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Get Hopping with froggeR

Source: vignettes/hopping-into-quarto.Rmd
hopping-into-quarto.Rmd

Introduction

froggeR streamlines Quarto workflows by providing a robust, user-friendly framework for project setup and document creation. Leverage Quarto branding within your projects with froggeR’s added functionality. This vignette demonstrates how froggeR can enhance your productivity while maintaining project consistency.

# Install from GitHub
install.packages("kyleGrealis/froggeR")

Core Features

Project setup often involves repetitive tasks that can impede your analysis workflow. froggeR addresses this by providing:

  • Automated project initialization with quarto_project()
  • Reusable project configurations through settings()
  • Replicate Quarto project brand styling with write_brand() and save_brand()
  • Configurable document templates via write_quarto()
  • Consistent styling with write_scss()
  • Enhanced version control setup
  • Easily add project documentation templates to any existing project, even those not initialized by froggeR.

SPOILER ALERT!!

All of the components listed below are available when you begin your Quarto projects with:

froggeR::quarto_project()

Save time on building a project structure, formatting, branding, and trying to redo that super awesome YAML you did a few weeks back. Start with froggeR now and get yourself dialed in for all future projects!

Quick Start Guide

Create a new Quarto project with a single command:

>> froggeR::quarto_project(name = "frogs")
This will create a new Quarto default project as a folder named frogs in
/home/kyle.
Do you want to proceed (Y/n)? 
Y
✔ Created Quarto project directory: frogs
✔ Created _quarto.yml
ℹ Copying existing froggeR settings...
✔ Created _variables.yml
ℹ Copying existing froggeR brand settings...
✔ Created _brand.yml
✔ Copying existing froggeR logos.
✔ Created custom.scss
✔ Created .gitignore
✔ Created README.md
✔ Created dated_progress_notes.md
✔ Created frogs.qmd with examples
✔ Created references.bib
✔ froggeR project setup complete. Opening in new session...

This command initializes a complete project structure with all necessary components:

Project Components

  1. Quarto Document
    • Pre-configured YAML header
    • Examples for adding brand logo, HTML in-document cross-references, and HTML links
    • Example for adding citations and references
  2. Style Sheet
    • Modern design elements
    • Customizable components
    • Clear documentation
  3. Project Configuration
    • _quarto.yml that is enhanced to simplify individual Quarto file YAML by centralizing document options. These can be changed on a per-document basis as well.
    • _variables.yml for consistent user metadata
    • _brand.yml for consistent project branding metadata
    • .gitignore for secure version control

When you start your first Quarto project with froggeR, you’re choosing fast & efficient templating over tedious replication of project documents. froggeR provides the ability to create project-level metadata (stored in _quarto.yml, _variables.yml, and _brand.yml files). This metadata allows users to reproduce a consistent structure & style across many Quarto projects. The _quarto.yml file serves as a central project structure file where you can set project-level Quarto document defaults such as toggling familiar rendering settings (i.e., format options, code-tools, page-layout).

You can then reuse personal metadata by modifying the _variables.yml file. These values are then used by _quarto.yml where the name value in _variables.yml is pulled into the project YAML as name: "{{< var name >}}". When you render the document, your actual name is displayed in the output. Adding your email, a personal or company URL, or your ORCID is just the same – the _variables.yml file is composed of key:value pairs. You can also create & use variables if you follow the format.

Now, this may seem like a lot of work for a basic Quarto project. You may be correct since the first project will take an extra few minutes of populating the _variables.yml file with your information and adjusting the _quarto.yml for project-level settings. However, once you froggeR::save_variables(), all of this work will be replicated immediately the next time you use froggeR to create your Quarto projects!

I’m sure you can envision many more ways to use metadata to your advantage. This isn’t a “froggeR-thing”… the great team working on Quarto is to thank!

Note: Deleting key:value pairs in the _variables.yml file requires you to also remove the corresponding fields in the _quarto.yml. It is recommended to comment out or leave blank the fields in _variables.yml that are not needed.

See vignette("customizing-quarto", package = "froggeR") for more detailed configuration options.

Customization

Document Settings

You may choose to setup your froggeR metadata before creating your first project.

Manage your document settings with the interactive configuration tool (see ?froggeR::settings for all options):

# Check, display, or update your settings
>> froggeR::settings()

froggeR settings options: 

1: Check for config files
2: Display current settings
3: Show how to update settings
4: Show how to reuse settings across projects
5: More information about settings

Selection: 
1

ℹ Run froggeR::write_variables() to create project-level settings.

To create and open the _variables.yml file for immediate customization, run:

# Create project-level metadata
froggeR::write_variables()

You will then see the file open with hints provided on how to fill in and use. Remember, it’s better (and safer) to leave fields blank than to delete them… but you can remove the first two comment lines.

