diff --git a/materials/_quarto.yml b/materials/_quarto.yml index 76b499ab..3d49da10 100755 --- a/materials/_quarto.yml +++ b/materials/_quarto.yml @@ -3,8 +3,8 @@ project: output-dir: _book book: - title: "Fundamentals in Data Management for Qualitative and Quantitative Arctic Research" - subtitle: "January 27-31, 2025" + title: "Reproducible Approaches to Arctic Research Using R" + subtitle: "February 24-28, 2025" reader-mode: false # NoteHD: cover image is not working @@ -28,24 +28,20 @@ book: chapters: - index.qmd # preface - - 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 # 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 + - session_01.qmd # ADC intro and R Setup + - session_02.qmd # Quarto + - session_03.qmd # DMP and Data Submission + - session_04.qmd # git intro + - session_05.qmd # Data Modeling + - session_06.qmd # Dplyr + - session_07.qmd # git collaboration + - session_08.qmd # Publishing analysis and data viz + - session_09.qmd # Practice I + - session_10.qmd # Functions and packages + - session_11.qmd # Thinking preferences and FAIR/CARE + - session_12.qmd # Practice II and portals + - session_13.qmd # Geospatial + - session_14.qmd # reproducible papers bibliography: book.bib diff --git a/materials/session_01.qmd b/materials/session_01.qmd index 453958b8..0ed40ed1 100644 --- a/materials/session_01.qmd +++ b/materials/session_01.qmd @@ -1,5 +1,5 @@ --- -title: "Introduction to the Arctic Data Center" +title: "Introduction to the Arctic Data Center and RStudio Server Setup" title-block-banner: true format: html: @@ -7,3 +7,5 @@ format: --- {{< include /sections/adc-intro-to-policies.qmd >}} + +{{< include /sections/rstudio-server-setup.qmd >}} diff --git a/materials/session_02.qmd b/materials/session_02.qmd index 4e87f5aa..cbec4170 100644 --- a/materials/session_02.qmd +++ b/materials/session_02.qmd @@ -1,9 +1,9 @@ --- -title: "RStudio Server Setup" +title: "Introduction to Quarto" title-block-banner: true --- -{{< include /sections/rstudio-server-setup.qmd >}} +{{< include /sections/r-intro-quarto.qmd >}} diff --git a/materials/session_03.qmd b/materials/session_03.qmd index ad1c0082..db644533 100644 --- a/materials/session_03.qmd +++ b/materials/session_03.qmd @@ -1,8 +1,10 @@ --- -title: "Introduction to R Programming" +title: "Data Management Plans & Submitting to the Arctic Data Center" title-block-banner: true execute: eval: true --- -{{< include /sections/intro-r-programming.qmd >}} +{{< include /sections/data-management-plans-reduced.qmd >}} + +{{< include /sections/metadata-adc-data-documentation-hands-on.qmd >}} diff --git a/materials/session_04.qmd b/materials/session_04.qmd index c7865326..a57efbc6 100644 --- a/materials/session_04.qmd +++ b/materials/session_04.qmd @@ -1,5 +1,5 @@ --- -title: "Thinking Preferences & Social Aspects of Collaboration" +title: "Introduction to git and GitHub" title-block-banner: true execute: eval: false @@ -14,7 +14,7 @@ format: -{{< include /sections/collaboration-thinking-preferences.qmd >}} +{{< include /sections/git-github-intro.qmd >}} + -{{< include /sections/collaboration-social-data-policies.qmd >}} diff --git a/materials/session_05.qmd b/materials/session_05.qmd index 86b8bdb4..51ff09ec 100644 --- a/materials/session_05.qmd +++ b/materials/session_05.qmd @@ -1,6 +1,6 @@ --- -title: "Writing Data Management Plans" +title: "Data Modeling Essentials" title-block-banner: true --- -{{< include /sections/data-management-plans-reduced.qmd >}} +{{< include /sections/data-modeling.Rmd >}} diff --git a/materials/session_06.qmd b/materials/session_06.qmd index 940f0d70..fb10007e 100644 --- a/materials/session_06.qmd +++ b/materials/session_06.qmd @@ -1,6 +1,6 @@ --- -title: "Literate Analysis with Quarto" +title: "Cleaning and Wrangling Data" title-block-banner: true --- -{{< include /sections/r-intro-quarto.qmd >}} \ No newline at end of file +{{< include /sections/data-cleaning-manipulation-tidyverse.Rmd >}} \ No newline at end of file diff --git a/materials/session_07.qmd b/materials/session_07.qmd index