update

[smasongarrison]

This pull request updates the full_data_workflow.Rmd vignette to improve reproducibility, clarity, and output formatting for the demonstration of discordant-kinship regression. The changes include switching to a synthetic dataset for analysis, enhancing table and regression output formatting, and adding explanatory text and equations to better guide users through the workflow.

Data workflow and reproducibility improvements:

• Replaces the original wide data (df_wide) with a new synthetic dataset (df_synthetic) generated from filtered cousin pairs, ensuring full reproducibility and clarity of the workflow. This includes setting a random seed and constructing new variables such as ages and weights for siblings. [1] [2] [3]
• Updates all downstream analysis steps (e.g., OLS regression, discordant regression) to use the new df_synthetic dataset instead of the original data. [1] [2] [3]

Output formatting and presentation:

• Improves table outputs throughout the vignette by specifying the number of digits and adding captions for clarity, and uses glimpse() for more informative data previews. [1] [2] [3] [4]
• Changes regression output from plain text to HTML-formatted tables using stargazer for all model summaries, improving readability and consistency. [1] [2] [3] [4]

Documentation and clarity enhancements:

• Adds LaTeX equations to clearly present regression model specifications for standard, between-family, and discordant-kinship regressions. [1] [2] [3]
• Expands explanatory text to clarify the ordering of siblings and the interpretation of discordant regression, and provides guidance on using the helper function for discordant regression.

Minor code and style cleanups:

• Standardizes the use of slice() for table previews and removes commented-out or unused code for improved readability. [1] [2] [3] [4]

These changes make the vignette more robust, user-friendly, and easier to follow for those learning or demonstrating discordant-kinship regression.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.16%. Comparing base (07287ab) to head (2acb65f).
⚠️ Report is 14 commits behind head on main.

Additional details and impacted files

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+ Coverage   88.33%   91.16%   +2.83%     
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  Files           7        7              
  Lines         840      849       +9     
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+ Hits          742      774      +32     
+ Misses         98       75      -23     

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[Copilot]

Pull Request Overview

Updates the full_data_workflow.Rmd vignette to make the discordant-kinship regression demo reproducible and clearer by switching to a synthetic dataset, improving output formatting, and adding explanatory text and equations.

• Switches analysis to a reproducible synthetic dataset generated via kinsim
• Replaces text outputs with HTML tables via stargazer and adds equations/explanations
• Cleans up table previews and standardizes formatting (digits, captions, slice)

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[Copilot]

The preceding text states 'Below we default to the long path for reproducibility,' but the code now defaults to df_synthetic. Also, the inline comment 'if you followed the pedigree path' is inaccurate for df_synthetic. Please update the prose and inline comment to reflect the new default and data source (e.g., 'synthetic data generated above').

[Copilot]

Pull Request Overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 6 comments.

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[Copilot]

sessioninfo does not export sessionInfo(); the function is session_info(). Use sessioninfo::session_info() (or utils::sessionInfo() if you intend the base function) to avoid a knit error.

Suggested change

	sessioninfo::sessionInfo()
	sessioninfo::session_info()

[Copilot]

Pull Request Overview

Copilot reviewed 24 out of 26 changed files in this pull request and generated 6 comments.

Comments suppressed due to low confidence (1)

man/discord_data.Rd:1

• The documentation sets a default for pair_identifiers (c("_s1","_s2")), but the implementation of discord_data() still requires pair_identifiers as a mandatory argument. Either add the default in the function signature or revert the Rd to reflect that it is required, to avoid confusing users and potential vignette failures if the argument is omitted.

% Generated by roxygen2: do not edit by hand

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