Deterministic journal submission profiles — journal-submission-profiles • popgenVCF

Creates, validates, applies, reports, renders, and writes deterministic journal submission profiles. Profiles encode explicit structural and packaging requirements without rewriting scientific content.

Usage

new_journal_profile(id = "generic", required_roles = c("manuscript_source"),
  optional_roles = character(), filenames = NULL,
  description = "Generic popgenVCF journal submission profile",
  version = "1.0", journal = description, publisher = NA_character_,
  status = c("generic", "verified", "deprecated"),
  source_url = NA_character_, source_date = NA_character_,
  required_sections = c("abstract", "introduction", "methods", "results", "discussion"),
  optional_sections = character(),
  required_declarations = c(
    "data_availability", "software_availability", "reproducibility",
    "funding", "author_contributions", "competing_interests"
  ),
  required_companions = character(), title_max_chars = NA_integer_,
  abstract_max_words = NA_integer_, keyword_min = 0L,
  keyword_max = NA_integer_, highlight_min = 0L,
  highlight_max = NA_integer_, highlight_max_chars = NA_integer_,
  graphical_abstract = FALSE, figure_max = NA_integer_,
  table_max = NA_integer_, supplementary_max = NA_integer_,
  allowed_figure_extensions = c("pdf", "png", "tif", "tiff", "svg"),
  filename_pattern = NA_character_, overrides = list())

validate_journal_profile(x)

generic_journal_profile()

journal_profile(name = c("research-article", "short-communication", "data-note"))

apply_journal_profile(plan, profile = generic_journal_profile())

validate_journal_submission(profile, manuscript, companions = NULL,
  graphical_abstract = NULL, strict = FALSE)

render_journal_profile(profile)

write_journal_profile(profile, directory, overwrite = FALSE)

Arguments

id: Stable profile identifier.
required_roles, optional_roles: Semantic submission roles.
filenames: Named role-to-filename character vector.
description: Human-readable profile description.
version: Version identifier for the encoded requirements.
journal: Journal or generic profile name.
publisher: Publisher name, when applicable.
status: Profile status: generic, verified, or deprecated.
source_url, source_date: Versioned source and verification date for named profiles.
required_sections, optional_sections: Manuscript section requirements.
required_declarations: Required declaration names.
required_companions: Required companion document names.
title_max_chars, abstract_max_words, keyword_min, keyword_max: Title, abstract, and keyword limits.
highlight_min, highlight_max, highlight_max_chars: Highlight constraints.
graphical_abstract: A logical requirement when constructing a profile, or an optional graphical abstract specification when validating a submission.
figure_max, table_max, supplementary_max: Maximum artifact counts.
allowed_figure_extensions: Allowed figure filename extensions.
filename_pattern: Optional regular expression for submission filenames.
overrides: Named author-supplied requirement overrides.
x: A journal profile or written profile directory.
name: Built-in generic profile name.
plan: A submission-plan data frame with role and destination columns.
profile: A validated journal profile.
manuscript: A validated canonical manuscript.
companions: Optional submission companion record.
strict: Whether failed requirements raise an error.
directory: Parent output directory.
overwrite: Whether an existing profile directory may be replaced.

Value

A journal profile, a profile-aware submission plan, a deterministic completeness report, Markdown text, a normalized output directory, or TRUE invisibly.