Run pointblank validation on a Biota table

Applies pointblank validation rules to check data quality and schema compliance for an eData Biota table. Checks that core identifier and biota-specific fields are non-null, environmental compartments indicate biota, and that species group, tissue, lifestage, and gender values are within their controlled vocabularies.

Usage

pb_validate_biota(data, actions = action_levels(), agent = TRUE)

Arguments

data

Data frame containing Biota table data to validate

actions

Action levels for pointblank agent (only used when agent = TRUE)

agent

Logical. If TRUE (default), returns a pointblank agent object. If FALSE, returns the validated data with validation failures removed.

Value

If agent = TRUE, a pointblank agent object containing validation results. If agent = FALSE, the input data with validation failures removed.

Details

Validation thresholds are configured using pointblank::action_levels().

See also

pb_validate_edata_table() for the underlying validation framework, pb_validate_all_edata_tables() to validate all tables at once, example_biota_tibble() for an example Biota table.

Other validation: pb_validate_CREED_data_relevance(), pb_validate_CREED_data_reliability(), pb_validate_CREED_scores(), pb_validate_all_edata_tables(), pb_validate_campaign(), pb_validate_edata_table(), pb_validate_measurements(), pb_validate_methods(), pb_validate_parameters(), pb_validate_reference(), pb_validate_samples(), pb_validate_sites()

Examples

if (FALSE) { # \dontrun{
pb_validate_biota(example_biota_tibble())
} # }