Package index • krt

Create and edit a table

Build a Key Resources Table and its records.

new_krt() krt_new() is_krt(): Create a Key Resources Table
add_resource() update_resource() remove_resource() get_resource(): Add, update, remove, or get a resource in a KRT
new_resource() is_resource(): Create a resource record
new_approval() add_approval(): Create and add an ethics or governance approval
new_contributor() add_contributor(): Create and add a contributor
krt_meta() `krt_meta<-`(): Get or set KRT metadata
krt_example: An example Key Resources Table
as.data.frame(<krt_tbl>): Coerce a KRT to a data frame (a rectangular view)
summary(<krt_tbl>): Summarize a KRT

The field registry and controlled vocabularies.

all_fields() field_spec() fields_for_type() field_label(): Key Resources Table field registry
coerce_field(): Coerce a field value to its declared type.
krt_vocab(): Access a KRT controlled vocabulary
krt_resource_types() krt_new_or_reuse() krt_statuses() krt_approval_types() krt_roles() krt_redaction_levels(): KRT controlled vocabularies
vocab_match(): Match a value against a controlled vocabulary

validate_krt(): Validate a Key Resources Table
krt_preflight(): Pre-flight release readiness check for a Key Resources Table
register_validator(): Register a validation rule
list_validators(): List registered validation rules
krt_validation_report: The validation report object
as.data.frame(<krt_validation_report>): Convert a validation report to a data frame
summary(<krt_validation_report>): Summarize a validation report
resource_signature(): Normalized signature of a resource
find_duplicates(): Find duplicate resources in a KRT

id_parse(): Parse and classify an identifier string
rrid_type(): Resource type implied by an RRID
parse_compound_identifier(): Parse a compound identifier string into typed fields
compose_identifier(): Compose a compound identifier string from a resource's typed fields
is_pending_identifier(): Is a value the ASAP "identifier pending" placeholder?
normalize_ids(): Normalize identifiers to canonical forms
resolve_rrid() resolve_doi() resolve_orcid() resolve_pubmed() resolve_ror() resolve_cellosaurus(): Resolve identifiers against public registries
resolve_id(): Resolve any identifier by detecting its scheme
register_resolver(): Register an identifier resolver
list_resolvers(): List registered resolver schemes
krt_suggest(): Suggest canonical names and identifiers from public authorities
register_suggest_source(): Register an autocomplete source
list_suggest_sources(): List autocomplete sources

krt_profiles(): List available profiles
get_profile(): Retrieve a registered profile
load_profile() is_profile(): Load a profile from a directory
krt_profile_info(): Describe a profile
apply_mapping(): Map one resource to a profile's columns
project_profile(): Project a KRT onto a profile as a data frame
mapping_lossy_fields(): Fields lost or folded when projecting to a profile
krt_profile_license() krt_profile_sources() krt_profile_attribution(): Licensing of a profile
krt_attribution(): Attribution text for a table's profile
krt_write_attribution(): Write attribution to a file
krt_audit_licenses(): Audit the licenses of the package and its bundled assets

redact_krt(): Redact sensitive fields for public sharing
redaction_policy(): The default redaction policy
redaction_default(): Default redaction strength for a profile's public exports
append_provenance(): Append a provenance entry to a KRT
krt_provenance(): Provenance of a KRT
as_prov_json(): Export the provenance graph as PROV-JSON
as_rocrate(): Export a KRT as an RO-Crate 1.1 metadata document
as_rdf(): Export a KRT as RDF (JSON-LD or Turtle)

extract_krt(): Extract a Key Resources Table from a manuscript
scan_identifiers(): Scan free text for research identifiers
extract_candidates(): Extract candidate resources from text (regex engine)
read_input_text(): Read manuscript text and tables from an input
detect_existing_krt(): Detect and parse a Key Resources Table embedded in a document
extract_llm(): Extract resources from text with an LLM
krt_llm() format(<krt_llm>) print(<krt_llm>): Configure an LLM for extraction
register_llm_provider(): Register an LLM provider
list_llm_providers(): List registered LLM providers
fetch_fulltext(): Fetch manuscript full text

krt_cli(): Run the krt command-line interface
launch_krt(): Launch the interactive KRT editor
register_profile(): Register an output profile
krt_plugins: Extend krt with plugins
krt_plugin_api(): The krt plugin API
validate_plugin_contract(): Check that an object satisfies a plugin contract

KRT-class: The KRT S4 class
as_krt() as_KRT(): Coerce to and from the S4 KRT class
krt_as_dataframe(): Coerce a KRT's resources to a DataFrame (Bioconductor)