Deterministic publication PCA and ordination outputs — publication_ordination

Creates and validates deterministic publication contracts around authoritative PCA and ordination results, including stable sample ordering, metadata alignment, variance tables, loadings, group centroids, source-data exports, figure-style bindings, captions, provenance, and mutation detection.

Usage

new_publication_ordination_spec(
  method = "pca",
  axis_columns = c("PC1", "PC2"),
  sample_id_column = "sample_id",
  group_column = NULL,
  region = c("none", "centroid", "ellipse", "hull"),
  labels = FALSE,
  source_data_format = "tsv",
  version = "1.0.0"
)

validate_publication_ordination_spec(spec)

new_publication_ordination_output(
  spec,
  coordinates,
  metadata = NULL,
  variance_explained = NULL,
  variance_explained_unit = c("auto", "fraction", "percent"),
  loadings = NULL,
  result_fingerprint,
  figure_binding = NULL
)

validate_publication_ordination_output(output, spec)

publication_ordination_caption(output, spec)

publication_ordination_report(output, spec)

Arguments

method: Stable PCA or ordination method name.
axis_columns: Ordered coordinate columns to publish.
sample_id_column: Coordinate and metadata sample identity column.
group_column: Optional aligned metadata grouping column.
region: Deterministic group-region policy.
labels: Whether sample labels are requested.
source_data_format: Stable machine-readable source-data format.
version: Specification version.
spec: A publication ordination specification.
coordinates: Authoritative PCA or ordination coordinates.
metadata: Optional sample metadata.
variance_explained: Optional variance proportions or percentages.
variance_explained_unit: "auto" (default) guesses fraction vs. percent from whether the published axes' values sum to at most 1 – ambiguous, and wrong, for a genuine small percentage. Pass "fraction" or "percent" explicitly when the unit is known, to bypass the guess entirely.
loadings: Optional loading matrix or data frame.
result_fingerprint: Fingerprint of the authoritative scientific result.
figure_binding: Optional publication figure-style binding.
output: A publication ordination output.

Value

Constructors return fingerprinted publication ordination records. Validators return TRUE invisibly. Caption and report functions return deterministic character output.