Canonical core analysis result objects — core

Creates, validates, adapts, tabulates, serializes, and restores stable canonical result objects for PCA, IBS/MDS, neighbour-joining trees, diversity, FST, AMOVA, DAPC, and isolation-by-distance analyses.

Usage

new_core_result(analysis, payload, parameters = list(), provenance = list(),
  metadata = NULL, validation = NULL,
  artifacts = new_artifact_manifest(), class_name = NULL)

validate_core_result(x)

new_pca_result(coordinates, eigenvalues, ...)
new_ibs_result(similarity, distance = 1 - similarity, mds = NULL, ...)
new_tree_result(tree, distances = NULL, ...)
new_diversity_result(statistics, ...)
new_fst_result(global_fst, pairwise, confidence_intervals = NULL, ...)
new_amova_result(components, statistics = NULL, ...)
new_dapc_result(coordinates, assignments = NULL, discriminant = NULL, ...)
new_ibd_result(distances, mantel_statistic, p_value = NA_real_,
  permutations = NA_integer_, ...)

as_core_result(analysis, x, parameters = list(), provenance = list(),
  metadata = NULL, validation = NULL, artifacts = new_artifact_manifest())

core_result_table(x)
save_core_result(x, path)
read_core_result(path)
# S3 method for class 'PopgenVCFCoreResult'
print(x, ...)

Arguments

analysis: Stable analysis identifier.
payload: Named list containing analysis-specific statistical results.
parameters: Named list of analysis parameters.
provenance: Named list describing software, inputs, commands, and runtime.
metadata: Optional sample or population metadata data frame.
validation: Optional data frame containing check and passed.
artifacts: A PopgenVCFArtifactManifest.
class_name: Optional analysis-specific S3 class name.
x: A canonical result, or an existing analysis output for adaptation.
coordinates: Sample coordinate data frame containing sample_id.
eigenvalues: Numeric PCA eigenvalues.
similarity: Symmetric IBS similarity matrix.
distance: Symmetric IBS-derived distance matrix.
mds: Optional MDS coordinates.
tree: Neighbour-joining or other tree representation.
distances: Optional tree distances, or an IBD pairwise-distance data frame.
statistics: Analysis statistics or optional AMOVA statistics.
global_fst: Finite global FST estimate.
pairwise: Pairwise FST data frame.
confidence_intervals: Optional FST confidence intervals.
components: AMOVA variance-component data frame.
assignments: Optional DAPC assignments.
discriminant: Optional DAPC discriminant model.
mantel_statistic: Finite Mantel statistic.
p_value: Optional Mantel permutation p-value.
permutations: Optional number of Mantel permutations.
path: RDS file path.
...: Additional arguments passed to new_core_result().

Value

Constructors and adapters return a validated analysis-specific object inheriting from PopgenVCFCoreResult. core_result_table() returns a data table, save_core_result() returns the path invisibly, and read_core_result() returns a validated canonical result.