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Infer Salmon Data Package artifacts from resource tables

infer_salmon_datapackage_artifacts.Rd

Infers column dictionaries, table metadata, candidate code lists, and dataset-level metadata in a single step from one or more raw data tables.

Usage

infer_salmon_datapackage_artifacts(
  resources,
  dataset_id = "dataset-1",
  table_id = "table_1",
  guess_types = TRUE,
  seed_semantics = TRUE,
  semantic_sources = c("smn", "gcdfo", "ols", "nvs"),
  semantic_max_per_role = 1,
  seed_verbose = TRUE,
  seed_codes = NULL,
  seed_table_meta = NULL,
  seed_dataset_meta = NULL,
  semantic_code_scope = c("factor", "all", "none")
)

Arguments

resources

Either a named list of data frames (one per resource table) or a single data frame (converted internally to a one-table list).

dataset_id

Dataset identifier applied to all inferred metadata.

table_id

Name used when resources is a single data frame.

guess_types

Logical; if TRUE (default), infer value_type for each dictionary column.

seed_semantics

Logical; if TRUE, run suggest_semantics() and attach semantic suggestions to the returned dictionary.

semantic_sources

Vector of vocabulary sources passed to suggest_semantics().

semantic_max_per_role

Maximum number of suggestions retained per I-ADOPT role.

seed_verbose

Logical; if TRUE, emit progress messages while seeding semantic suggestions.

seed_codes

Optional codes.csv-style seed metadata.

seed_table_meta

Optional tables.csv-style seed metadata.

seed_dataset_meta

Optional dataset.csv-style seed metadata.

semantic_code_scope

Character string controlling which codes.csv rows are sent through suggest_semantics() during one-shot seeding. "factor" (default) only analyzes codes sourced from factor/categorical columns in the original data frame(s); "all" analyzes all inferred or supplied code rows; "none" skips code-level semantic suggestions.

Value

A named list with the following components:

  • resources: Named list of input tables

  • dict: Inferred dictionary tibble

  • table_meta: Inferred table metadata tibble

  • codes: Inferred candidate codes tibble

  • dataset_meta: Inferred dataset metadata one-row tibble

  • semantic_suggestions: Semantic suggestion tibble (or NULL)

Details

This is a convenience helper for biologists who want to get from raw data frames to package-ready metadata artifacts with one call.

Examples

if (FALSE) { # \dontrun{
resources <- list(
  catches = data.frame(
    station_id = c("A", "B"),
    species = c("Coho", "Chinook"),
    count = c(10L, 20L),
    sample_date = as.Date(c("2024-01-01", "2024-01-02"))
  ),
  stations = data.frame(
    station_id = c("A", "B"),
    latitude = c(49.8, 49.9),
    longitude = c(-124.4, -124.5)
  )
)

artifacts <- infer_salmon_datapackage_artifacts(
  resources,
  dataset_id = "demo-1",
  seed_semantics = TRUE,
  seed_verbose = TRUE
)

dict <- artifacts$dict
table_meta <- artifacts$table_meta
codes <- artifacts$codes
dataset_meta <- artifacts$dataset_meta
} # }