[smasongarrison]

This pull request significantly updates the vignettes/plots.Rmd vignette to use synthetic data and new variable names, shifting the focus from socioeconomic status (SES) and flu vaccinations to "Behavior" and "depressiveness" in kinship pairs. The code and narrative are revised throughout to reflect this new context, including data loading, processing, variable naming, and plot labeling. The changes also streamline the workflow by using synthetic datasets and the discord_data() function for data generation and preparation.

Key changes include:

1. Data Source and Structure Updates

• Replaces the NLSY79 flu/SES data with synthetic datasets (mz_signif, mz_nonsignif) and generates discordant kin data using discord_data(), focusing on "Behavior" and "depressiveness" as the primary variables. [1] [2]
• Updates all data preparation and cleaning steps to use these new variables and data structures, removing references to the original SES/flu variables. [1] [2]

2. Variable and Grouping Name Refactoring

• Renames variables and grouping factors throughout the code and text, e.g., s00_h40_mean → Behavior_mean, flu_total_mean → depressiveness_mean, ses_diff_group → mom_diff_group, to match the new synthetic data context. [1] [2]

3. Plot and Label Updates

• Revises all plot code to use the new variable names and updates plot titles, axis labels, and legends to refer to "Behavior" and "depressiveness" instead of SES and flu vaccinations. [1] [2] [3] [4] [5] [6] [7] [8]

4. Narrative and Documentation Alignment

• Updates the vignette text to explain the new variables, describe the synthetic data, and clarify the interpretation of plots in terms of "Behavior" and "depressiveness" differences between kin, rather than SES and flu. [1] [2] [3] [4]

5. Code Cleanup and Output Enhancements

• Removes obsolete code related to the original data and adds code to save generated plots as PNG files for documentation purposes.

These changes modernize the vignette, making it more generalizable and focused on illustrating patterns in synthetic kinship data using the discord_data() workflow.

[codacy-production]

Up to standards ✅

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.20%. Comparing base (86513d1) to head (1625811).

Additional details and impacted files

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##             main      #58   +/-   ##
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  Coverage   91.20%   91.20%           
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  Files           7        7           
  Lines         853      853           
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  Hits          778      778           
  Misses         75       75           

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