setting up initial book structure for coreR

materials/_quarto.yml

@@ -3,8 +3,8 @@ project:
   output-dir: _book
 
 book: 
-  title: "NCEAS coreR for Delta Science Program"
-  subtitle: "June 10 - 13, 2024"
+  title: "NCEAS Learning Hub’s coreR Course"
+  subtitle: "October  - 11, 2024"
   reader-mode: false
 
   # NoteHD: cover image is not working
@@ -23,30 +23,32 @@ book:
       - icon: twitter
         href: https://twitter.com/ucsb_nceas
       - icon: github
-        href: https://github.com/NCEAS/nceas-training/tree/2024-06-delta
+        href: https://github.com/NCEAS/nceas-training/tree/2024-10-coreR
 
   chapters:
     - index.qmd # preface 
     - 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 # Tidy data
-    - session_07.qmd # Cleaning and Wrangling
-    - session_08.qmd # Practice Session I - joins
-    - session_09.qmd # Collaborating with Git
-    - session_10.qmd # Data Management
-    - session_11.qmd # Publishing to the Web
-    - session_12.qmd # Intro to Data Viz
-    - session_13.qmd # Spatial Data
+    - session_04.qmd # Intro to R & RStudio
+    - session_05.qmd # Literate Analysis
+    - session_06.qmd # Lego Activity + Discussion
+    - session_07.qmd # Intro to Git and GitHub
+    - session_08.qmd # Tidy Data
+    - session_09.qmd # Cleaning and Wrangling
+    - session_10.qmd # Practice Session I - joins
+    - session_11.qmd # Collaborating with Git 
+    - session_12.qmd # Publishing to the Web
+    - session_13.qmd # Intro to Data Viz
     - session_14.qmd # Practice Session II -lobter report 
-    - session_15.qmd # Shiny
-    - session_16.qmd # Reproducibility and Provenence
-    - session_17.qmd # Appendix: Set up in personla comp
-    - session_18.qmd # Intro to R & RStudio
-    # - session_19.qmd # Spatial Data
-    # - session_20.qmd # Repro and Provenance
+    - session_15.qmd # Data Management
+    - session_16.qmd # Spatial Data
+    - session_17.qmd # Functions and Packages
+    - session_18.qmd # Practice Functions and Packages
+    - session_19.qmd # Office Hour Guidelines
+    - session_20.qmd # GitHub for Project management
+    - session_21.qmd # Repro and Provenance
+    # - session_22.qmd # Appendix: Set up in personla comp
 
 
 

materials/index.qmd

@@ -4,35 +4,33 @@
 
 ![](cover.png){width="80%" fig-align="center"}
 
-![](images/delta/delta-logo.png){width="80%" fig-align="center"}
 
 :::
 
-## About the course {.unnumbered}
-As part of a collaboration between NCEAS and the Delta Science Program, this course has been adapted from [NCEAS coreR course](https://www.nceas.ucsb.edu/learning-hub/core-r), an in-person immersion in R programming for environmental data science. Researchers will gain experience with essential data science tools and best practices to increase their capacity as collaborators, reproducible coders, and open scientists.
+## Welcome! {.unnumbered}
+coreR is a five-day immersion in R programming for environmental data science. Researchers will gain experience with essential data science tools and best practices to increase their capacity as collaborators, reproducible coders, and open scientists.
 
+### Course Learning Objectives
+-   Effectively manage data using `tidy` data practices and developing quality metadata
+-   Establish best practices and utilize tools like Git & GitHub, and Data Management Plans to optimize your collaboration
+-   Better communicate scientific analyses and results using Markdown, GitHub webpages, and R packages like `ggplot` and `leaflet`
+-   Increase your familiarity and confidence with data science tools
 
-## NCEAS Expertise
+### Week's Schedule
 
-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).
+:::{.column-body-outset}
+<!-- ![](images/schedule.png) -->
+:::
 
-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.
 
