Author, Validate, and Export Key Resources Tables
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘krt’ version 0.1.0
Help Pages
A C D E F G I K L M N P R S U V W
-- A --
| add_approval | Create and add an ethics or governance approval |
| add_contributor | Create and add a contributor |
| add_resource | Add, update, remove, or get a resource in a KRT |
| all_fields | Key Resources Table field registry |
| append_provenance | Append a provenance entry to a KRT |
| apply_mapping | Map one resource to a profile's columns |
| as.data.frame.krt_tbl | Coerce a KRT to a data frame (a rectangular view) |
| as.data.frame.krt_validation_report | Convert a validation report to a data frame |
| as_KRT | Coerce to and from the S4 'KRT' class |
| as_krt | Coerce to and from the S4 'KRT' class |
| as_prov_json | Export the provenance graph as PROV-JSON |
| as_rdf | Export a KRT as RDF (JSON-LD or Turtle) |
| as_rocrate | Export a KRT as an RO-Crate 1.1 metadata document |
-- C --
| coerce_field | Coerce a field value to its declared type. |
| compose_identifier | Compose a compound identifier string from a resource's typed fields |
-- D --
| detect_existing_krt | Detect and parse a Key Resources Table embedded in a document |
-- E --
| export_asap | Export a KRT in the ASAP six-column format |
| export_citation | Export citable resources as RIS or BibTeX |
| export_krt | Export a Key Resources Table |
| export_tabular | Export a KRT as a delimited table or spreadsheet |
| extract_candidates | Extract candidate resources from text (regex engine) |
| extract_krt | Extract a Key Resources Table from a manuscript |
| extract_llm | Extract resources from text with an LLM |
-- F --
| fetch_fulltext | Fetch manuscript full text |
| fields_for_type | Key Resources Table field registry |
| field_label | Key Resources Table field registry |
| field_registry | Key Resources Table field registry |
| field_spec | Key Resources Table field registry |
| find_duplicates | Find duplicate resources in a KRT |
| format.krt_llm | Configure an LLM for extraction |
-- G --
| get_profile | Retrieve a registered profile |
| get_resource | Add, update, remove, or get a resource in a KRT |
-- I --
| id_parse | Parse and classify an identifier string |
| import_asap | Import an ASAP or Cell Press Key Resources Table |
| import_krt | Import a Key Resources Table from a file or string |
| import_tabular | Import a generic tabular Key Resources Table |
| is_krt | Create a Key Resources Table |
| is_pending_identifier | Is a value the ASAP "identifier pending" placeholder? |
| is_profile | Load a profile from a directory |
| is_resource | Create a resource record |
-- K --
| KRT-class | The 'KRT' S4 class |
| krt_approval_types | KRT controlled vocabularies |
| krt_as_dataframe | Coerce a KRT's resources to a DataFrame (Bioconductor) |
| krt_attribution | Attribution text for a table's profile |
| krt_audit_licenses | Audit the licenses of the package and its bundled assets |
| krt_cli | Run the krt command-line interface |
| krt_deposit_figshare | Deposit a KRT to Figshare |
| krt_deposit_zenodo | Deposit a KRT to Zenodo |
| krt_diff | Diff two Key Resources Tables |
| krt_example | An example Key Resources Table |
| krt_import_elabftw | Import resources from an eLabFTW experiment |
| krt_import_protocolsio | Import a protocol from protocols.io |
| krt_llm | Configure an LLM for extraction |
| krt_merge | Merge Key Resources Tables |
| krt_meta | Get or set KRT metadata |
| krt_meta<- | Get or set KRT metadata |
| krt_new | Create a Key Resources Table |
| krt_new_or_reuse | KRT controlled vocabularies |
| krt_plugins | Extend krt with plugins |
| krt_plugin_api | The krt plugin API |
| krt_preflight | Pre-flight release readiness check for a Key Resources Table |
| krt_profiles | List available profiles |
| krt_profile_attribution | Licensing of a profile |
| krt_profile_info | Describe a profile |
| krt_profile_license | Licensing of a profile |
| krt_profile_sources | Licensing of a profile |
| krt_provenance | Provenance of a KRT |
| krt_redaction_levels | KRT controlled vocabularies |
| krt_resource_types | KRT controlled vocabularies |
| krt_roles | KRT controlled vocabularies |
| krt_statuses | KRT controlled vocabularies |
| krt_suggest | Suggest canonical names and identifiers from public authorities |
| krt_tbl | Create a Key Resources Table |
| krt_validation_report | The validation report object |
| krt_vocab | Access a KRT controlled vocabulary |
| krt_vocabularies | KRT controlled vocabularies |
| krt_write | Export a Key Resources Table |
| krt_write_attribution | Write attribution to a file |
-- L --
| launch_krt | Launch the interactive KRT editor |
| list_llm_providers | List registered LLM providers |
| list_resolvers | List registered resolver schemes |
| list_suggest_sources | List autocomplete sources |
| list_validators | List registered validation rules |
| load_profile | Load a profile from a directory |
-- M --
| mapping_lossy_fields | Fields lost or folded when projecting to a profile |
-- N --
| new_approval | Create and add an ethics or governance approval |
| new_contributor | Create and add a contributor |
| new_krt | Create a Key Resources Table |
| new_resource | Create a resource record |
| normalize_ids | Normalize identifiers to canonical forms |
-- P --
| parse_compound_identifier | Parse a compound identifier string into typed fields |
| print.krt_llm | Configure an LLM for extraction |
| project_profile | Project a KRT onto a profile as a data frame |
-- R --
| read_input_text | Read manuscript text and tables from an input |
| read_krt_json | Read a KRT from canonical JSON |
| read_krt_yaml | Read a KRT from canonical YAML |
| redaction_default | Default redaction strength for a profile's public exports |
| redaction_policy | The default redaction policy |
| redact_krt | Redact sensitive fields for public sharing |
| register_llm_provider | Register an LLM provider |
| register_profile | Register an output profile |
| register_resolver | Register an identifier resolver |
| register_suggest_source | Register an autocomplete source |
| register_validator | Register a validation rule |
| remove_resource | Add, update, remove, or get a resource in a KRT |
| render_krt | Render a KRT as a formatted table |
| resolvers | Resolve identifiers against public registries |
| resolve_cellosaurus | Resolve identifiers against public registries |
| resolve_doi | Resolve identifiers against public registries |
| resolve_id | Resolve any identifier by detecting its scheme |
| resolve_orcid | Resolve identifiers against public registries |
| resolve_pubmed | Resolve identifiers against public registries |
| resolve_ror | Resolve identifiers against public registries |
| resolve_rrid | Resolve identifiers against public registries |
| resource_signature | Normalized signature of a resource |
| rrid_type | Resource type implied by an RRID |
-- S --
| scan_identifiers | Scan free text for research identifiers |
| summary.krt_tbl | Summarize a KRT |
| summary.krt_validation_report | Summarize a validation report |
-- U --
| update_resource | Add, update, remove, or get a resource in a KRT |
-- V --
| validate_krt | Validate a Key Resources Table |
| validate_plugin_contract | Check that an object satisfies a plugin contract |
| vocab_match | Match a value against a controlled vocabulary |
-- W --
| write_krt_json | Write a KRT to canonical JSON |
| write_krt_yaml | Write a KRT to canonical YAML |