Restructure book for 2025-01-arctic fundamentals course

.gitignore

@@ -17,4 +17,7 @@
 *.html
 
 # geospatial lesson files
-rosm.cache/*
+rosm.cache/*
+
+# Session build files
+session_*_files/*

materials/_quarto.yml

@@ -3,8 +3,8 @@ project:
   output-dir: _book
 
 book: 
-  title: "NCEAS Learning Hub’s coreR Course"
-  subtitle: "October 7-11, 2024"
+  title: "Fundamentals in Data Management for Qualitative and Quantitative Arctic Research"
+  subtitle: "January 27-31, 2025"
   reader-mode: false
 
   # NoteHD: cover image is not working
@@ -23,33 +23,28 @@ book:
       - icon: twitter
         href: https://twitter.com/ucsb_nceas
       - icon: github
-        href: https://github.com/NCEAS/nceas-training/tree/2024-10-coreR
+        href: https://github.com/NCEAS/nceas-training/tree/2025-01-arctic
 
   chapters:
     - index.qmd # preface 
-    - session_01.qmd # Introduction
-    - session_02.qmd # R Setup
-    - session_03.qmd # Git and GitHub set up
-    - 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_01.qmd # ADC intro
+    - session_02.qmd # R Setup 
+    - session_03.qmd # Intro to R programming
+    - session_04.qmd # Thinking preferencees + Social aspects of collab
+    - session_05.qmd # DMP
+    - session_06.qmd # Literate analysis
+    - session_07.qmd # ADC-Fundamental practice 1 
+    - session_08.qmd # Data Modeling and 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 # 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
-
+    - session_10.qmd # Intro Data Viz
+    - session_11.qmd # Ethical Data Collection
+    - session_12.qmd # ADC-Fundamentals practice 2
+    - session_13.qmd # Text data
+    - session_14.qmd # Census data
+    - session_15.qmd # Metadata best practices & publishing
+    - session_16.qmd # Data portals
+    - session_17.qmd # Survey Workflows
+    - session_18.qmd # Repro and Provenance
 
 
 bibliography: book.bib
@@ -62,4 +57,4 @@ format:
   # pdf:
   #   documentclass: scrreprt
 
-editor: visual
+editor: visual

materials/index.qmd

@@ -1,36 +1,20 @@
-<!-- # Preface {.unnumbered} -->
-
 ::: column-margin
+![](images/arctic-data-center.png){width="80%" fig-align="center"}
+:::
 
+::: column-margin
 ![](cover.png){width="80%" fig-align="center"}
-
-
 :::
 
-## 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
--   Increase your familiarity and confidence with data science tools
--   Overview of tools you can use within the R programming language and RStudio interface
--   Effectively manage data using `tidy` data practices and understanding the importance of quality metadata
--   Establish best practices and utilize tools like Git & GitHub to optimize collaboration
--   Better communicate scientific analyses and results using Markdown, GitHub webpages, and R packages like `ggplot` and `leaflet`
-
-
-### Week's Schedule
-
-
-![](images/schedule.png)
-
+## About the course {.unnumbered}
 
-## NCEAS Expertise
-
-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.
+This 5-day in-person workshop will provide researchers with an overview of reproducible and ethical research practices, steps and methods for more easily documenting and preserving their data at the Arctic Data Center, and an introduction to programming in R. Special attention will be paid to qualitative data management, including practices working with sensitive data. Example datasets will draw from natural and social sciences, and methods for conducting reproducible research will be discussed in the context of both qualitative and quantitative data. Responsible and reproducible data management practices will be discussed as they apply to all aspects of the data life cycle. This includes ethical data collection and data sharing, data sovereignty, and the [CARE](https://www.gida-global.org/care) principles. The CARE principles are guidelines that help ensure open data practices (like the FAIR principles) appropriately engage with Indigenous Peoples’ rights and interests.
 
+## Week's Schedule
 
+::: column-body-outset
+![](images/schedule.png){.lightbox width=100%}
+:::
 
 ## Code of Conduct
 
@@ -42,15 +26,8 @@ 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:** Matthew B. Jones, Angie Garcia, Nicole Greco, Justin Kadi, Jim Regetz (2025), Fundamentals in Data Management for Qualitative and Quantitative Arctic Research. Arctic Data Center & NCEAS Learning Hub. URL <https://learning.nceas.ucsb.edu/2025-01-arctic>.
 
-**Citation:** Camila Vargas Poulsen, Casey Ohara, Shayna Sura (2024), NCEAS coreR for Delta Science Program, October 2024, NCEAS Learning Hub. URL <https://learning.nceas.ucsb.edu/2024-10-coreR>.
-
-**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.
-
-
+**Additional contributors:** Ben Bolker, Amber E. Budden, Julien Brun, Samantha Csik, Halina Do-Linh, Natasha Haycock-Chavez, S. Jeanette Clark, Julie Lowndes, Stephanie Hampton, Samanta Katz, Erin McLean, Bryce Mecum, Casey O'Hara, Deanna Pennington, Karthik Ram, Jim Regetz, Tracy Teal, Camila Vargas-Poulsen, Daphne Virlar-Knight, Leah Wasser.
 
