Validate Catch at Taxon Level

Flags outliers in catch_kg by comparing values to upper bounds computed per gear + catch_taxon group (via get_catch_bounds_taxon). Rows with catch_kg above the bound receive a numeric alert code and optionally have their catch_kg set to NA.

Usage

validate_catch_taxa(data, k = 3, flag_value = 4)

Arguments

data

A data frame containing (at least) submission_id, gear, catch_taxon, and catch_kg.

k

A numeric parameter passed to LocScaleB; used for computing outlier bounds in get_catch_bounds_taxon.

flag_value

A numeric value to assign when catch_kg exceeds the upper bound. Default is 4.

Value

A data frame with the columns:

submission_id

Carried from the input data.

catch_taxon

Carried from the input data.

catch_kg

Potentially modified if outlier.

alert_catch

The alert code flag_value for outliers, or NA_real_ if no outlier.

Details

1. Calls get_catch_bounds_taxon to retrieve outlier bounds for each gear + catch_taxon group.

2. Joins these bounds to data on gear and catch_taxon.

3. Rowwise, checks if catch_kg is greater than the bound upper.up. If so, sets alert_catch = flag_value and optionally replaces catch_kg with NA_real_.

See also

get_catch_bounds_taxon, LocScaleB

Examples

if (FALSE) { # \dontrun{
catch_alert <- validate_catch_taxa(data, k = 3, flag_value = 4)
head(catch_alert)
} # }