diff --git a/.github/ISSUE_TEMPLATE/course-template-feature-request.md b/.github/ISSUE_TEMPLATE/course-template-feature-request.md deleted file mode 100644 index 144b755..0000000 --- a/.github/ISSUE_TEMPLATE/course-template-feature-request.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Course Template Feature Request -about: Suggest an idea for the course templates -title: '' -labels: '' -assignees: cansavvy - ---- - -## Is your feature request related to a problem? Please describe. - - -## Describe the solution you'd like - - -## Describe alternatives you've considered - - -## Additional context - diff --git a/.github/ISSUE_TEMPLATE/course-template-problem-report.md b/.github/ISSUE_TEMPLATE/course-template-problem-report.md deleted file mode 100644 index ca8c382..0000000 --- a/.github/ISSUE_TEMPLATE/course-template-problem-report.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -name: Course Template Problem Report -about: Create a report to help improve the template and its documentation -title: Problem -labels: bug -assignees: cansavvy - ---- - -## Describe what is not working with the template or is unclear in the documentation - - -## Please link to the specific course repository you are working on - -## To Reproduce - - -## Expected behavior - - -## Github actions links - - -## Screenshots - - -## Additional context - diff --git a/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md b/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md deleted file mode 100644 index 22e87ea..0000000 --- a/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md +++ /dev/null @@ -1,14 +0,0 @@ ---- -name: Add your new course to syncs/OTTR updates -about: Provide information about your new course (which uses the OTTR template) so that we can enroll it in OTTR updates -title: '' -labels: '' -assignees: cansavvy - ---- - -## What is the name of your new repository? - - -## What username or organization is your new repository associated with? - diff --git a/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md b/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md deleted file mode 100644 index 80a5065..0000000 --- a/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md +++ /dev/null @@ -1,26 +0,0 @@ ---- -name: Update your course's info for syncs/OTTR updates -about: Provide information about your moved/renamed course (which uses the OTTR template) so that it can continue to be enrolled in OTTR updates -title: '' -labels: '' -assignees: cansavvy - ---- - - - -## If the name of your repository was changed ... - -### What was the old name? - - -### What is the new name? - - -## If the repository was moved ... - -### What was the original username or organization your repository was associated with? - - -### What is the new username or organization your repository was associated with? - diff --git a/.github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md b/.github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md deleted file mode 100644 index b0196ee..0000000 --- a/.github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -name: Add new repository to sync -about: Enroll your repository for OTTR updates -title: OTTR Updates Enrollment -labels: '' -assignees: cansavvy ---- - -Added __ repository to sync.yml in order to enroll in OTTR updates. diff --git a/.github/course_README_template.md b/.github/course_README_template.md deleted file mode 100644 index 1c9ccdf..0000000 --- a/.github/course_README_template.md +++ /dev/null @@ -1,24 +0,0 @@ -# {Course Name} - -This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template). - -You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.} - -If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/). - -## About this course - -This course introduces {info on what this course introduces} - -## Learning Objectives - -This course will teach learners to: - -- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here} -- {More learning objectives} - -## Encountering problems? - -If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}. - -Creative Commons License
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise. diff --git a/.github/sync.yml b/.github/sync.yml deleted file mode 100755 index 9510ba2..0000000 --- a/.github/sync.yml +++ /dev/null @@ -1,167 +0,0 @@ -# Candace Savonen Aug 2021 -# For info on how to update this file see: https://github.com/marketplace/actions/repo-file-sync-action#%EF%B8%8F-sync-configuration - -group: - - files: - - source: .github/workflows/ - dest: .github/workflows/ - deleteOrphaned: true - exclude: | - send-updates.yml - test-send-updates.yml - starting-course.yml - release-notes.yml - docker-test.yml - docker-build.yml - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - - source: .github/ISSUE_TEMPLATE/course-problem-report.md - dest: .github/ISSUE_TEMPLATE/course-problem-report.md - - source: .github/ISSUE_TEMPLATE/course-content-add.md - dest: .github/ISSUE_TEMPLATE/course-content-add.md - - source: .github/ISSUE_TEMPLATE/url-error.md - dest: .github/ISSUE_TEMPLATE/url-error.md - - source: style-sets - dest: style-sets - - source: assets/box_images/ - dest: assets/box_images/ - - source: resources/exclude_files.txt - dest: resources/exclude_files.txt - # Repositories to receive changes - repos: | - jhudsl/Documentation_and_Usability - jhudsl/Informatics_Research_Leadership - jhudsl/Data_Management_for_Cancer_Research - jhudsl/Computing_for_Cancer_Informatics - jhudsl/Adv_Reproducibility_in_Cancer_Informatics - jhudsl/Reproducibility_in_Cancer_Informatics - jhudsl/Dissemination_and_Engagement - fhdsl/Cancer_Clinical_Informatics - jhudsl/Machine_Learning_for_Cancer_Informatics - jhudsl/Cancer_Informatics_Data_Visualization - jhudsl/Cancer_Genome_Informatics - fhdsl/Cancer_Imaging_Informatics - datatrail-jhu/DataTrail_Template - abyzovlab/CNVpytor-course - tmm211/dsp-terra-mooc-test2 - fhdsl/Choosing_Genomics_Tools - fhdsl/NIH_Data_Sharing - fhdsl/FH_Cluster_Guide - fhdsl/Using_Leanpub - fhdsl/Ethical_Data_Handling_for_Cancer_Research - fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles - fhdsl/Design_of_Data_Analysis - fhdsl/Tools_for_Reproducible_Workflows_in_R - fhdsl/Introduction_to_reproducible_research - mccoy-lab/hgv_modules - griffithlab/pVACtools_Intro_Course - griffithlab/CIVIC_SVI_Course - PracticalGenomics/cogaps-on-sciserver - fhdsl/AI_for_Efficient_Programming - fhdsl/AI_for_Decision_Makers - griffithlab/Immuno_Workflow_Course - fhdsl/Intro_to_R - fhdsl/Intro_to_Command_Line - fhdsl/Intro_to_Git_GitHub - fhdsl/WDL_Workflows_Guide - fhdsl/Intermediate-Git-GitHub - fhdsl/GitHub_Automation_for_Scientists - williamtmillsiv/introduction_to_bioinformatics - fhdsl/OTTR_Quarto - fhdsl/bench_to_bytes - fhdsl/Intermediate_R - fhdsl/DataViz_Practice - fhdsl/DataViz_Considerations -###ADD NEW REPO HERE following the format above# - -### These are custom groups for syncing -- not all files needs to be synced - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/pull-request.yml - dest: .github/workflows/pull-request.yml - repos: | - jhudsl/OTTR_Template_Website - - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/delete-preview.yml - dest: .github/workflows/delete-preview.yml - - source: .github/workflows/send-updates.yml - dest: .github/workflows/send-updates.yml - - source: .github/workflows/test-send-updates.yml - dest: .github/workflows/test-send-updates.yml - - source: scripts/make_screenshots.R - dest: scripts/make_screenshots.R - - source: scripts/switch_sync_repo.R - dest: scripts/switch_sync_repo.R - repos: | - jhudsl/OTTR_Quizzes - - - files: - - source: .github/workflows/ - dest: .github/workflows/ - exclude: | - starting-course.yml - release-notes.yml - - source: .github/switch_sync_repo.R - dest: .github/switch_sync_repo.R - - source: .github/ISSUE_TEMPLATE/course-problem-report.md - dest: .github/ISSUE_TEMPLATE/course-problem-report.md - - source: .github/ISSUE_TEMPLATE/course-content-add.md - dest: .github/ISSUE_TEMPLATE/course-content-add.md - - source: code_of_conduct.md - dest: code_of_conduct.md - - source: assets/box_images/ - dest: assets/box_images/ - - source: assets/style.css - dest: assets/style.css - - source: assets/toc_close.css - dest: assets/toc_close.css - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - - source: style-sets/fhdasl/ - dest: style-sets/fhdasl/ - repos: | - jhudsl/AnVIL_Template - - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/ - dest: .github/workflows/ - deleteOrphaned: true - - source: .github/switch_sync_repo.R - dest: .github/switch_sync_repo.R - - source: .github/automatic-issues/ - dest: .github/automatic-issues/ - - source: assets/box_images/ - dest: assets/box_images/ - - source: assets/style.css - dest: assets/style.css - - source: assets/toc_close.css - dest: assets/toc_close.css - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - repos: | - C-MOOR/C-MOOR_Template - - - files: - - source: config_automation.yml - dest: config_automation.yml - - source: .github/workflows/ - dest: .github/workflows/ - deleteOrphaned: true - - source: .github/switch_sync_repo.R - dest: .github/switch_sync_repo.R - - source: assets/box_images/ - dest: assets/box_images/ - - source: scripts/ - dest: scripts/ - deleteOrphaned: true - repos: | - opencasestudies/OCS_Guide diff --git a/.github/workflows/send-updates.yml b/.github/workflows/send-updates.yml deleted file mode 100644 index f636dc0..0000000 --- a/.github/workflows/send-updates.yml +++ /dev/null @@ -1,45 +0,0 @@ -# Candace Savonen Aug 2021 - -name: Sync Files - -on: - release: - types: - - published - workflow_dispatch: - inputs: - prtag: - description: 'Tag to use?' - required: true - default: 'null' - -jobs: - sync: - runs-on: ubuntu-latest - steps: - - name: Checkout Repository - uses: actions/checkout@v4 - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - - name: Get the version - id: get_tag - run: | - if [ github.event.inputs.prtag == 'null' ] - then - echo "version=$(echo $GITHUB_REF | cut -d / -f 3)" >> $GITHUB_OUTPUT - fi - if [ github.event.inputs.prtag != 'null' ] - then - echo "version=${{ github.event.inputs.prtag }}" >> $GITHUB_OUTPUT - fi - - - name: Run Mechanics File Sync - uses: BetaHuhn/repo-file-sync-action@v1.17.21 - with: - GH_PAT: ${{ secrets.GH_PAT }} - COMMIT_BODY: release-${{ steps.get_tag.outputs.version }} diff --git a/.github/workflows/starting-course.yml b/.github/workflows/starting-course.yml deleted file mode 100644 index 144aa3d..0000000 --- a/.github/workflows/starting-course.yml +++ /dev/null @@ -1,144 +0,0 @@ -# Code adapted from https://github.com/JetBrains/intellij-platform-plugin-template/blob/deb171483598ee8a5d7621154db880e87b4db4ef/.github/workflows/template-cleanup.yml -# by Candace Savonen for this repository. - -name: Starting a new course - -on: - push: - branches: [ main, staging ] - workflow_dispatch: - -jobs: - # Run cleaning process only if workflow is triggered by not being in the Bookdown template anymore - template-cleanup: - name: Template Cleanup - runs-on: ubuntu-latest - if: github.event.repository.name != 'OTTR_Template' - steps: - - name: checkout repo - uses: actions/checkout@v4 - - - name: Login as jhudsl-robot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.email "itcrtrainingnetwork@gmail.com" - git config --global user.name "jhudsl-robot" - -##### Delete Template-specific files that aren't needed for new courses - - # Cleanup Template-specific bits - - name: Cleanup - run: | - # Cleanup - mv .github/course_README_template.md README.md - rm -rf \ - .github/workflows/report-maker.yml \ - .github/workflows/send-updates.yml \ - .github/workflows/test-send-updates.yml \ - .github/sync.yml \ - .github/test-sync.yml \ - .github/workflows/starting-course.yml \ - .github/ISSUE_TEMPLATE/course-template-problem-report.md \ - .github/ISSUE_TEMPLATE/course-template-feature-request.md \ - .github/ISSUE_TEMPLATE/new-course-add-to-sync.md \ - .github/ISSUE_TEMPLATE/update-course-info-for-sync.md \ - .github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md \ - resources/code_output \ - resources/screenshots \ - resources/course_screenshots \ - resources/gs_slides \ - resources/image_to_slide_key.tsv \ - resources/images/02-chapter_of_course_files \ - resources/images/03-test_cases_files \ - resources/images/04-figures_files \ - resources/chapt_screen_images \ - Course_Name.rds \ - code_of_conduct.md \ - CONTRIBUTING.md \ - docs/*.html \ - docs/*.md \ - manuscript/* - - - # Commit modified files - - name: Commit deleted files - id: commit_it - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.email "itcrtrainingnetwork@gmail.com" - git config --global user.name "jhudsl-robot" - git add . - git commit -m "Template cleanup" - pushed_it=true - git push || pushed_it=false - echo "pushed_it=$pushed_it" >> $GITHUB_OUTPUT - - # If main is already protected, then file a PR - - name: Create PR with deleted files - if: steps.commit_it.outputs.pushed_it == 'false' - uses: peter-evans/create-pull-request@v3 - id: pr - with: - commit-message: Delete unnecessary files - signoff: false - branch: auto_copy_rendered_files - delete-branch: true - title: 'Automatic course set up' - body: | - ### Description: - This PR was initiated by the github actions. It helps set up this repository to be ready to write your course. - It deletes some remnant files you don't need for your course but were used when this was a template. - labels: | - automated - reviewers: $GITHUB_ACTOR - token: ${{secrets.GH_PAT}} - -##### Filing issues! - - # Issue for what repository settings need to be set - - name: New Course - Set Repository Settings - uses: peter-evans/create-issue-from-file@v4 - with: - title: New Course - Set Repository Settings - content-filepath: .github/automatic-issues/set-repo-settings.md - labels: automated training issue - - # Issue for what needs to be edited - - name: New Course - Templates to Edit - uses: peter-evans/create-issue-from-file@v4 - with: - title: New Course - Templates to Edit - content-filepath: .github/automatic-issues/templates-to-edit.md - labels: automated training issue - - # Issue for how to enroll repo for updates - - name: New Course - Template Update Enrollment - uses: peter-evans/create-issue-from-file@v4 - with: - title: New Course - Template Update Enrollment - content-filepath: .github/automatic-issues/update-enrollment.md - labels: automated training issue - - # Issue for adding a method of feedback - - name: Reminder - Add a method of user feedback - uses: peter-evans/create-issue-from-file@v4 - with: - title: Reminder - Add user feedback method - content-filepath: .github/automatic-issues/add-feedback-method.md - labels: automated training issue - - - name: Get organization name - id: get_org_name - run: | - org_name=$(dirname ${{github.repository}}) - echo "org_name=$org_name" >> $GITHUB_OUTPUT - echo $org_name - - # Issue for adding the course to the jhudsl library - - name: Reminder - Add to jhudsl library - if: ${{ steps.get_org_name.outputs.org_name == 'jhudsl' }} - uses: peter-evans/create-issue-from-file@v4 - with: - title: Reminder - Add to jhudsl library - content-filepath: .github/automatic-issues/add-to-library.md - labels: automated training issue diff --git a/.github/workflows/test-send-updates.yml b/.github/workflows/test-send-updates.yml deleted file mode 100644 index 61e6b71..0000000 --- a/.github/workflows/test-send-updates.yml +++ /dev/null @@ -1,40 +0,0 @@ -# Candace Savonen Aug 2021 - -name: Test Sync Files - -on: - workflow_dispatch: - inputs: - repo: - description: 'What repo to test on e.g. jhudsl/OTTR_Template_Test' - required: true - default: 'jhudsl/OTTR_Template_Test' - -jobs: - test-sync: - runs-on: ubuntu-latest - container: - image: jhudsl/base_ottr:main - - steps: - - name: Checkout Repository - uses: actions/checkout@master - - - name: Login as github actions bot - run: | - git config --global --add safe.directory $GITHUB_WORKSPACE - git config --global user.name 'github-actions[bot]' - git config --global user.email 'github-actions[bot]@users.noreply.github.com' - - - name: Set up test-sync.yml - run: | - cp .github/sync.yml .github/test-sync.yml - # Switch out repo argument - Rscript --vanilla .github/switch_sync_repo.R --repo ${{ github.event.inputs.repo }} - - - name: Run Mechanics File Sync - uses: BetaHuhn/repo-file-sync-action@v1.17.21 - with: - GH_PAT: ${{ secrets.GH_PAT }} - COMMIT_BODY: "test-run" - CONFIG_PATH: .github/test-sync.yml diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md deleted file mode 100644 index c71331e..0000000 --- a/CONTRIBUTING.md +++ /dev/null @@ -1,123 +0,0 @@ -# Want to contribute to OTTR? - -## Code of Conduct - -The [Contributor Covenant Code of Conduct can be found here](https://github.com/jhudsl/OTTR_Template/blob/main/code_of_conduct.md) - -## What are the different OTTR repositories/resources? - -Open-source Tools for Training Resources (OTTR) are a set of GitHub repositories designed to offer efficiency and flexibility in creating and maintaining training resources for courses and informatics tools. Below different repositories and resources that part of the OTTR universe are listed with brief explanations of what they do. The repositories and resources are split between "Functionality" and "Documentation" where the "Functionality" section focuses on the repositories or code that make OTTR functional; and the "Documentation" section focuses on the resources that explain how to use and maintain OTTR. - -### Functionality -#### OTTR_Template - -The [OTTR_Template repository](https://github.com/jhudsl/OTTR_Template) is a template used to create OTTR courses, specifically when you're writing one course, but publishing it in three places: (bookdown/website), Leanpub, and Coursera. If used with [a pull request model](https://www.ottrproject.org/writing_content_courses.html#about-ottr-and-pull-requests), courses built with the template will be checked for spelling errors and periodically for broken URLs, and can be previewed and automatically rendered after updates. - -#### OTTR_Quizzes - -The [OTTR_Quizzes repository](https://github.com/jhudsl/OTTR_Quizzes) can be used when you want your course quizzes to remain private rather being housed in a public, open source repository. Use of this repository is in conjunction with the main OTTR_Template. All edits and additions to non-quiz content should take place - -#### OTTR_Template_Website - -The [OTTR_Template_Website repository](https://github.com/jhudsl/OTTR_Template_Website) is a template used to create OTTR websites. Like the main OTTR_Template, if used with [a pull request model](https://www.ottrproject.org/writing_content_courses.html#about-ottr-and-pull-requests), websites built with the template will be checked for spelling errors and periodically for broken URLs, and can be previewed and automatically rendered after updates. Unlike the main OTTR_Template, it only produces a website as output. - -#### ottr-reports - -The [ottr-reports repository](https://github.com/jhudsl/ottr-reports) houses the functionality for reporting the results of the GitHub Action checks on spelling, URLs, and quiz formatting. - -#### ottr-docker - -The [ottr_docker repository](https://github.com/jhudsl/ottr_docker) holds the Dockerfiles for docker images available for use with OTTR. - -#### ottrpal - -The [ottrpal repository](https://github.com/jhudsl/ottrpal) provides the functionality to convert an OTTR course to files ready for use in Leanpub and Coursera - -#### cow - -The [cow repository](https://github.com/jhudsl/cow) isn't officially an OTTR repository, but is a GitHub API wrapper in R which has additional functions to help wrangle GitHub published courses like OTTR courses. - -### Documentation - -#### ottrproject.org - -The [ottrproject.org repository](https://github.com/jhudsl/ottrproject.org) renders the [OTTR documentation website](https://www.ottrproject.org/). The repository is generated from the [OTTR_Template_Website template](https://github.com/jhudsl/OTTR_Template_Website). - -#### OTTR paper - -There's an [OTTR paper](https://pubmed.ncbi.nlm.nih.gov/37207236/) published in the Journal of Statistics and Data Science Education by C. Savonen, C. Wright, A. Hoffman, et al. in 2023. [For information on citing the manuscript, see here](https://www.ottrproject.org/index.html#how-to-cite-ottr) - -#### Cheatsheets - -TBA - -#### Videos - -TBA - -## How should you suggest changes or alert us about problems? - -There are various ways in which you can request or suggest changes to OTTR. Below we discuss ways in which you can make suggestions or requests, but leave the implementation to others or implement the suggestions yourselves. - -### You want to make suggestions, but leave the implementation to someone else - -If you want to alert us about an issue or make suggestions, you can open a GitHub Issue or submit a response in our [OTTR Feedback Google Form](https://forms.gle/jGQnd5oemHWyuUq28). - -If you aren't sure what repository the suggestion pertains to -- or if the suggestion pertains to multiple repositories file it to the [`OTTR_Template` repo](https://github.com/jhudsl/OTTR_Template/issues/new/choose). - -#### GitHub Issues - -Open an issue describing the bug or feature request for the relevant repository using the following links. - -| Repository | Issues Link | -|:---------------------:|:---------------------------------------------------------------------------:| -| OTTR_Template | [Open an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose) | -| OTTR_Quizzes | [Open an issue here](https://github.com/jhudsl/OTTR_Quizzes/issues/new/choose) | -| OTTR_Template_Website | [Open an issue here](https://github.com/jhudsl/OTTR_Template_Website/issues/new/choose)| -| ottr-reports | [Open an issue here](https://github.com/jhudsl/ottr-reports/issues/new/choose) | -| ottr-docker | [Open an issue here](https://github.com/jhudsl/ottr_docker/issues/new/choose) | -| ottrpal | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose) | -| cow | [Open an issue here](https://github.com/jhudsl/cow/issues/new/choose) | -| ottrproject.org | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose) | - -##### Description of choices for issue type (if given) - -Most of the links above will directly open an issue for you to fill out a description of the problem or request, but several of the repositories provide choices (and related description templates) for the type of issue you want to open. Those choices could include the following: - -* **Feature Request** or **Course Template Feature Request**: Use this issue if you want to make a suggestion for an addition. -* **Problem Report** or **Course Template Problem Report**: