Getting started with metasalmon • metasalmon

Overview

The metasalmon package helps salmon scientists wrap their analysis-ready tables into portable, ontology-aware Salmon Data Packages. A Salmon Data Package is a Frictionless Data Package extended with salmon-specific semantic fields (IRIs, concept schemes) that link your data to the DFO Salmon Ontology.

Quick Example

library(metasalmon)

# Load your data
df <- readr::read_csv("your-data.csv")

# Infer a starter dictionary
dict <- infer_dictionary(df, dataset_id = "my-dataset", table_id = "my-table")

# Validate it
validate_dictionary(dict)

# Create a package
resources <- list(main_table = df)
dataset_meta <- tibble::tibble(
  dataset_id = "my-dataset",
  title = "My Dataset",
  description = "Description here",
  # ... other fields
)
table_meta <- tibble::tibble(
  dataset_id = "my-dataset",
  table_id = "main_table",
  file_name = "main_table.csv",
  # ... other fields
)

pkg_path <- create_salmon_datapackage(
  resources, dataset_meta, table_meta, dict,
  path = "output-package"
)

Learn More

Functions workflow: See vignette("functions-workflow") for a detailed walkthrough
GPT collaboration: See vignette("gpt-collaboration") for using AI assistance
Package reference: Browse function documentation with ?infer_dictionary

Package Layout

R/: Core functions for dictionary inference/validation, package creation/reading
inst/extdata/: Example data files for tests and vignettes
tests/testthat/: Automated tests
vignettes/: Long-form documentation