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Per-AOI species presence with bcfp species-group expansion

Source: R/lnk_presence.R
lnk_presence.Rd

Reads a single AOI's row from a wsg_species_presence tibble and returns structured presence info: the per-species TRUE/FALSE flags from the row, expanded by user-supplied species groups so that "any group member present" promotes the whole group to present. Mirrors bcfp's wsg_salmon / wsg_ct_dv_rb JOIN logic in load_streams_access.sql — useful as input to per-species pipeline loops that should skip absent species.

Usage

lnk_presence(
  wsg_species_presence,
  aoi,
  groups = list(salmon = c("ch", "cm", "co", "pk", "sk"), ct_dv_rb = c("ct", "dv", "rb"))
)

Arguments

wsg_species_presence

Data frame or tibble matching the loaded$wsg_species_presence shape (per lnk_load_overrides()): watershed_group_code, then per-species columns (bt, ch, ...), plus optional notes. Values may be character ("t"/""/NA, the CSV-bundled form) or logical (TRUE/FALSE/NA, the PostgreSQL form). notes and watershed_group_code are excluded from the species list.

aoi

Character. Watershed group code (e.g. "ADMS").

groups

Named list of character vectors. Each name is a group tag (e.g. "salmon"); each value lists species codes that share group-presence semantics. Default mirrors bcfp:

  • salmon = c("ch", "cm", "co", "pk", "sk")

  • ct_dv_rb = c("ct", "dv", "rb")

A species in a group is reported present iff any group member is present in the AOI row. Pass list() to disable expansion.

Value

A list with:

  • aoi: echo of input.

  • row: the raw 1-row tibble for aoi.

  • present: character vector of species codes present after group expansion.

  • absent: character vector of species codes not present.

  • is_present(sp): vectorised function returning TRUE for species in present.

Details

Coexists with lnk_pipeline_species(), which returns the intersection of cfg$species with AOI-present species as a plain vector. lnk_presence() is the structured / group-aware sibling.

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_pipeline_species()

Examples

if (FALSE) { # \dontrun{
loaded <- lnk_load_overrides(lnk_config("default_extrabreaks"))

# ADMS — BT + salmon-group + ct_dv_rb-group present.
pres <- lnk_presence(loaded$wsg_species_presence, "ADMS")
pres$present                           # bt, ch, co, sk + cm, pk (group-expanded)
pres$absent                            # st, wct, gr, ko
pres$is_present(c("bt", "st", "cm"))   # TRUE FALSE TRUE

# ELKR — salmon all NULL, no group expansion fires.
pres <- lnk_presence(loaded$wsg_species_presence, "ELKR")
pres$is_present("ch")                  # FALSE

# Disable group expansion.
pres <- lnk_presence(loaded$wsg_species_presence, "ADMS",
                     groups = list())
pres$is_present("cm")                  # FALSE (only literal cm column matters)
} # }