Author

Affiliation

Ronald (Ryy) Glenn Thomas

UCSD

1 Guide to Building, Submitting, and Managing the zzlongplot R Package

1.1 Step 1: Setting Up the Package Structure

1. Create a New Package Directory:

   • Use usethis to create a package directory:

     usethis::create_package("path/to/zzlongplot")

   • This sets up the necessary directory structure with folders like R/ and files like DESCRIPTION.

2. Add the Core Script:
   • Place the zzlongplot.R file in the R/ directory.
3. Set Up the DESCRIPTION File:

   • Edit the DESCRIPTION file to include metadata about the package. Use usethis::use_description() to create and fill this file:

     usethis::use_description(fields = list(
       Title = "Flexible Longitudinal Plotting in R",
       Description = "Provides tools for generating observed and change plots in longitudinal datasets.",
       Version = "0.1.0",
       Author = "Your Name [aut, cre]",
       Maintainer = "Your Name <your_email@example.com>",
       License = "MIT",
       Encoding = "UTF-8"
     ))

4. Add Dependencies:

   • List package dependencies in the DESCRIPTION file under Imports. For example:

     Imports:
       dplyr,
       ggplot2,
       patchwork

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1.2 Step 2: Document the Package

1. Add Roxygen2 Comments:
   • Ensure all functions in zzlongplot.R have Roxygen2 comments for documentation.
2. Generate Documentation:

   • Run:

     devtools::document()

   • This creates help files in the man/ directory and updates the NAMESPACE file.

3. Create a Vignette:

   • Add the vignette to introduce the package:

     usethis::use_vignette("Introduction_to_zzlongplot")

   • Place the provided zzlongplot-vignette.Rmd file in the vignettes/ directory and build it:

     devtools::build_vignettes()

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1.3 Step 3: Test the Package

1. Add Unit Tests:

   • Use usethis to set up a testing framework:

     usethis::use_testthat()

   • Place the test-zzlongplot.R file in tests/testthat/.

2. Run Tests:

   • Run all tests:

     devtools::test()

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1.4 Step 4: Check the Package

1. Build and Check:

   • Build the package:

     devtools::build()

   • Check the package for CRAN compliance:

     devtools::check()

2. Fix Issues:
   • Address any warnings or errors reported by devtools::check().

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1.5 Step 5: Submit to CRAN

1. Prepare for Submission:

   • Ensure the package passes R CMD check with no warnings, errors, or notes.

   • Compress the package into a .tar.gz file using:

     devtools::build()

2. Submit to CRAN:
   • Go to the CRAN submission page.
   • Upload the .tar.gz file and fill out the required metadata.
3. Respond to Feedback:
   • CRAN maintainers might request changes. Address them promptly and resubmit if needed.

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1.6 Step 6: Set Up a GitHub Repository

1. Initialize a Git Repository:

   • In the package directory, run:

     git init
     git add .
     git commit -m "Initial commit"

2. Create a Repository on GitHub:

   • Use the GitHub website or the gh CLI tool:

     gh repo create yourusername/zzlongplot --public --source=.

3. Push the Code:

   • Push the code to GitHub:

     git branch -M main
     git push -u origin main

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1.7 Step 7: Manage the Development Repository

1. Add Version Control:

   • Use Git for version control. For example, create a branch for new features:

     git checkout -b feature-new-plot

2. Tag Releases:

   • Tag versions for releases:

     git tag -a v0.1.0 -m "First release"
     git push origin v0.1.0

3. Add Continuous Integration:

   • Set up GitHub Actions for testing:

     usethis::use_github_action_check_standard()

4. Publish Development Versions:
   • Use GitHub to manage development versions and issues.

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1.8 Step 8: Maintain the Package

1. Address Issues:
   • Monitor and address issues reported by users.
2. Update the Package:
   • For updates, increment the version number in DESCRIPTION and tag the new version.

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