Make sure everything passes devtools::check()

[whelena]

Description

Minor changes to pass devtools::check()

Checklist

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[Copilot]

Pull request overview

This pull request makes minor fixes to ensure the package passes devtools::check() validation. The changes correct vignette configuration, standardize graphics function parameter names, rename internal helper functions, and add missing package imports.

Changes:

• Updated vignette engine specification and output format for consistency
• Corrected parameter names in graphics device functions to match R documentation
• Renamed internal angle calculation functions for clarity
• Added missing package imports to NAMESPACE

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
vignettes/ManuscriptFigures.Rmd	Updated vignette engine to knitr::rmarkdown and changed output format to html_document for consistency with other vignettes
R/save.plot.R	Corrected parameter names from file to filename for png(), tiff(), and svg() functions to match R documentation
R/angles.R	Renamed internal functions split.equal.angle and split.equal.x.dist to divide.equal.angle and divide.equal.x.dist
NAMESPACE	Added missing imports: tail from utils, rnorm and runif from stats, and rgb from grDevices

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[tnyamaguchi]

LGTM!