Publication companion bundles — publication-companion • popgenVCF

Create validated, checksummed publication companion plans and directories from reproducible popgenVCF projects without recomputing scientific analyses.

Usage

publication_style(style = "generic")

new_publication_bundle(project, style = "generic", title = project$name)

validate_publication_bundle(x)

generate_publication_bundle(
  project,
  directory,
  style = "generic",
  title = project$name,
  include_project = TRUE,
  include_fair = TRUE,
  overwrite = FALSE
)

set_project_publication_bundle(project, bundle)

Arguments

style: A built-in style identifier or custom publication profile.
project: A validated PopgenVCFProject.
title: Optional manuscript title.
x: A publication bundle plan or written directory.
directory: Output directory.
include_project: Include the portable analysis project.
include_fair: Include embedded FAIR metadata when available.
overwrite: Permit replacement of a non-empty output directory.
bundle: A validated PopgenVCFPublicationBundle.

Value

Style and plan constructors return validated objects. The generator returns the normalized publication directory invisibly. Validators return TRUE invisibly or fail with an integrity error.

Details

Built-in profiles include generic, Nature, Molecular Ecology, G3, BMC, and PLOS. Profiles control labels and citation conventions only; they do not claim full journal submission-template compliance. Scientific files are copied from the immutable artifact lineage, and every written file is protected by SHA256 in publication-manifest.tsv.