 
-<!-- *June 10 - 13, 2024* -->
 
-### Learning Objectives
--   Effectively manage data using `tidy` data practices
--   Implement reproducible scientific workflows throughout all aspects of a project
--   Establish best practices and utilize tools like Git & GitHub to optimize your collaboration
--   Better communicate scientific analyses and results using Markdown, GitHub webpages, and R packages like `ggplot2` and `Shiny`
-- Increase your familiarity and confidence with data science tools
+## NCEAS Expertise
 
-### Week's Schedule
+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).
+
+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.
 
-:::{.column-body-outset}
-![](images/schedule.png)
-:::
 
 
 ## Code of Conduct
@@ -45,6 +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/).
 
+**UPDATE**
 **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.

materials/session_04.qmd

@@ -1,5 +1,5 @@
 ---
-title: "Literate Analysis with Quarto"
+title: "Introduction to R & RStudio"
 title-block-banner: true
 # execute: 
 #   eval: false
@@ -14,5 +14,5 @@ title-block-banner: true
 
 
 
-{{< include /sections/r-intro-quarto.qmd >}}
+{{< include /sections/intro-r-programming.qmd >}}
 

materials/session_05.qmd

@@ -1,12 +1,8 @@
 ---
-title: "Intro to Git and GitHub"
+title: "Literate Analysis with Quarto"
 title-block-banner: true
 ---
 
 
 
-
-
-
-
-{{< include /sections/git-github-intro.qmd >}}
+{{< include /sections/r-intro-quarto.qmd >}}

materials/session_06.qmd

@@ -1,5 +1,5 @@
 ---
-title: "Tidy Data"
+title: "Reproducibility: a Lego activity"
 title-block-banner: true
 format:
   html:
@@ -9,4 +9,4 @@ format:
 
 
 
-{{< include /sections/intro-tidy-data.qmd >}}
+<!-- {{< include /sections/intro-tidy-data.qmd >}} -->

materials/session_07.qmd

@@ -1,8 +1,8 @@
 ---
-title: "Cleaning and Wrangling Data"
+title: "Introduction to Git and GtiHub"
 title-block-banner: true
 ---
 
 
-{{< include /sections/clean-wrangle-data.qmd >}}
+{{< include /sections/git-github-intro.qmd >}}
 

materials/session_08.qmd

@@ -1,20 +1,12 @@
 ---
-title: "Practice Session I"
+title: "Tidy Data"
 title-block-banner: true
-execute: 
-  eval: false
-format:
-  html:
-    code-link: true
-    code-fold: true
-    code-summary: "Answer"
-    code-overflow: wrap
 ---
 
 
+{{< include /sections/intro-tidy-data.qmd >}}
 
-
-{{< include /sections/r-practice-tidy-data-joins.qmd >}}
+<!-- {{< include /sections/r-practice-tidy-data-joins.qmd >}} -->
 
 
 

materials/session_09.qmd

@@ -1,14 +1,10 @@
 ---
-title: "Collaborating with Git and GitHub"
+title: "Cleaning and Wrangling Data"
 title-block-banner: true
-execute:
-  eval: false
 ---
 
-{{< include /sections/git-collab-merge-conflicts.qmd >}}
 
-
-<!--{{< include /sections/intro-tidy-data.qmd >}}-->
+{{< include /sections/clean-wrangle-data.qmd >}}
 
 
 

materials/session_10.qmd

@@ -1,17 +1,15 @@
 ---
-title: "Data Management Essentials"
+title: "Practice Session I"
 title-block-banner: true
-execute: 
+execute:
   eval: false
+format:
+  html:
+    code-link: true
+    code-fold: true
+    code-summary: "Answer"
+    code-overflow: wrap
 ---
 
 
-<!-- ::: {.callout-note} -->
-<!-- You can download the slides for this session [here](files/2024-03-github-for-project-management.pdf). -->
-<!-- ::: -->
-
-
-
-
-
-{{< include /sections/data-management-essentials.qmd >}}
+{{< include /sections/r-practice-tidy-data-joins.qmd >}}

materials/session_11.qmd

@@ -1,10 +1,10 @@
 ---
-title: "Publishing your Analysis to the Web"
+title: "Collaborating with Git and GitHub"
 title-block-banner: true
 ---
 
