Package index • eDataDRF

Initialise tibbles

Create empty versions of the format’s tables as R tibble objects

initialise_campaign_tibble(): Initialise campaign tibble
initialise_references_tibble(): Initialise references tibble
initialise_sites_tibble(): Initialise sites tibble
initialise_parameters_tibble(): Initialise parameters tibble
initialise_compartments_tibble(): Initialise compartments tibble
initialise_methods_tibble(): Initialise methods tibble
initialise_samples_tibble(): Initialise samples tibble
initialise_biota_tibble(): Initialise biota tibble
initialise_measurements_tibble(): Initialise measurements tibble
initialise_CREED_data_tibble(): Initialise CREED criteria data tibble
initialise_CREED_scores_tibble(): Initialise CREED scores tibble

Controlled vocabulary

Vectors (and sometimes tibbles) of controlled vocabulary

CREED_choices_vocabulary(): CREED assessment scores controlled vocabulary
altitude_units_vocabulary(): Altitude units controlled vocabulary
analytical_protocols_vocabulary(): Analytical protocols controlled vocabulary
areas_vocabulary(): Ocean controlled vocabulary (wrapper for ocean_vocabulary())
coordinate_systems_vocabulary(): Coordinate systems controlled vocabulary
countries_vocabulary(): Countries controlled vocabulary
data_source_vocabulary(): Controlled vocabulary for data sources
environ_compartments_sub_vocabulary(): Environmental compartment sub-categories controlled vocabulary
environ_compartments_vocabulary(): Environmental compartments controlled vocabulary
extraction_protocols_vocabulary(): Extraction protocols controlled vocabulary
fractionation_protocols_vocabulary(): Fractionation protocols controlled vocabulary
gender_vocabulary(): Gender controlled vocabulary
geographic_features_sub_vocabulary(): Geographic feature sub-categories controlled vocabulary
geographic_features_vocabulary(): Geographic features controlled vocabulary
lifestage_vocabulary(): Life stages controlled vocabulary
measured_categories_vocabulary(): Measured categories controlled vocabulary
measured_flag_vocabulary(): Measurement flags controlled vocabulary
measured_types_vocabulary(): Measured types controlled vocabulary
ocean_vocabulary(): Ocean controlled vocabulary
parameter_types_sub_vocabulary(): Parameter type sub-categories controlled vocabulary
parameter_types_vocabulary(): Parameter types controlled vocabulary
parameter_unit_vocabulary(): Parameter units and conversion factors vocabulary
parameters_vocabulary(): Sampled parameters controlled vocabulary
protocol_categories_vocabulary(): Protocol categories controlled vocabulary
protocol_options_vocabulary(): All protocols controlled vocabulary
reference_type_vocabulary(): Controlled vocabulary for reference types
sampling_protocols_vocabulary(): Sampling protocols controlled vocabulary
species_groups_vocabulary(): Species groups controlled vocabulary
species_names_vocabulary(): Species names controlled vocabulary
tissue_types_vocabulary(): Tissue types controlled vocabulary
uncertainty_types_vocabulary(): Uncertainty types controlled vocabulary

Character limits

Character limits for some inputs

reference_character_limits(): Reference field character limits

Generate IDs

Generate ID strings based on abbreviated titles

abbreviate_string(): Abbreviate string to first n words with case formatting
generate_reference_id(): Generate Reference ID
generate_protocol_id(): Generate a semi-unique string ID for a protocol based on its type, name, the campaign name, and a sequence number

Export

Export tables as zipped CSV files

get_dataset_display_name(): Get Dataset Display Name
export_campaign_zip(): Export Multiple Datasets as ZIP of CSV Files

Example data

Functions to generate example data

example_CREED_relevance_tibble(): Create Example CREED Relevance Tibble
example_CREED_reliability_tibble(): Create Example CREED Reliability Tibble
example_CREED_scores_tibble(): Create Example CREED Scores Tibble
example_biota_tibble(): Create Example Biota Tibble
example_campaign_tibble(): Create Example Campaign Tibble
example_compartments_tibble(): Create Example Compartments Tibble
example_measurements_tibble(): Create Example Measurements Tibble
example_methods_tibble(): Create Example Methods Tibble
example_parameters_tibble(): Create Example Parameters Tibble
example_references_tibble(): Create Example References Tibble
example_samples_tibble(): Create Example Samples Tibble
example_sites_tibble(): Create Example Sites Tibble
creed_tibble_to_mock_input(): Convert CREED Tibble to Mock Input List

Validation

Functions using {pointblank} to validate data

pb_validate_all_edata_tables(): Validate all eData tables at once
pb_validate_edata_table(): Run pointblank validation on an eData table
col_vals_in_set_verbose(): Wrapper for col_vals_in_set with enhanced error reporting