Package index • metasalmon

Start Here

One-shot package creation from raw tables

metasalmon-package metasalmon: metasalmon: Utilities for Salmon Data Packages
create_sdp(): Create a Salmon Data Package directly from raw tables
infer_salmon_datapackage_artifacts(): Infer Salmon Data Package artifacts from resource tables
read_salmon_datapackage(): Read a Salmon Data Package
validate_salmon_datapackage(): Validate a Salmon Data Package end to end

Manual writing when you already have the SDP metadata tables assembled

write_salmon_datapackage(): Write a Salmon Data Package from preassembled metadata

Infer, validate, and apply semantic data dictionaries

infer_dictionary(): Infer a starter dictionary from a data frame
validate_dictionary(): Validate a salmon data dictionary
apply_salmon_dictionary(): Apply a salmon dictionary to a data frame
apply_semantic_suggestions(): Apply semantic suggestions into a dictionary

Semantic suggestion, vocabulary search, and ranking benchmark capabilities

suggest_semantics(): Suggest semantic annotations for a dictionary
chat_decomposition(): Interactive decomposition review for measurement variables
find_terms(): Find candidate terms across external vocabularies
sources_for_role(): Get recommended sources for a given role
benchmark_term_ranking_fixtures(): Benchmark semantic term ranking against fixture cases
deduplicate_proposed_terms(): Deduplicate proposed ontology terms

Fetch the ontology and validate semantic coverage

Detect missing terms, route SMN, GCDFO, profile, or uncertain requests, and draft curator-reviewed GitHub issues

detect_semantic_term_gaps(): Detect candidate and LLM-identified semantic term gaps
render_ontology_term_request(): Render GitHub-ready ontology term request payloads
submit_term_request_issues(): Submit rendered ontology term requests as GitHub issues

Crosswalk legacy NuSEDS method labels to canonical method families

nuseds_enumeration_method_crosswalk(): NuSEDS enumeration method crosswalk
nuseds_estimate_method_crosswalk(): NuSEDS estimate method crosswalk

Darwin Core Data Package mapping and export helpers

suggest_dwc_mappings(): Suggest Darwin Core Data Package mappings for dictionary columns
dwc_dp_build_descriptor(): Build a DwC-DP datapackage descriptor (export helper)

HNAP-aware EDH XML export helpers for Enterprise Data Hub workflows

edh_build_hnap_xml(): Build HNAP-aware metadata XML for DFO Enterprise Data Hub export
edh_build_iso19139_xml(): Deprecated alias for edh_build_hnap_xml()
write_edh_xml_from_sdp(): Rebuild HNAP-aware EDH XML from a reviewed Salmon Data Package

Validated SSSOM concept alignments and ordered measurement decompositions

read_sssom_mapping_set(): Read a reviewed SSSOM mapping set
write_sdp_sssom(): Write reviewed SSSOM mapping sets into a Salmon Data Package
validate_sdp_sssom(): Validate SDP SSSOM artifacts
read_sdp_measurement_decompositions(): Read ordered measurement decompositions from a Salmon Data Package
write_sdp_measurement_decompositions(): Write ordered measurement decompositions into a Salmon Data Package
validate_sdp_measurement_decompositions(): Validate ordered SDP measurement-decomposition artifacts

SOSA procedures, measure-specific observation structures, and closed reproducibility sidecars

read_sdp_methods(): Read an SDP SOSA procedure registry
write_sdp_methods(): Write an SDP SOSA procedure registry
validate_sdp_methods(): Validate an SDP SOSA procedure registry
read_sdp_observation_structures(): Read measure-specific SDP observation structures
write_sdp_observation_structures(): Write measure-specific SDP observation structures
validate_sdp_observation_structures(): Validate measure-specific SDP observation structures
extract_sdp_observations(): Extract normalized logical observations from an SDP
read_sdp_reproducibility_manifest(): Read an SDP reproducibility manifest
write_sdp_reproducibility_manifest(): Write a closed reproducibility manifest into a Salmon Data Package
validate_sdp_reproducibility_manifest(): Validate an SDP reproducibility manifest

Reviewed EML 2.2.0 export and verified DataONE/KNB publication

write_eml_from_sdp(): Write reviewed EML 2.2.0 metadata from a Salmon Data Package
publish_sdp_to_knb(): Publish a reviewed Salmon Data Package to production KNB

Authenticate once and read CSVs from private GitHub repositories

Access ICES reference codes and vocabulary

Version and update helpers

check_for_updates(): Check whether a newer metasalmon release is available