Use this issue if you want to report a problem or possible improvement. -* **New Content Idea**: This is a template meant for opening an issue in an OTTR course, so that someone can suggest an additional topic or idea for that specific course. It can be used for general suggestions for content. -* **Course Problem Report**: This is a template meant for opening an issue in an OTTR course, so that someone can point out a problem or suggest an improvement for that specific course. It shouldn't be used for opening an issue in one of these repos. - -##### Assign an OTTR maintainer - -Assign an OTTR maintainer (`@cansavvy` or `@carriewright11` or `@avahoffman`) to the issue. If you aren't sure who the issue pertains to, assign `@cansavvy` and she'll make sure it gets to the right person. - -#### Google Form - -This [OTTR Feedback Google Form](https://docs.google.com/forms/d/e/1FAIpQLSfcc_h1MPfCOWyQup4Z76lzlBGz8cAkDQmBiqfxqOZ4_4lCkQ/viewform) can be used to ask questions about any problems you encounter or submit feedback such as ideas or requests for improvements. - -### You want to make suggestions, and implement them yourself! - -If you want to implement an improvement or fix a problem, open a branch, make the changes to the code there, and then open a pull request. [See this chapter "Using Version Control with GitHub"](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/using-version-control-with-github.html) from our Advanced Reproducibility course for more information on this pull request model if needed. - -#### Request Review - -Make sure to request review of your pull request from an OTTR maintainer (`@cansavvy` or `@carriewright11` or `@avahoffman`). - -## What if you want to make several courses with similar branding using OTTR? - -If you plan to use the OTTR template several times for related courses within an organization and want each to have a shared branding or functionality variation, you may want to make your own template from the OTTR_Template, incorporating the stylistic changes in your spinoff template before making specific courses from the spinoff template. - -OTTR_Template --> Spinoff_Template (Make stylistic changes, mark as a template repository) --> Course Repository - -Examples that have done this include: - -| Spinoff template | Link | -|:------------------:|:-------------------------------------------------------------------------:| -| AnVIL Template | [GitHub Source Code](https://github.com/jhudsl/AnVIL_Template) | -| DataTrail Template | [GitHub Source Code](https://github.com/datatrail-jhu/DataTrail_Template) | -|Quarto website| [GitHub Source Code](https://github.com/fhdsl/OTTR_Quarto)| -|Metric collection dashboard template| [GitHub Source Code](https://github.com/fhdsl/metricminer-dashboard)| - -If you are interested in this and have questions, reach out to the OTTR maintainers by filing a GitHub issue and assigning `@cansavvy`, `@carriewright11`, and `@avahoffman`. diff --git a/Course_Name.rds b/Course_Name.rds deleted file mode 100644 index 561ed0d..0000000 Binary files a/Course_Name.rds and /dev/null differ diff --git a/README.md b/README.md index 8c59ad3..1c9ccdf 100644 --- a/README.md +++ b/README.md @@ -1,32 +1,24 @@ -## OTTR for Courses! +# {Course Name} -Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada: +This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template). -The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_. +You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.} -_This template and guide helps you_: +If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/). -- Edit and write a course in [RMarkdown files](https://rmarkdown.rstudio.com/) and have it published to multiple different platforms: - - [Leanpub](https://leanpub.com/bookstore?type=course) - - [Bookdown](https://bookdown.org/) - - [Coursera](https://www.coursera.org/) -- Have [Github action robots](https://www.ottrproject.org/customize-robots.html) do your repetitive tasks like spell check and re-rendering. -- Use [automagic conversion](https://github.com/jhudsl/ottrpal) to ease the lift of prepping the material for different platforms' formats. -- Use [our Docker image](https://hub.docker.com/repository/docker/jhudsl/base_ottr) for consistency across authors as well as to help you [avoid dependency hell](https://en.wikipedia.org/wiki/Dependency_hell). +## About this course -[See the OTTR pre-print here!](https://arxiv.org/abs/2203.07083) +This course introduces {info on what this course introduces} - +## Learning Objectives -## Courses that have been made using this template: -- [Documentation and Usability](https://jhudatascience.org/Documentation_and_Usability/) -- [Leadership for Cancer Informatics Research](https://jhudatascience.org/Informatics_Research_Leadership/) -- [Reproducibility in Cancer Informatics](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/) -- [Advanced Reproducibility in Cancer Informatics](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/) +This course will teach learners to: -## To Get Started -- Go to the [ottrproject.org](https://www.ottrproject.org/). -- Check out the [rendered version of the template](https://jhudatascience.org/OTTR_Template/). -- Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform. -- Please take a look at the [code of conduct](./code_of_conduct.md). -- If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated. +- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here} +- {More learning objectives} + +## Encountering problems? + +If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}. + +Creative Commons License
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise. diff --git a/code_of_conduct.md b/code_of_conduct.md deleted file mode 100644 index c4b61f6..0000000 --- a/code_of_conduct.md +++ /dev/null @@ -1,130 +0,0 @@ - -# Contributor Covenant Code of Conduct - -## Our Pledge - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, -nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -## Our Standards - -Examples of behavior that contributes to a positive environment for our -community include: - -* Demonstrating empathy and kindness toward other people -* Being respectful of differing opinions, viewpoints, and experiences -* Giving and gracefully accepting constructive feedback -* Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -* Focusing on what is best not just for us as individuals, but for the - overall community - -Examples of unacceptable behavior include: - -* The use of sexualized language or imagery, and sexual attention or - advances of any kind -* Trolling, insulting or derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or email - address, without their explicit permission -* Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Enforcement Responsibilities - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -## Scope - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to Jeff Leek at jtleek@hey.com. -All complaints will be reviewed and investigated promptly and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -## Enforcement Guidelines - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -### 1. Correction - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -### 2. Warning - -**Community Impact**: A violation through a single incident or series -of actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or -permanent ban. - -### 3. Temporary Ban - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -### 4. Permanent Ban - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within -the