df9834d7..dd8066bf 100644 --- a/materials/session_07.qmd +++ b/materials/session_07.qmd @@ -1,8 +1,8 @@ --- -title: "R Practice: Literate Analysis " +title: "Collaborating with git and GitHub" title-block-banner: true execute: - eval: false + eval: true # format: # html: # code-link: true @@ -11,4 +11,4 @@ execute: # code-overflow: wrap --- -{{< include /sections/exercise-intro-programming-socialsci.qmd >}} \ No newline at end of file +{{< include /sections/git-collab-merge-conflicts.qmd >}} \ No newline at end of file diff --git a/materials/session_08.qmd b/materials/session_08.qmd index a00cbbd8..87a3f736 100644 --- a/materials/session_08.qmd +++ b/materials/session_08.qmd @@ -1,5 +1,5 @@ --- -title: "Data Modeling / Tidy Data" +title: "Publishing Analysis to the Web and Data Visualization" title-block-banner: true format: html: @@ -7,4 +7,6 @@ format: code-link: true --- -{{< include /sections/data-modeling-socialsci.qmd >}} +{{< include /sections/git-github-publishing-analysis.qmd >}} + +{{< include /sections/visualization-ggplot-leaflet.qmd >}} diff --git a/materials/session_09.qmd b/materials/session_09.qmd index a4f60fdb..6f38d992 100644 --- a/materials/session_09.qmd +++ b/materials/session_09.qmd @@ -1,5 +1,5 @@ --- -title: "Cleaning and Wrangling Data" +title: "Practice Session I" title-block-banner: true execute: eval: false @@ -11,4 +11,4 @@ format: code-overflow: wrap --- -{{< include /sections/clean-wrangle-data.qmd >}} +{{< include /sections/r-practice-clean-wrangle-visualize.qmd >}} diff --git a/materials/session_10.qmd b/materials/session_10.qmd index eac85f15..4fe58b04 100644 --- a/materials/session_10.qmd +++ b/materials/session_10.qmd @@ -1,9 +1,11 @@ --- -title: "Intro to Data Visualization" +title: "Writing Functions and Packages" title-block-banner: true format: html: code-overflow: wrap --- -{{< include /sections/visualization-ggplot-leaflet.qmd >}} +{{< include /sections/r-creating-functions.qmd >}} + +{{< include /sections/r-creating-packages.qmd >}} \ No newline at end of file diff --git a/materials/session_11.qmd b/materials/session_11.qmd index 9995fa5a..9f5e0f82 100644 --- a/materials/session_11.qmd +++ b/materials/session_11.qmd @@ -1,6 +1,8 @@ --- -title: "Ethical Data Collection" +title: "Thinking Preferences and Ethical Data Collection" title-block-banner: true --- +{{< include /sections/collaboration-thinking-preferences-short.qmd >}} + {{< include /sections/data-ethics-eloka-2023.qmd >}} diff --git a/materials/session_12.qmd b/materials/session_12.qmd index 8d9cfd2f..fa42160a 100644 --- a/materials/session_12.qmd +++ b/materials/session_12.qmd @@ -1,8 +1,10 @@ --- -title: "R Practice: Cleaning and Wrangling" +title: "R Practice II and Data Portals" title-block-banner: true execute: eval: false --- -{{< include /sections/exercise-tidyverse-socialsci.qmd >}} +{{< include /sections/r-practice-function-cleaning-data.qmd >}} + +{{< include /sections/adc-creating-data-portals.qmd >}} diff --git a/materials/session_13.qmd b/materials/session_13.qmd index f37b4b95..65eae920 100644 --- a/materials/session_13.qmd +++ b/materials/session_13.qmd @@ -1,5 +1,5 @@ --- -title: "Working with Text Data in R" +title: "Working with Spatial Data" title-block-banner: true # execute: # eval: false @@ -11,4 +11,4 @@ title-block-banner: true # code-overflow: wrap --- -{{< include /sections/intro-tidy-text-data.qmd >}} +{{< include /sections/geospatial-vector-analysis.qmd >}} diff --git a/materials/session_14.qmd b/materials/session_14.qmd index 95cae438..d71ad874 100644 --- a/materials/session_14.qmd +++ b/materials/session_14.qmd @@ -1,6 +1,6 @@ --- -title: "U.S Census Data in R" +title: "Reproducibility and Provenance" title-block-banner: true --- -{{< include /sections/census-data.qmd >}} \ No newline at end of file +{{< provenance-reproducibility-datapaper.qmd >}} \ No newline at end of file diff --git a/materials/session_15.qmd b/materials/session_15.qmd deleted file mode 100644 index cf7a65ca..00000000 --- a/materials/session_15.qmd +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Metadata