# You do not need to use quotes around values.
# You may edit any value or leave it blank.
name: 
email: 
orcid: 
url: #https://example.com
affiliations:

Save this file then run froggeR::save_variables() to store this configuration file in your operating system’s (OS) configuration file location (i.e., in Linux, this is $HOME/.config/froggeR/config.yml). This reinforce’s froggeR’s goal to increase your effeciency now and for future projects.

These settings flow through your projects in this order:

  1. config.yml stores your permanent settings (exact location depends on your OS)
  2. froggeR reads these when creating new projects
  3. Settings populate _variables.yml in your project
  4. Quarto documents use these variables automatically
How froggeR manages settings across projects (config.yml)
How froggeR manages settings across projects (config.yml)

Note: While you can update these settings at any time, most users find they only need to set them once or very infrequently.

Congratulations! You’ve just made your next Quarto project with froggeR even easier! But how? Well, let’s have a little fun: delete the _variables.yml in your local project you just created. Don’t worry… we’ll make it reappear, but this time you will not need to reinput the value fields. Once again, run froggeR::write_variables() and voila! You should see your saved config file that matches the one you just deleted… and it’s already filled in!

This is froggeR’s main benefit: making Quarto documents and projects easier the next time too. Later we’ll see how froggeR::quarto_project() will pull this information the next time while setting up the entire project structure. You can skip ahead to the vignette, if you like.

Create a Quarto document with examples

Quickly create a Quarto document that includes examples for adding your brand logo, section and other within-document cross-references, hyperlinks, and references with froggeR::write_quarto(example = TRUE). This opens a new file with the default name of “Untitled-1.qmd”.

The template will open:

Quarto template with examples
Quarto template with examples

Visual Styling

Customize your document appearance with SCSS:

froggeR::write_scss()

This creates a custom.scss file with commented-out examples. Uncomment and modify these to customize your document’s appearance. For more information on Quarto styling, refer to:

Advanced Usage

Project Documentation

Generate comprehensive project documentation:

froggeR::write_readme()
froggeR::write_notes()

The README template was designed for academia in mind (notice the references to “PI”, or principle investigator, within the file), but is adaptable to meet your needs. There are sections for explaining how to use your project, what the directories and files contain, and created so you can focus more on creating content.

We’ve included a dated_progress_notes.md file. A study with sample size N=1 has demonstrated that this has really helped me the study participant refresh memory after a few weeks away from a project.

Best Practices

For optimal results with froggeR:

  1. Use metadata in your projects
    • Follow guide to save your metadata in the configuration file
    • Initialize projects with quarto_project() or write_quarto()
    • Review Quarto documentation to really open up your projects
  2. Project Organization
    • Use consistent naming conventions
    • Maintain clear directory structure
    • Document project changes
  3. Version Control
    • Review .gitignore settings
    • Update progress notes regularly
    • Maintain README documentation
  4. Styling
    • Test SCSS changes before implementation
    • Document custom styling decisions
    • Use variables for consistency

Troubleshooting and FAQs

Common Issues

  1. Q: My YAML isn’t rendering correctly in the Quarto document.

    A: Ensure that your _variables.yml file is properly formatted. Check for any extra spaces or incorrect indentation.

  2. Q: The SCSS styles aren’t applying to my document.

    A: Make sure the SCSS file is properly linked in your YAML header. Remember, the order of the styles sheets matters. During the initialization of froggeR::write_quarto(custom_yaml = TRUE), the custom.scss will override anything set in the default styling. The same applies if another SCSS sheet is added – it will override all SCSS files listed above it. Check the console for any error messages during rendering.

  3. Q: I’m getting an error when trying to create a new project.

    A: Ensure you have the latest version of froggeR and Quarto installed. Also, check if you have write permissions in the target directory.

Tips for Smoother Projects

  • Always review the generated files after project creation to ensure everything is set up as expected.
  • When customizing SCSS, make small changes and render frequently to see the effects.
  • Keep your froggeR settings up-to-date, especially when working across multiple projects.

For more specific issues, consult the documentation or reach out through the GitHub issue tracker.

Getting Help

Need assistance? Several resources are available:

Future Developments

froggeR is continuously evolving to meet the needs of the R and Quarto community. Some exciting features on our roadmap include:

  • Quarto Dashboard Integration: Streamlined creation and management of interactive Quarto dashboards.
  • Enhanced Version Control Integration: More robust Git integration features.
  • Expanded Customization Options: Additional templates and styling options for diverse project needs.
  • Collaborative Tools: Features to enhance team workflows and project sharing.

Stay tuned to our GitHub repository for updates and new releases. We welcome feature requests and feedback from our user community to help shape the future of froggeR!

Summary

froggeR provides a streamlined approach to Quarto project management, offering:

  • Efficient project initialization
  • Consistent document styling
  • Secure version control
  • Comprehensive documentation

Happy analyzing! 🐸

Elevating your Quarto workflow with automated excellence