diff --git a/materials/_quarto.yml b/materials/_quarto.yml index efa8dab6..33caadc9 100755 --- a/materials/_quarto.yml +++ b/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 diff --git a/materials/index.qmd b/materials/index.qmd index f5a3de1a..5017bf49 100644 --- a/materials/index.qmd +++ b/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} + +::: -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. - -### 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 . **Additional contributors:** Ben Bolker, Amber E. Budden, Julien Brun, Samantha Csik, Halina Do-Linh, Natasha Haycock-Chavez, S. 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Binary files /dev/null and b/materials/session_03_files/figure-pdf/unnamed-chunk-7-1.pdf differ diff --git a/materials/session_04.qmd b/materials/session_04.qmd index a2547b73..01092bcc 100644 --- a/materials/session_04.qmd +++ b/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 >}} diff --git a/materials/session_05.qmd b/materials/session_05.qmd index b2d6da5c..6a3452f8 100644 --- a/materials/session_05.qmd +++ b/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 >}} diff --git a/materials/session_06.qmd b/materials/session_06.qmd index c755f1e1..ec3d710b 100644 --- a/materials/session_06.qmd +++ b/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 >}} + diff --git a/materials/session_07.qmd b/materials/session_07.qmd index 1404010f..f7988789 100644 --- a/materials/session_07.qmd +++ b/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 >}} diff --git a/materials/session_08.qmd b/materials/session_08.qmd index baecc940..c1c6f1c6 100644 --- a/materials/session_08.qmd +++ b/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 >}} + diff --git a/materials/session_09.qmd b/materials/session_09.qmd index a450ed1e..d1527ca6 100644 --- a/materials/session_09.qmd +++ b/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/clean-wrangle-data.qmd >}} diff --git a/materials/session_10.qmd b/materials/session_10.qmd index 79767d07..cbef2779 100644 --- a/materials/session_10.qmd +++ b/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 --- - - - - - - - - -{{< include /sections/data-management-essentials.qmd >}} +{{< include /sections/r-practice-tidy-data-joins.qmd >}} diff --git a/materials/session_11.qmd b/materials/session_11.qmd index 1776d457..6d12d75d 100644 --- a/materials/session_11.qmd +++ b/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 >}} diff --git a/materials/session_12.qmd b/materials/session_12.qmd index 1701b072..67ccbc44 100644 --- a/materials/session_12.qmd +++ b/materials/session_12.qmd @@ -1,5 +1,5 @@ --- -title: "Data Visualization" +title: "Publishing to the Web" title-block-banner: true --- @@ -7,4 +7,4 @@ title-block-banner: true -{{< include /sections/visualization-delta.qmd >}} +{{< include /sections/git-github-publishing-analysis.qmd >}} diff --git a/materials/session_13.qmd b/materials/session_13.qmd index cba16a70..8e57c7da 100644 --- a/materials/session_13.qmd +++ b/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 >}} diff --git a/materials/session_14.qmd b/materials/session_14.qmd index e997c144..9bf24e03 100644 --- a/materials/session_14.qmd +++ b/materials/session_14.qmd @@ -12,6 +12,4 @@ format: --- - - {{< include /sections/r-practice-clean-wrangle-visualize.qmd >}} diff --git a/materials/session_15.qmd b/materials/session_15.qmd index fd8bc0f8..a5ee49dc 100644 --- a/materials/session_15.qmd +++ b/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 >}} diff --git a/materials/session_16.qmd b/materials/session_16.qmd index 73817a8a..d15f12ef 100644 --- a/materials/session_16.qmd +++ b/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 >}} + diff --git a/materials/session_17.qmd b/materials/session_17.qmd index d67b2d05..e560405b 100644 --- a/materials/session_17.qmd +++ b/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 >}} \ No newline at end of file diff --git a/materials/session_18.qmd b/materials/session_18.qmd index 7626a89e..90acddd2 100644 --- a/materials/session_18.qmd +++ b/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 >}} \ No newline at end of file + \ No newline at end of file diff --git a/materials/session_19.qmd b/materials/session_19.qmd index 37cb5821..6990dcd8 100644 --- a/materials/session_19.qmd +++ b/materials/session_19.qmd @@ -1,5 +1,5 @@ --- -title: "Working with Spatial Data" +title: "Office Hour" title-block-banner: true --- @@ -7,6 +7,6 @@ title-block-banner: true -{{< include /sections/geospatial-vector-analysis.qmd >}} + diff --git a/materials/session_20.qmd b/materials/session_20.qmd index 64f53fc5..1337c00d 100644 --- a/materials/session_20.qmd +++ b/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 >}} \ No newline at end of file + \ No newline at end of file diff --git a/materials/session_21.qmd b/materials/session_21.qmd new file mode 100644 index 00000000..64f53fc5 --- /dev/null +++ b/materials/session_21.qmd @@ -0,0 +1,9 @@ +--- +title: "Reproducibility & Provenance" +title-block-banner: true +--- + + + + +{{< include /sections/provenance-reproducibility-datapaper.qmd >}} \ No newline at end of file