community. - -## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], -version 2.0, available at -[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0]. - -Community Impact Guidelines were inspired by -[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. - -For answers to common questions about this code of conduct, see the FAQ at -[https://www.contributor-covenant.org/faq][FAQ]. -Translations are available at [https://www.contributor-covenant.org/translations][translations]. - -[homepage]: https://www.contributor-covenant.org -[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html -[Mozilla CoC]: https://github.com/mozilla/diversity -[FAQ]: https://www.contributor-covenant.org/faq -[translations]: https://www.contributor-covenant.org/translations diff --git a/docs/01-intro.md b/docs/01-intro.md deleted file mode 100644 index 7fe3484..0000000 --- a/docs/01-intro.md +++ /dev/null @@ -1,99 +0,0 @@ - - - -# Introduction - - -## Motivation - - -## Target Audience - -The course is intended for ... - -## Curriculum - -The course covers... - - - -``` r -devtools::session_info() -``` - -``` -## ─ Session info ─────────────────────────────────────────────────────────────── -## setting value -## version R version 4.3.2 (2023-10-31) -## os Ubuntu 22.04.4 LTS -## system x86_64, linux-gnu -## ui X11 -## language (EN) -## collate en_US.UTF-8 -## ctype en_US.UTF-8 -## tz Etc/UTC -## date 2024-06-26 -## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) -## -## ─ Packages ─────────────────────────────────────────────────────────────────── -## package * version date (UTC) lib source -## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0) -## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) -## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) -## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) -## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) -## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) -## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) -## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) -## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) -## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) -## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) -## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) -## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) -## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) -## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) -## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) -## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0) -## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) -## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) -## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) -## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) -## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) -## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) -## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) -## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) -## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0) -## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f) -## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) -## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) -## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) -## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) -## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) -## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) -## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) -## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) -## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) -## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) -## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) -## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) -## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) -## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) -## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) -## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) -## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) -## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) -## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) -## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) -## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) -## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) -## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) -## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) -## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) -## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) -## -## [1] /usr/local/lib/R/site-library -## [2] /usr/local/lib/R/library -## -## ────────────────────────────────────────────────────────────────────────────── -``` diff --git a/docs/02-chapter_of_course.md b/docs/02-chapter_of_course.md deleted file mode 100644 index 49e0cd6..0000000 --- a/docs/02-chapter_of_course.md +++ /dev/null @@ -1,369 +0,0 @@ - -# A new chapter - -If you haven't yet read the getting started Wiki pages; [start there](https://www.ottrproject.org/getting_started.html). - -To see the rendered version of this chapter and the rest of the template, see here: https://jhudatascience.org/OTTR_Template/. - -Every chapter needs to start out with this chunk of code: - - - - -## Learning Objectives - -Every chapter also needs Learning objectives that will look like this: - -This chapter will cover: - -- {You can use https://tips.uark.edu/using-blooms-taxonomy/ to define some learning objectives here} -- {Another learning objective} - -## Libraries - -For this chapter, we'll need the following packages attached: - -*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). - - -``` r -library(magrittr) -``` - -## Topic of Section - -You can write all your text in sections like this, using `##` to indicate a new header. you can use additional pound symbols to create lower levels of headers. - -See [here](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf) for additional general information about how you can format text within R Markdown files. In addition, see [here](https://pandoc.org/MANUAL.html#pandocs-markdown) for more in depth and advanced options. - -### Subtopic - -Here's a subheading (using three pound symbols) and some text in this subsection! - -## Code examples - -You can demonstrate code like this: - - -``` r -output_dir <- file.path("resources", "code_output") -if (!dir.exists(output_dir)) { - dir.create(output_dir) -} -``` - -And make plots too: - - -``` r -hist_plot <- hist(iris$Sepal.Length) -``` - -![](resources/images/02-chapter_of_course_files/figure-docx/unnamed-chunk-4-1.png) - -You can also save these plots to file: - - -``` r -png(file.path(output_dir, "test_plot.png")) -hist_plot -``` - -``` -## $breaks -## [1] 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 -## -## $counts -## [1] 5 27 27 30 31 18 6 6 -## -## $density -## [1] 0.06666667 0.36000000 0.36000000 0.40000000 0.41333333 0.24000000 0.08000000 -## [8] 0.08000000 -## -## $mids -## [1] 4.25 4.75 5.25 5.75 6.25 6.75 7.25 7.75 -## -## $xname -## [1] "iris$Sepal.Length" -## -## $equidist -## [1] TRUE -## -## attr(,"class") -## [1] "histogram" -``` - -``` r -dev.off() -``` - -``` -## png -## 2 -``` - -## Image example - -How to include a Google slide. It's simplest to use the `ottrpal` package: - - -![](resources/images/02-chapter_of_course_files/figure-docx//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png){width=100%} - -But if you have the slide or some other image locally