Resolve the Species Set for an AOI

The species the config classifies, filtered to those present in the AOI. Used by lnk_pipeline_classify() and lnk_pipeline_connect() to pick which species to run, and exposed for callers that need to derive the same list outside the pipeline (e.g. a custom compare_bcfishpass_wsg() that queries bcfishpass reference tables only for these species).

Usage

lnk_pipeline_species(cfg, loaded, aoi)

Arguments

cfg

An lnk_config object from lnk_config().

loaded

Named list of tibbles from lnk_load_overrides(). Carries parameters_fresh and wsg_species_presence.

aoi

Character. AOI identifier — today a watershed group code (e.g. "BULK") matched against loaded$wsg_species_presence$watershed_group_code.

Value

Character vector of species codes. Empty when neither config nor AOI carries species.

Details

The returned set is the intersection of:

• cfg$species — species the rules YAML classifies (parsed at lnk_config() load time)

• species flagged present for aoi in loaded$wsg_species_presence — the wide-form presence table where each species column (bt, ch, cm, ...) holds "t" for present and "f" for absent

When loaded$wsg_species_presence is not populated the function returns cfg$species unfiltered. When the AOI is not found in the table the function returns character(0).

See also

Other pipeline: lnk_pipeline_access(), lnk_pipeline_break(), lnk_pipeline_classify(), lnk_pipeline_connect(), lnk_pipeline_crossings(), lnk_pipeline_load(), lnk_pipeline_mapping_code(), lnk_pipeline_prepare(), lnk_pipeline_run(), lnk_pipeline_setup(), lnk_presence()

Examples

cfg    <- lnk_config("bcfishpass")
loaded <- lnk_load_overrides(cfg)
#> Warning: incomplete final line found by readTableHeader on '/home/runner/work/_temp/Library/link/extdata/configs/bcfishpass/overrides/cabd_blkey_xref.csv'
lnk_pipeline_species(cfg, loaded, "BULK")
#> [1] "BT" "CH" "CO" "PK" "SK" "ST"
lnk_pipeline_species(cfg, loaded, "ADMS")
#> [1] "BT" "CH" "CO" "SK"