Build Grammateus semantic report elements — grammateus_report

grammateus_report_element() creates a low-level Grammateus-shaped semantic report element from R data. grammateus_qc_report_elements() builds the standard floundeR QC report element set for run metadata, QC summaries, flowcell/yield/quality/barcode evidence, POD5 integrity, BAM evidence, library-preparation evidence, report-card findings, methods, limitations, appendices, and provenance. These helpers do not render HTML or PDF and do not require private Grammateus runtime assets.

Usage

grammateus_report_element(
  element_id,
  element_type = c("table", "section", "methods", "limitations", "appendix",
    "provenance"),
  title,
  caption = NULL,
  data = NULL,
  body = NULL,
  methods_note = NULL,
  source_hash = NULL,
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL
)

grammateus_qc_report_elements(
  run_metadata = NULL,
  qc_summary = NULL,
  flowcell_density = NULL,
  yield_over_time = NULL,
  quality_distribution = NULL,
  barcode_balance = NULL,
  pod5_integrity = NULL,
  bam_alignment_summary = NULL,
  bam_validation = NULL,
  bam_index = NULL,
  bam_sort = NULL,
  library_preparation = NULL,
  report_card_findings = NULL,
  methods = NULL,
  limitations = NULL,
  appendices = NULL,
  provenance = NULL,
  produced_by = "floundeR",
  producer_version = NULL,
  produced_at_utc = Sys.time(),
  run_id = NULL
)

Arguments

element_id: Stable lower-snake-case identifier with an element-type prefix such as table_, section_, methods_, limitations_, appendix_, or provenance_.
element_type: Semantic element type.
title: Human-readable element title.
caption: Required caption for table-like report elements.
data: Optional data frame or list payload.
body: Optional character body for text-like elements.
methods_note: Optional methods note.
source_hash: Optional SHA-256 hash for the source data. When omitted, a deterministic hash is computed from data and body.
produced_by: Producing software or service name.
producer_version: Producing software version.
produced_at_utc: Production timestamp.
run_id: Optional upstream run, workflow, or analysis identifier.
run_metadata, qc_summary, flowcell_density, yield_over_time, quality_distribution, barcode_balance, pod5_integrity, bam_alignment_summary, bam_validation, bam_index, bam_sort, library_preparation, report_card_findings: Optional QC evidence tables.
methods: Optional methods text.
limitations: Optional limitations table or text.
appendices: Optional named list of appendix tables or text.
provenance: Optional provenance table or list.

Value

A flounder_grammateus_report_element list, or a flounder_grammateus_report_element_bundle containing named elements.