downloaded you can also use HTML like this: - -Major point!! example image - -## Video examples -You may also want to embed videos in your course. If alternatively, you just want to include a link you can do so like this: - -Check out this [link to a video](https://www.youtube.com/embed/VOCYL-FNbr0) using markdown syntax. - -### Using `knitr` - -To embed videos in your course, you can use `knitr::include_url()` like this: -Note that you should use `echo=FALSE` in the code chunk because we don't want the code part of this to show up. If you are unfamiliar with [how R Markdown code chunks work, read this](https://rmarkdown.rstudio.com/lesson-3.html). - - - - -### Using HTML - - - -### Using `knitr` - - - -### Using HTML - - - -## Website Examples - -Yet again you can use a link to a website like so: - -[A Website](https://yihui.org) - -You might want to have users open a website in a new tab by default, especially if they need to reference both the course and a resource at once. - -[A Website](https://yihui.org){target="_blank"} - -Or, you can embed some websites. - -### Using `knitr` - -This works: - - - - -### Using HTML - - - - -If you'd like the URL to show up in a new tab you can do this: - -``` -LinkedIn -``` - -## Citation examples - -We can put citations at the end of a sentence like this [@rmarkdown2021]. -Or multiple citations [@rmarkdown2021, @Xie2018]. - -but they need a ; separator [@rmarkdown2021; @Xie2018]. - -In text, we can put citations like this @rmarkdown2021. - -## Stylized boxes - -Occasionally, you might find it useful to emphasize a particular piece of information. To help you do so, we have provided css code and images (no need for you to worry about that!) to create the following stylized boxes. - -You can use these boxes in your course with either of two options: using HTML code or Pandoc syntax. - -### Using `rmarkdown` container syntax - -The `rmarkdown` package allows for a different syntax to be converted to the HTML that you just saw and also allows for conversion to LaTeX. See the [Bookdown](https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html) documentation for more information [@Xie2020]. Note that Bookdown uses Pandoc. - - -``` -::: {.notice} -Note using rmarkdown syntax. - -::: -``` - -::: {.notice} -Note using rmarkdown syntax. - -::: - -As an example you might do something like this: - -::: {.notice} -Please click on the subsection headers in the left hand -navigation bar (e.g., 2.1, 4.3) a second time to expand the -table of contents and enable the `scroll_highlight` feature -([see more](introduction.html#scroll-highlight)) -::: - - -### Using HTML - -To add a warning box like the following use: - -``` -
-Followed by the text you want inside -
-``` - -This will create the following: - -
- -Followed by the text you want inside - -
- -Here is a `
` box: - -
- -Note text - -
- -Here is a `
` box: - -
- -GitHub text - -
- - -Here is a `
` box: - -
- -dictionary text - -
- - -Here is a `
` box: - -
- -reflection text - -
- - -Here is a `
` box: - -
- -Work in Progress text - -
- - -## Dropdown summaries - -
You can hide additional information in a dropdown menu -Here's more words that are hidden. -
- -## Print out session info - -You should print out session info when you have code for [reproducibility purposes](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html). - - -``` r -devtools::session_info() -``` - -``` -## ─ Session info ─────────────────────────────────────────────────────────────── -## setting value -## version R version 4.3.2 (2023-10-31) -## os Ubuntu 22.04.4 LTS -## system x86_64, linux-gnu -## ui X11 -## language (EN) -## collate en_US.UTF-8 -## ctype en_US.UTF-8 -## tz Etc/UTC -## date 2024-06-26 -## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) -## -## ─ Packages ─────────────────────────────────────────────────────────────────── -## package * version date (UTC) lib source -## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0) -## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) -## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) -## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) -## curl 5.2.0 2023-12-08 [1] RSPM (R 4.3.0) -## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) -## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) -## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) -## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) -## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) -## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) -## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) -## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) -## highr 0.10 2022-12-22 [1] RSPM (R 4.3.0) -## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) -## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) -## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) -## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) -## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0) -## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) -## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) -## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) -## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) -## magrittr * 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) -## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) -## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) -## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) -## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0) -## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f) -## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) -## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) -## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) -## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) -## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) -## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) -## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) -## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) -## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) -## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) -## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) -## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) -## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) -## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) -## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) -## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) -## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) -## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2) -## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) -## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) -## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) -## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) -## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) -## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) -## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) -## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) -## -## [1] /usr/local/lib/R/site-library -## [2] /usr/local/lib/R/library -## -## ────────────────────────────────────────────────────────────────────────────── -``` - -[many links]: https://github.com/jhudsl/OTTR_Template diff --git a/docs/404.html b/docs/404.html deleted file mode 100644 index 4b2d9ea..0000000 --- a/docs/404.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - Page not found | Course Name - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Page not found

