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Settle persisted habitat flags on link's access

Source: R/lnk_habitat_gate.R
lnk_habitat_gate.Rd

Sets accessible, spawning, rearing, lake_rearing and wetland_rearing FALSE in <table_habitat>_<sp> wherever <table_access>.access_<sp> is 0, for one watershed group, so the habitat flags agree with the access a consumer reads.

Usage

lnk_habitat_gate(
  conn,
  aoi,
  table_habitat,
  table_access,
  table_streams,
  species,
  overlay = NULL,
  table_access_prior = NULL
)

Arguments

conn

A DBI::DBIConnection object.

aoi

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

table_habitat

Character. Schema-qualified prefix of the per-species habitat tables: <table_habitat>_<sp> (e.g. "fresh_default.streams_habitat").

table_access

Character. Schema-qualified streams_access table.

table_streams

Character. Schema-qualified streams table (measures and length_metre).

species

Character vector of species codes to settle.

overlay

A data frame in user_habitat_classification's shape (species_code, blue_line_key, downstream_route_measure, upstream_route_measure, spawning, rearing), or NULL for none.

table_access_prior

Character or NULL. Schema-qualified table of id_segment, watershed_group_code and access_<sp> as they were before the recompute that precedes this call. NULL leaves n_lifted_settled NA.

Value

A data frame, one row per species and flag: species, flag, n_segments and km set from TRUE to FALSE, and n_lifted_settled (per species, repeated on its rows).

Details

The two columns are built at different times from different barrier sets (link#349). fresh's accessible, which gates spawning and rearing inside frs_habitat_classify(), is computed once per group from that group's own breaks: metre-rounded positions, within the group only, lifted by the group's own overrides. access_<sp> is link's, built from every group's persisted barriers and overrides and re-settled after a multi-host run (lnk_access() with merge = TRUE). access_<sp> is the authoritative one, and this step makes the habitat flags follow it.

Rows that user_habitat_classification marks as known habitat keep their spawning / rearing (bcfishpass forces known habitat whatever the model says, and so does fresh::frs_habitat_overlay()); their accessible is still set FALSE. Pass the loaded table as overlay when the bundle applies the overlay. The match is the overlay's own: same blue_line_key, the segment's measure range inside the overlay row's.

The settle is one-way. A segment it blanks gets its habitat back only from a re-model of the group: when a later recompute lifts a segment (access_<sp> 0 to 1 or 2) whose accessible is FALSE, its habitat is missing until then. Pass the access values from before the recompute as table_access_prior and those segments are counted in n_lifted_settled.

See also

lnk_access(), lnk_pipeline_run()

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(), lnk_presence()

Examples

if (FALSE) { # \dontrun{
conn <- lnk_db_conn()
cfg <- lnk_config("default")
loaded <- lnk_load_overrides(cfg)

# After a recompute of DUNC's access in fresh_default:
lnk_habitat_gate(conn, aoi = "DUNC",
  table_habitat = "fresh_default.streams_habitat",
  table_access  = "fresh_default.streams_access",
  table_streams = "fresh_default.streams",
  species = lnk_pipeline_species(cfg, loaded, "DUNC"),
  overlay = loaded$user_habitat_classification)
} # }