Package index • metasalmon

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One-shot package creation from raw tables

metasalmon-package metasalmon: metasalmon: Utilities for Salmon Data Packages
metasalmon_configuration metasalmon-options: Configure MetaSalmon
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

Advanced Package Assembly

Manual writing when you already have the SDP metadata tables assembled

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

Dictionary Functions

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

Review and Edit (in R)

Review the seeded IRIs in the console, decide them in a script, fill in the remaining metadata, and write it all back — no spreadsheet required

review_semantics(): Review semantic suggestions in the console
accept_suggestion() reject_suggestion(): Decide a semantic review slot
apply_sdp_semantics(): Write semantic review decisions into a package
review_metadata(): Report the metadata a package still needs, with the call that fills it
set_sdp_dataset() set_sdp_table() set_sdp_column() set_sdp_code(): Fill in a package's free-text metadata
semantic_suggestions(): Semantic suggestions attached to a dictionary or package
semantic_llm_assessments(): Target-level LLM assessments attached to a dictionary

Harness Review (packet and ingest)

Model judgement runs outside the package: write a review packet, have your harness judge it, and read the assessments back

write_semantic_review_packet(): Write a semantic review packet for a harness to judge
ingest_semantic_assessments(): Ingest a harness's semantic assessments

Semantic Helpers

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

Ontology + Validation

Fetch the ontology and validate semantic coverage

fetch_salmon_ontology(): Fetch the Salmon Domain Ontology with caching
validate_semantics(): Validate semantics with graceful gap reporting
verify_sdp_semantic_iris(): Verify selected HTTP semantic IRIs in a Salmon Data Package
suggest_facet_schemes(): Suggest facet schemes for proposed terms

Term Request Workflow

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

NuSEDS Helpers

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
nuseds_estimate_classification_crosswalk(): NuSEDS estimate classification crosswalk

Darwin Core (DwC-DP)

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)

Enterprise Data Hub (EDH)

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

Semantic Review Supplements

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

Extended SDP Structure and Reproducibility

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

migrate_sdp_methods(): Migrate an sdp-0.2.0 package's method metadata to sdp-0.3.0
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

Public Catalogue Metadata

Bounded public query captures with provenance receipts; no source-object fetch, submission or semantic approval

capture_catalogue_query(): Capture a bounded public catalogue metadata query

EML and KNB

Reviewed EML 2.2.0 export and verified DataONE/KNB publication, starting from the semantic closure both require

write_sdp_semantic_closure(): Write the reviewed semantic closure for a Salmon Data Package
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 KNB

GitHub Access

Authenticate once and read CSVs from private GitHub repositories

ms_setup_github(): Set up GitHub access for private repositories
github_raw_url(): Build a stable raw GitHub URL
read_github_csv(): Read a CSV from a GitHub repository
read_github_csv_dir(): Read all CSV files from a GitHub directory

ICES Vocabulary

Access ICES reference codes and vocabulary

ices_vocab: ICES controlled vocabularies (code lists)
ices_code_types(): List ICES code types
ices_codes(): List ICES codes for a code type
ices_find_code_types(): Find ICES code types by text match
ices_find_codes(): Find ICES codes within a code type by text match

Maintenance

Version and update helpers

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