/session_01.qmd b/materials/session_01.qmd
@@ -1,9 +1,9 @@
 ---
-title: "Seminar Series Recap and Reproducibility"
+title: "Welcome: Let's Talk About Reproducibility"
 title-block-banner: true
 format:
   html:
     code-overflow: wrap
 ---
 
-{{< include /sections/activity-reproducibility-lego.qmd >}}
+<!-- {{< include /sections/activity-reproducibility-lego.qmd >}} -->
diff --git a/materials/session_02.qmd b/materials/session_02.qmd
@@ -1,11 +1,12 @@
 ---
-title: "Data Visualization"
+title: "RStudio Server Setup"
 title-block-banner: true
 
 ---
 
 
-{{< include /sections/visualization-ggplot-leaflet.qmd >}}
+
+{{< include /sections/rstudio-server-setup.qmd >}}
 
 
 

diff --git a/materials/session_03.qmd b/materials/session_03.qmd
@@ -1,9 +1,10 @@
 ---
-title: "Text Analysis in R"
+title: "Git and GitHub Setup"
 title-block-banner: true
 ---
 
 
 
-{{< include /sections/text-analysis-ohara.qmd >}}
+
+{{< include /sections/git-setup.qmd >}}
 
diff --git a/materials/session_04.qmd b/materials/session_04.qmd
@@ -1,5 +1,5 @@
 ---
-title: "Accesing Survey Data Using a Reproducible Workflow"
+title: "Literate Analysis with Quarto"
 title-block-banner: true
 # execute: 
 #   eval: false
@@ -15,5 +15,5 @@ title-block-banner: true
 
 
 
-{{< include /sections/survey-workflow.qmd >}}
+{{< include /sections/r-intro-quarto.qmd >}}
 
diff --git a/materials/session_05.qmd b/materials/session_05.qmd
@@ -1,5 +1,5 @@
 ---
-title: "Visualizing Spatial Data"
+title: "Intro to Git and GitHub"
 title-block-banner: true
 ---
 
@@ -9,4 +9,4 @@ title-block-banner: true
 
 
 
-{{< include /sections/visualization-geospatial-basemaps.qmd >}}
+{{< include /sections/git-github-intro.qmd >}}
diff --git a/materials/session_06.qmd b/materials/session_06.qmd
@@ -1,14 +1,14 @@
 ---
-title: "GitHub for Project Management"
+title: "Data Management Essentials"
 title-block-banner: true
 execute: 
   eval: false
 ---
 
 
-::: {.callout-note}
-You can download the slides for this session [here](files/2024-03-github-for-project-management.pdf).
-:::
+<!-- ::: {.callout-note} -->
+<!-- You can download the slides for this session [here](files/2024-03-github-for-project-management.pdf). -->
+<!-- ::: -->
 
 
-<!--{{< include /sections/visualization-quarto-dashboards.qmd >}}-->
+{{< include /sections/data-management-essentials.qmd >}}
diff --git a/materials/session_07.qmd b/materials/session_07.qmd
@@ -1,11 +1,11 @@
 ---
-title: "Publishing to the Web"
+title: "Collaborating with Git and GitHub"
 title-block-banner: true
 execute:
   eval: false
 ---
 
-{{< include /sections/git-github-publishing-analysis.qmd >}}
+{{< include /sections/git-collab-merge-conflicts.qmd >}}
 
 
 <!--{{< include /sections/intro-tidy-data.qmd >}}-->
diff --git a/materials/session_08.qmd b/materials/session_08.qmd
@@ -1,14 +1,14 @@
 ---
-title: "Git Workflows"
+title: "Tidy Data"
 title-block-banner: true
 format:
   html:
     code-overflow: wrap
     code-link: true
 ---
 
+<!---CHECK which version we want-->
 
+{{< include /sections/intro-tidy-data.qmd >}}
 
-{{< include /sections/git-pull-requests-branches.qmd >}}
 
-{{< include /sections/git-workflows.qmd >}}
diff --git a/materials/session_09.qmd b/materials/session_09.qmd
@@ -1,9 +1,9 @@
 ---
-title: "Science Communication: Message Box"
+title: "Cleaning and Wrangling Data"
 title-block-banner: true
 ---
 
 
-{{< include /sections/communication.qmd >}}
+{{< include /sections/clean-wrangle-data.qmd >}}
+
 
-<!--{{< include /sections/git-collab-merge-conflicts.qmd >}}-->
diff --git a/materials/session_10.qmd b/materials/session_10.qmd
@@ -1,15 +1,20 @@
 ---
-title: "Quarto Dashboards"
+title: "Practice Session"
 title-block-banner: true
+execute: 
+  eval: false
 format:
   html:
+    code-link: true
+    code-fold: true
+    code-summary: "Answer"
     code-overflow: wrap
 ---
 
 
+<!-- CHECK all looks good-->
 
-
-{{< include /sections/visualization-quarto-dashboards.qmd >}}
+{{< include /sections/r-practice-clean-wrangle-visualize.qmd >}}
 
 
 

diff --git a/materials/session_11.qmd b/materials/session_11.qmd
@@ -1,18 +1,10 @@
 ---
-title: "Practice Session"
+title: "Publishing your Analysis to the Web"
 title-block-banner: true
-execute: 
-  eval: false
-format:
-  html:
-    code-link: true
-    code-fold: true
-    code-summary: "Answer"
-    code-overflow: wrap
 ---
 
 
-{{< include /sections/r-practice-clean-wrangle-visualize.qmd >}}
+{{< include /sections/git-github-publishing-analysis.qmd >}}
 
 
 
diff --git a/materials/session_12.qmd b/materials/session_12.qmd
@@ -1,11 +1,10 @@
 ---
-title: "Reproducibility and Provenance"
+title: "Data Visualization"
 title-block-banner: true
-execute:
-  eval: false
+
 ---
 
 
 
 
-{{< include /sections/provenance-reproducibility-datapaper.qmd >}}
+{{< include /sections/visualization-delta.qmd >}}
diff --git a/materials/session_13.qmd b/materials/session_13.qmd
@@ -1,8 +1,8 @@
 ---
-title: "Check and Set your PAT"
+title: "Working with Spatial Data"
 title-block-banner: true
 ---
 
 
-{{< include /sections/github-check-pat.qmd >}}
+{{< include /sections/geospatial-vector-analysis.qmd >}}