Best Practices and Data Publishing" -title-block-banner: true ---- - -{{< include /sections/metadata-adc-data-documentation-socialsci.qmd >}} diff --git a/materials/session_16.qmd b/materials/session_16.qmd deleted file mode 100644 index 6b88b229..00000000 --- a/materials/session_16.qmd +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: "Creating Data Portals" -title-block-banner: true -format: - html: - code-link: true - code-overflow: wrap ---- - -{{< include /sections/adc-creating-data-portals.qmd >}} diff --git a/materials/session_17.qmd b/materials/session_17.qmd deleted file mode 100644 index 2854ebbb..00000000 --- a/materials/session_17.qmd +++ /dev/null @@ -1,14 +0,0 @@ ---- -title: "Reproducible Survey Workflow" -title-block-banner: true -execute: - eval: false -format: - html: - code-link: true - code-fold: true - code-summary: "Answer" - code-overflow: wrap ---- - -{{< include /sections/survey-workflow.qmd >}} diff --git a/materials/session_18.qmd b/materials/session_18.qmd deleted file mode 100644 index 109dc817..00000000 --- a/materials/session_18.qmd +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Provenance and Reproducibility" -title-block-banner: true ---- - -{{< include /sections/provenance-reproducibility-datapaper.qmd >}} diff --git a/materials/session_19.qmd b/materials/session_19.qmd deleted file mode 100644 index 078f417d..00000000 --- a/materials/session_19.qmd +++ /dev/null @@ -1,36 +0,0 @@ ---- -title: "Office Hour" -title-block-banner: true ---- - - -## Steps {.unnumbered} - -1. Go over the [Installing R and Git in your computer](https://learning.nceas.ucsb.edu/2024-10-coreR/session_22.html) session and make sure you have everything installed and updated. - -2. Introduce your GitHub credentials to your local computer. Follow the steps in [Git and GitHub Setup](https://learning.nceas.ucsb.edu/2024-10-coreR/session_03.html) section. - -3. Create a new repository on GitHub. It is up to you if you you named it something related to a project you are working or something more like a test-repo. - -4. Clone your GitHub repository into your local computer. Create a new RProject (with version control) - -5. Modify the README file. Provide a title to your project and a description. `Stage (add)` - `Commit` - `Pull` - `Push` your changes. - -6. Add sub-folders to your project. We have talked throughout the course the importance of organization, ultimately, it is up to you how you organize your project. - -7. Add data into your project and create a script (or Quarto doc) - -8. Read in your data and start working with it! - - -:::callout-important -## About gitignore - -If your data is too large you might wanna consider adding your the folder where your data live to the `gitignore` file. This way, Git will not track that file. GitHub has a size limit to 100 mb. This mean your will not be able to push files over that limit. This is when the `gitignore` comes handy. -::: - - - - - - diff --git a/materials/session_20.qmd b/materials/session_20.qmd deleted file mode 100644 index c8a88f78..00000000 --- a/materials/session_20.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: "GitHub for Project Management" -title-block-banner: true ---- - - - -{{< include /sections/git-project-management.qmd >}} \ No newline at end of file diff --git a/materials/session_21.qmd b/materials/session_21.qmd deleted file mode 100644 index 69a531dc..00000000 --- a/materials/session_21.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: "Reproducibility & Provenance" -title-block-banner: true ---- - - - -{{< include /sections/provenance-reproducibility-datapaper.qmd >}} \ No newline at end of file diff --git a/materials/session_22.qmd b/materials/session_22.qmd deleted file mode 100644 index 1d7bd39d..00000000 --- a/materials/session_22.qmd +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: "Installing R and Git in your computer" -title-block-banner: true ---- - - -{{< include /sections/r-git-install-guide.qmd >}} \ No newline at end of file