Package index • eDataDRF

Initialise tibbles

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

initialise_campaign_tibble(): Initialise an 8x0 tibble for storing organisational and date metadata
initialise_references_tibble(): Initialise an 18x0 tibble for storing metadata on scientific literature
initialise_sites_tibble(): Initialise an 13x0 tibble for storing geographical metadata
initialise_parameters_tibble(): Initialise an 10x0 tibble for storing metadata on sampled parameters: stressors, quality, etc.
initialise_compartments_tibble(): Initialise an 3x0 tibble for storing metadata on sampled environmental compartment
initialise_methods_tibble(): Initialise an 5x0 tibble for storing metadata on scientific/sampling methods and protocols
initialise_samples_tibble(): Initialise an 11x0 tibble for storing combinations of sites, dates, parameters, and compartments sampled
initialise_biota_tibble(): Initialise an 14x0 tibble for storing biota metadata
initialise_measurements_tibble(): Initialise an 26x0 tibble for storing measurement data
initialise_CREED_data_tibble(): Initialise an 6x0 tibble for storing CREED assessment data
initialise_CREED_scores_tibble(): Initialise an 5x0 tibble for storing a data source's overall CREED score

Controlled vocabulary

Vectors (and sometimes tibbles) of controlled vocabulary

CREED_choices_vocabulary(): Controlled vocabulary for CREED scores, CREED table
altitude_units_vocabulary(): Controlled vocabulary for the ALTITUDE_UNIT column, Sites table
analytical_protocols_vocabulary(): Controlled vocabulary for PROTOCOL_TYPE and PROTOCOL_NAME columns (analytical), Methods table
areas_vocabulary(): Ocean controlled vocabulary (wrapper for ocean_vocabulary())
coordinate_systems_vocabulary(): Controlled vocabulary for the SITE_COORDINATE_SYSTEM column, Sites table
countries_vocabulary(): Controlled vocabulary for the COUNTRY_ISO column, Sites table
data_source_vocabulary(): Controlled vocabulary for the DATA_SOURCE column, References table
environ_compartments_sub_vocabulary(): Controlled vocabulary for the ENVIRON_COMPARTMENT and ENVIRON_COMPARTMENT_SUB columns, Compartments table
environ_compartments_vocabulary(): Controlled vocabulary for the ENVIRON_COMPARTMENT column, Compartments table
extraction_protocols_vocabulary(): Controlled vocabulary for PROTOCOL_TYPE and PROTOCOL_NAME columns (extraction), Methods table
fractionation_protocols_vocabulary(): Controlled vocabulary for PROTOCOL_TYPE and PROTOCOL_NAME columns (fractionation), Methods table
gender_vocabulary(): Controlled vocabulary for the SAMPLE_SPECIES_GENDER column, Biota table
geographic_features_sub_vocabulary(): Controlled vocabulary for the SITE_GEOGRAPHIC_FEATURE_SUB column, Sites table
geographic_features_vocabulary(): Controlled vocabulary for the SITE_GEOGRAPHIC_FEATURE column, Sites table
lifestage_vocabulary(): Controlled vocabulary for the SAMPLE_SPECIES_LIFESTAGE column, Biota table
measured_categories_vocabulary(): Controlled vocabulary for the MEASURED_CATEGORY column, Compartments table
measured_flag_vocabulary(): Controlled vocabulary for MEASURED_FLAG, Measurements table
measured_types_vocabulary(): Controlled vocabulary for the MEASURED_TYPE column, Parameters table
ocean_vocabulary(): Controlled vocabulary for the OCEAN_IHO column, Sites table
parameter_types_sub_vocabulary(): Controlled vocabulary for the PARAMETER_TYPES_SUB column, Parameters table
parameter_types_vocabulary(): Controlled vocabulary for the PARAMETER_TYPES column, Parameters table
parameter_unit_vocabulary(): Controlled vocabulary for MEASURED_UNIT, LOQ_UNIT, and LOD_UNIT, with conversion factors and base units
parameters_vocabulary(): Data for PARAMETER_NAME, PARAMETER_TYPE, etc. in the Parameters table
protocol_categories_vocabulary(): Controlled vocabulary for PROTOCOL_CATEGORY column, Methods table
protocol_options_vocabulary(): Controlled vocabulary for PROTOCOL_TYPE and PROTOCOL_NAME columns (all), Methods table
reference_type_vocabulary(): Controlled vocabulary for the REFERENCE_TYPE column, References table
sampling_protocols_vocabulary(): Controlled vocabulary for PROTOCOL_TYPE and PROTOCOL_NAME columns (sampling), Methods table
species_groups_vocabulary(): Controlled vocabulary for the SPECIES_GROUP column, Biota table
species_names_vocabulary(): Controlled vocabulary for the SPECIES_NAME column, Biota table
tissue_types_vocabulary(): Controlled vocabulary for the SAMPLE_TISSUE column, Biota table
uncertainty_types_vocabulary(): Controlled vocabulary for the UNCERTAINTY_TYPE column, Measurements table

Generate IDs

Generate ID strings based on abbreviated titles, plus regex to check

abbreviate_string(): Generic function to abbreviate string to first n words with case formatting
generate_reference_id(): Generate compact reference ID (YYYYLNameFirstThreeWords) for REFERENCE_ID in References table
generate_protocol_id(): Generate a semi-unique string ID for a protocol (PROTOCOL_ID) based on its type, name, the campaign name, and a sequence number; used as a key between Methods and Measurements table.
generate_sample_id_with_components(): Generate compact Sample ID (SiteCode-ParamAbbrev-CompartmentAbbrev-Date-R-SubsampleAbbrev) for SAMPLE_ID in Samples table
sample_id_regex(): Regular expression to check generate_sample_id_with_components() protocol IDs for Samples table
protocol_id_regex(): Regular expression to check generate_protocol_id() protocol IDs for Methods table

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_CREED_data_relevance(): Run pointblank validation on a CREED Relevance data table
pb_validate_CREED_data_reliability(): Run pointblank validation on a CREED Reliability data table
pb_validate_all_edata_tables(): Validate all eData tables at once
pb_validate_biota(): Run pointblank validation on a Biota table
pb_validate_campaign(): Run pointblank validation on a Campaign table
pb_validate_CREED_scores(): Run pointblank validation on a CREED Scores table
pb_validate_edata_table(): Generic pointblank validation helper for eData tables
pb_validate_measurements(): Run pointblank validation on a Measurements table
pb_validate_methods(): Run pointblank validation on a Methods table
pb_validate_parameters(): Run pointblank validation on a Parameters table
pb_validate_reference(): Run pointblank validation on a Reference table
pb_validate_samples(): Run pointblank validation on a Samples table
pb_validate_sites(): Run pointblank validation on a Sites table