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The page you requested cannot be found (perhaps it was moved or renamed).

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You may want to try searching to find the page's new location, or use -the table of contents to find the page you are looking for.

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- All illustrations CC-BY. -
- All other materials CC-BY unless noted otherwise. -
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- - - - - - - - - - - - - diff --git a/docs/About.md b/docs/About.md deleted file mode 100644 index 362165b..0000000 --- a/docs/About.md +++ /dev/null @@ -1,125 +0,0 @@ - -# About the Authors {-} - -These credits are based on our [course contributors table guidelines](https://www.ottrproject.org/more_features.html#giving-credits-to-contributors). - -  -  - -|Credits|Names| -|-------|-----| -|**Pedagogy**|| -|Lead Content Instructor(s)|[FirstName LastName]| -|Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved| Delivered the course in some way - video or audio| -|Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved | If any other authors besides lead instructor| -|Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved| Wrote less than a chapter| -|Content Editor(s)/Reviewer(s) | Checked your content| -|Content Director(s) | Helped guide the content direction| -|Content Consultants (include chapter name/link in parentheses or word "General") - make new line if more than one chapter involved | Gave high level advice on content| -|Acknowledgments| Gave small assistance to content but not to the level of consulting | -|**Production**|| -|Content Publisher(s)| Helped with publishing platform| -|Content Publishing Reviewer(s)| Reviewed overall content and aesthetics on publishing platform| -|**Technical**|| -|Course Publishing Engineer(s)| Helped with the code for the technical aspects related to the specific course generation| -|Template Publishing Engineers|[Candace Savonen], [Carrie Wright], [Ava Hoffman]| -|Publishing Maintenance Engineer|[Candace Savonen]| -|Technical Publishing Stylists|[Carrie Wright], [Ava Hoffman], [Candace Savonen]| -|Package Developers ([ottrpal]) [Candace Savonen], [John Muschelli], [Carrie Wright]| -|**Art and Design**|| -|Illustrator(s)| Created graphics for the course| -|Figure Artist(s)| Created figures/plots for course| -|Videographer(s)| Filmed videos| -|Videography Editor(s)| Edited film| -|Audiographer(s)| Recorded audio| -|Audiography Editor(s)| Edited audio recordings| -|**Funding**|| -|Funder(s)| Institution/individual who funded course including grant number| -|Funding Staff| Staff members who help with funding| - -  - - -``` -## ─ Session info ─────────────────────────────────────────────────────────────── -## setting value -## version R version 4.3.2 (2023-10-31) -## os Ubuntu 22.04.4 LTS -## system x86_64, linux-gnu -## ui X11 -## language (EN) -## collate en_US.UTF-8 -## ctype en_US.UTF-8 -## tz Etc/UTC -## date 2024-06-26 -## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) -## -## ─ Packages ─────────────────────────────────────────────────────────────────── -## package * version date (UTC) lib source -## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) -## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) -## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) -## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) -## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) -## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) -## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) -## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) -## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) -## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) -## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) -## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) -## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) -## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) -## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) -## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) -## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) -## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) -## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) -## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) -## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) -## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) -## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) -## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) -## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) -## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) -## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) -## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) -## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) -## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) -## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) -## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) -## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) -## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) -## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) -## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) -## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) -## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) -## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) -## -## [1] /usr/local/lib/R/site-library -## [2] /usr/local/lib/R/library -## -## ────────────────────────────────────────────────────────────────────────────── -``` - - - -[FirstName LastName]: link to personal website -[John Muschelli]: https://johnmuschelli.com/ -[Candace Savonen]: https://www.cansavvy.com/ -[Carrie Wright]: https://carriewright11.github.io/ -[Ava Hoffman]: https://www.avahoffman.com/ - - - -[ottrpal]: https://github.com/jhudsl/ottrpal - - diff --git a/docs/References.md b/docs/References.md deleted file mode 100644 index 98d65dc..0000000 --- a/docs/References.md +++ /dev/null @@ -1,2 +0,0 @@ - -# References diff --git a/docs/a-new-chapter.html b/docs/a-new-chapter.html deleted file mode 100644 index eded3b2..0000000 --- a/docs/a-new-chapter.html +++ /dev/null @@ -1,609 +0,0 @@ - - - - - - - Chapter 2 A new chapter | Course Name - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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This chapter will cover:

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Major point!! example image

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2.6 Video examples

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2.6.1 Using knitr

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To embed videos in your course, you can use knitr::include_url() like this: -Note that you should use echo=FALSE in the code chunk because we don’t want the code part of this to show up. If you are unfamiliar with how R Markdown code chunks work, read this.

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References

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-Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown. -
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-Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown. -
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-Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook. -
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About the Authors

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These credits are based on our course contributors table guidelines.

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- ---- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
CreditsNames
Pedagogy
Lead Content Instructor(s)FirstName LastName
Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involvedDelivered the course in some way - video or audio
Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involvedIf any other authors besides lead instructor
Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involvedWrote less than a chapter
Content Editor(s)/Reviewer(s)Checked your content
Content Director(s)Helped guide the content direction
Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involvedGave high level advice on content
AcknowledgmentsGave small assistance to content but not to the level of consulting
Production
Content Publisher(s)Helped with publishing platform
Content Publishing Reviewer(s)Reviewed overall content and aesthetics on publishing platform
Technical
Course Publishing Engineer(s)Helped with the code for the technical aspects related to the specific course generation
Template Publishing EngineersCandace Savonen, Carrie Wright, Ava Hoffman
Publishing Maintenance EngineerCandace Savonen
Technical Publishing StylistsCarrie Wright, Ava Hoffman, Candace Savonen
Package Developers (ottrpal) Candace Savonen, John Muschelli, Carrie Wright
Art and Design
Illustrator(s)Created graphics for the course
Figure Artist(s)Created figures/plots for course
Videographer(s)Filmed videos
Videography Editor(s)Edited film
Audiographer(s)Recorded audio
Audiography Editor(s)Edited audio recordings
Funding
Funder(s)Institution/individual who funded course including grant number
Funding StaffStaff members who help with funding
-

 

-
## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value
-##  version  R version 4.3.2 (2023-10-31)
-##  os       Ubuntu 22.04.4 LTS
-##  system   x86_64, linux-gnu
-##  ui       X11
-##  language (EN)
-##  collate  en_US.UTF-8
-##  ctype    en_US.UTF-8
-##  tz       Etc/UTC
-##  date     2024-06-26
-##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
-## 
-## ─ Packages ───────────────────────────────────────────────────────────────────
-##  package     * version date (UTC) lib source
-##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
-##  bslib         0.6.1   2023-11-28 [1] RSPM (R 4.3.0)
-##  cachem        1.0.8   2023-05-01 [1] RSPM (R 4.3.0)
-##  cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
-##  devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
-##  digest        0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
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About this Course

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0.1 Available course formats

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This course is available in multiple formats which allows you to take it in the way that best suites your needs. You can take it for certificate which can be for free or fee.

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Chapter 1 Introduction

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1.1 Motivation

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1.2 Target Audience

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The course is intended for …

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1.3 Curriculum

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The course covers…

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devtools::session_info()
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Chapter 3 References

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-Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown. -
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Chapter 3 Topic of Section

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3.1 Subtopic

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References

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-Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown. -
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