 
-{{< include /sections/git-github-publishing-analysis.qmd >}}
+{{< include /sections/git-collab-merge-conflicts.qmd >}}
 
 
 

materials/session_12.qmd

@@ -1,10 +1,10 @@
 ---
-title: "Data Visualization"
+title: "Publishing to the Web"
 title-block-banner: true
 
 ---
 
 
 
 
-{{< include /sections/visualization-delta.qmd >}}
+{{< include /sections/git-github-publishing-analysis.qmd >}}

materials/session_13.qmd

@@ -1,10 +1,10 @@
 ---
-title: "Working with Spatial Data"
+title: "Data Visualization"
 title-block-banner: true
 ---
 
 
 
 
-{{< include /sections/geospatial-vector-analysis.qmd >}}
+{{< include /sections/visualization-delta.qmd >}}
 

materials/session_14.qmd

@@ -12,6 +12,4 @@ format:
 ---
 
 
-<!-- CHECK all looks good-->
-
 {{< include /sections/r-practice-clean-wrangle-visualize.qmd >}}

materials/session_15.qmd

@@ -1,5 +1,5 @@
 ---
-title: "Introduction to Shiny"
+title: "Data Management Essentials"
 title-block-banner: true
 execute: 
     eval: false
@@ -8,7 +8,7 @@ execute:
 
 
 
-{{< include /sections/shiny-intro.qmd >}}
+{{< include /sections/data-management-essentials.qmd >}}
 
 
 

materials/session_16.qmd

@@ -1,11 +1,11 @@
 ---
-title: "Reproducibility and Provenance"
+title: "Working with Spatial Data"
 title-block-banner: true
-# format:
-#   html: 
-#     code-link: true
-#     code-overflow: wrap
+format:
+  html:
+    code-link: true
+    code-overflow: wrap
 ---
 
-{{< include /sections/provenance-reproducibility-datapaper.qmd >}}
+<!-- {{< include /sections/geospatial-vector-analysis.qmd >}} -->
 

materials/session_17.qmd

@@ -1,8 +1,10 @@
 ---
-title: "Appendix: Install R and Git in your Computer"
+title: "Writing Functions and Packages"
 title-block-banner: true
 ---
 
 
 
-{{< include /sections/r-git-install-guide.qmd >}}
+{{< include /sections/r-creating-functions.qmd >}}
+
+{{< include /sections/r-creating-packages.qmd >}}

materials/session_18.qmd

@@ -1,8 +1,8 @@
 ---
-title: "Appendix: Intro to R & RStudio"
+title: "Practice Session III"
 title-block-banner: true
 ---
 
 
 
-{{< include /sections/intro-r-programming.qmd >}}
+<!-- {{< include /sections/intro-r-programming.qmd >}} -->

materials/session_19.qmd

@@ -1,12 +1,12 @@
 ---
-title: "Working with Spatial Data"
+title: "Office Hour"
 title-block-banner: true
 ---
 
 
 
 
 
-{{< include /sections/geospatial-vector-analysis.qmd >}}
+<!-- {{< include /sections/geospatial-vector-analysis.qmd >}} -->
 
 

materials/session_20.qmd

@@ -1,9 +1,9 @@
 ---
-title: "Reproducibility & Provenance"
+title: "GitHub for Project Management"
 title-block-banner: true
 ---
 
 
 
 
-{{< include /sections/provenance-reproducibility-datapaper.qmd >}}
+<!-- {{< include /sections/provenance-reproducibility-datapaper.qmd >}} -->

materials/session_21.qmd

@@ -0,0 +1,9 @@
+---
+title: "Reproducibility & Provenance"
+title-block-banner: true
+---
+
+
+
+
+{{< include /sections/provenance-reproducibility-datapaper.qmd >}}