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Build and render unified population-genomics reports

population_genomics_report.Rd

Discovers available canonical analyses, orders sections deterministically, records reproducibility metadata, writes a Quarto source document, and optionally renders HTML or PDF reports. Analyses not supplied are omitted automatically.

Usage

build_population_genomics_report_plan(
  results,
  title = "Population genomics report",
  include = NULL,
  exclude = NULL
)

validate_population_genomics_report_plan(x)

write_population_genomics_report(
  results,
  output_dir,
  title = "Population genomics report",
  formats = "html",
  render = TRUE,
  include = NULL,
  exclude = NULL
)

# S3 method for class 'PopgenVCFReportPlan'
print(x, ...)

Arguments

results

A non-empty list of canonical core or ancestry result objects, or an existing PopgenVCFReportPlan.

title

Report title.

include

Optional analysis identifiers to include.

exclude

Optional analysis identifiers to omit.

x

A PopgenVCFReportPlan.

output_dir

Directory for report sources and rendered outputs.

formats

Output formats. Supported values are "html" and "pdf".

render

Render through Quarto. Set to FALSE to create the deterministic plan, section manifest, and QMD source without requiring Quarto.

...

Unused.

Value

build_population_genomics_report_plan() returns a validated PopgenVCFReportPlan. validate_population_genomics_report_plan() returns x invisibly. write_population_genomics_report() returns a list containing the plan, artifact manifest, and output paths.