 This is a Quarto book. To learn more about Quarto books visit <https://quarto.org/docs/books>.
-
-
-
-

materials/session_01.qmd

@@ -1,10 +1,9 @@
 ---
-title: "Course Introduction"
+title: "Introduction to the Arctic Data Center"
 title-block-banner: true
 format:
   html:
     code-overflow: wrap
 ---
 
-
-{{< include /sections/reproducibility-intro.qmd >}}
+{{< include /sections/adc-intro-to-policies.qmd >}}

materials/session_02.qmd

@@ -5,11 +5,5 @@ title-block-banner: true
 ---
 
 
-
-
-
 {{< include /sections/rstudio-server-setup.qmd >}}
 
-
-
-

materials/session_03.qmd

@@ -1,11 +1,9 @@
 ---
-title: "Git and GitHub Setup"
+title: "Introduction to R Programming"
 title-block-banner: true
-code-annotations: hover
+execute: 
+  eval: false
 ---
 
-
-
-
-{{< include /sections/git-setup.qmd >}}
+{{< include /sections/intro-r-programming.qmd >}}
 

materials/session_04.qmd

@@ -1,17 +1,20 @@
 ---
-title: "Working in R & RStudio"
+title: "Thinking Preferences & Social Aspects of Collaboration"
 title-block-banner: true
-# execute: 
-#   eval: false
-# format:
-#   html:
-#     code-link: true
-#     code-fold: true
-#     code-summary: "Answer"
-#     code-overflow: wrap
+execute: 
+  eval: false
+format:
+  html:
+    code-link: true
+    code-fold: true
+    code-summary: "Answer"
+    code-overflow: wrap
 ---
 
 
 
-{{< include /sections/intro-r-programming.qmd >}}
 
+{{< include /sections/collaboration-thinking-preferences.qmd >}}
+
+
+{{< include /sections/collaboration-social-data-policies.qmd >}}

materials/session_05.qmd

@@ -1,8 +1,6 @@
 ---
-title: "Literate Analysis with Quarto"
+title: "Writing Data Management Plans"
 title-block-banner: true
 ---
 
-
-
-{{< include /sections/r-intro-quarto.qmd >}}
+{{< include /sections/data-management-plans-reduced.qmd >}}

materials/session_06.qmd

@@ -1,12 +1,6 @@
 ---
-title: "Reproducibility: a Lego activity"
+title: "Literate Analysis with Quarto"
 title-block-banner: true
-format:
-  html:
-    code-overflow: wrap
-    code-link: true
 ---
 
-
-
-<!-- {{< include /sections/intro-tidy-data.qmd >}} -->
+{{< include /sections/r-intro-quarto.qmd >}}

materials/session_07.qmd

@@ -1,8 +1,14 @@
 ---
-title: "Git and GitHub"
+title: "R Practice: Literate Analysis "
 title-block-banner: true
+execute:
+  eval: false
+# format:
+#   html: 
+#     code-link: true
+#     code-fold: true
+#     code-summary: "Example Code"
+#     code-overflow: wrap
 ---
 
-
-{{< include /sections/git-github-intro.qmd >}}
-
+{{< include /sections/exercise-intro-programming-socialsci.qmd >}}

materials/session_08.qmd

@@ -1,15 +1,10 @@
 ---
-title: "Tidy Data"
+title: "Data Modeling Essentials"
 title-block-banner: true
+format:
+  html:
+    code-overflow: wrap
+    code-link: true
 ---
 
-
-
-
-{{< include /sections/intro-tidy-data.qmd >}}
-
-<!-- {{< include /sections/r-practice-tidy-data-joins.qmd >}} -->
-
-
-
-
+{{< include /sections/data-modeling-socialsci.qmd >}}

materials/session_09.qmd

@@ -1,11 +1,14 @@
 ---
 title: "Cleaning and Wrangling Data"
 title-block-banner: true
+execute:
+  eval: false
+format:
+  html: 
+    code-link: true
+    code-fold: true
+    code-summary: "Answer"
+    code-overflow: wrap
 ---
 
-
-
 {{< include /sections/clean-wrangle-data.qmd >}}
-
-
-

materials/session_10.qmd

@@ -1,14 +1,9 @@
 ---
-title: "Practice Session: Joins"
+title: "Intro to Data Visualization"
 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-tidy-data-joins.qmd >}}
+{{< include /sections/visualization-ggplot-leaflet.qmd >}}

materials/session_11.qmd

@@ -1,10 +1,6 @@
 ---
-title: "Collaborating with Git and GitHub"
+title: "Ethical Data Collection"
 title-block-banner: true
 ---
 
-
-{{< include /sections/git-collab-merge-conflicts.qmd >}}
-
-
-
+{{< include /sections/data-ethics-eloka-2023.qmd >}}

materials/session_12.qmd

@@ -1,9 +1,8 @@
 ---
-title: "Publishing to the Web"
+title: "R Practice: Cleaning and Wrangling"
 title-block-banner: true
-
+execute:
+  eval: false
 ---
 
-
-
-{{< include /sections/git-github-publishing-analysis.qmd >}}
+{{< include /sections/exercise-tidyverse-socialsci.qmd >}}

materials/session_13.qmd

@@ -1,10 +1,14 @@
 ---
-title: "Data Visualization"
+title: "Working with Text Data in R"
 title-block-banner: true
+# execute:
+#   eval: false
+# format:
+#   html:
+#     code-link: true
+#     code-fold: true
+#     code-summary: "Answer"
+#     code-overflow: wrap
 ---
 
-
-
-
-{{< include /sections/visualization-delta.qmd >}}
-
+{{< include /sections/intro-tidy-text-data.qmd >}}

materials/session_14.qmd

@@ -1,16 +1,6 @@
 ---
-title: "Practice Session: Collaborative Report"
+title: "U.S Census Data in R"
 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/census-data.qmd >}}