Deterministic submission companion documents — submission-companions • popgenVCF

Creates, validates, renders, and checksum-verifies cover letters, highlights, and author declaration summaries without changing canonical manuscript content.

Usage

new_submission_companions(manuscript, journal = NULL, editor = NULL,
  significance = NULL, novelty = NULL, highlights = character(),
  suggested_reviewers = NULL, opposed_reviewers = NULL,
  confirmations = list(), max_highlights = 5L,
  max_highlight_characters = 125L)

validate_submission_companions(x, strict = TRUE)

write_submission_companions(companions, directory, overwrite = FALSE,
  strict = FALSE)

Arguments

manuscript: A canonical PopgenVCFManuscript object supplying the title, authors, corresponding-author metadata, and declarations.
journal: Optional target journal name supplied by the author. Missing values are retained as visible placeholders.
editor: Optional handling-editor name or salutation supplied by the author.
significance: Optional author-written statement describing the manuscript's significance. The function never generates this claim automatically.
novelty: Optional author-written statement describing the manuscript's novelty. The function never generates this claim automatically.
highlights: Character vector of author-supplied manuscript highlights in submission order.
suggested_reviewers: Optional reviewer records supplied by the author, including names and any available affiliation, email, or rationale fields.
opposed_reviewers: Optional records identifying reviewers the authors request be excluded, with author-supplied reasons.
confirmations: Named list of explicit author confirmations, such as originality, author approval, or absence of simultaneous submission.
max_highlights: Maximum permitted number of highlight entries.
max_highlight_characters: Maximum permitted character count for each highlight.
x: A PopgenVCFSubmissionCompanions object to validate.
strict: Logical flag. In strict mode, missing required author inputs and placeholders cause validation to fail; permissive mode reports them without failing.
companions: A validated PopgenVCFSubmissionCompanions object to write.
directory: Destination directory in which the isolated companions/ output is created.
overwrite: Logical flag controlling replacement of an existing companion-document output directory.

Value

new_submission_companions() returns a PopgenVCFSubmissionCompanions object. Validation returns TRUE invisibly. Writing returns the normalized output directory invisibly.