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Build per-segment per-species access from schema tables (portable)

Source: R/lnk_access.R
lnk_access.Rd

Schema-aware portable wrapper around lnk_pipeline_access() — the access twin of lnk_mapping_code(). Builds the per-species barriers_<sp>_access + per-source views internally (via lnk_barriers_views()) over table_barriers, then computes the wide streams_access shape for aoi and writes it to table_to.

Usage

lnk_access(
  conn,
  cfg,
  aoi,
  table_streams,
  table_barriers,
  table_to,
  merge = FALSE,
  presence = NULL,
  species = NULL
)

Arguments

conn

A DBI::DBIConnection to the local pipeline DB.

cfg

An lnk_config object.

aoi

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

table_streams

Character. Schema-qualified streams table (the segments).

table_barriers

Character. Schema-qualified unified barriers table. The per-species _access + source _unified views are built over it internally via lnk_barriers_views().

table_to

Character. Schema-qualified destination streams_access table. With merge = TRUE it must already exist (rows for aoi are UPDATEd in place).

merge

Logical. FALSE (default) overwrites table_to. TRUE surgically UPDATEs table_to's aoi rows (recompute; see Merge mode).

presence

An lnk_presence object or NULL. Per-species presence for aoi; pass-through to lnk_pipeline_access().

species

Character vector of species codes. Default cfg$species.

Value

conn invisibly.

Details

Works against working-schema tables (mid-pipeline) or persist-schema tables (ad-hoc / post-consolidate recompute) without modification — the caller passes explicit table_<role> names. The caller passes ONE table_barriers (the unified barriers table); the per-species access set and the source-typed views are derived from it internally, so no pre-built barriers_per_sp list is needed (that stays the lower-level lnk_pipeline_access() surface).

Merge (recompute) mode

merge = TRUE is the post-consolidate recompute (link#205). A WSG's accessibility depends on barriers downstream, possibly in another WSG (the provincial-accumulation property, RUNBOOK.md §5); when WSGs are modelled on separate hosts each sees only its own barriers, so the per-host streams_access can be wrong cross-WSG. Once all barriers are consolidated, merge = TRUE re-settles ONLY the cross-WSG columns (has_barriers_<sp>_dnstr, has_barriers_{anthropogenic,pscis,dams}_dnstr, dam_dnstr_ind) against the complete table_barriers, reusing the already-persisted streams + streams_habitat — far cheaper than a full lnk_pipeline_run() (which re-derives streams + habitat). It UPDATEs the existing table_to rows for aoi and preserves the within-WSG columns the recompute does not touch:

  • remediated_dnstr_ind (and has_barriers_remediations_dnstr) — depend on the working-schema crossings/remediations, correct from the prior compute and within-WSG in practice.

  • the observed-upstream distinction in access_<sp>: set to 0 when newly blocked, else kept at 2 where the prior compute had an observation, else 1.

observations/crossings are intentionally skipped (NULL): they only drive the access 1-vs-2 code + remediated_dnstr_ind (both preserved above); mapping_code's accessible = !has_barriers_<sp>_dnstr is independent of them.

merge = FALSE (default) overwrites table_to via lnk_pipeline_access() — first-compute, intended for a working / scratch table (it drops + recreates the target as a flat id_segment-keyed table, so do NOT point it at a persist table; use merge = TRUE for persist).

See also

lnk_mapping_code(), lnk_pipeline_access(), lnk_barriers_views()

Other compare: lnk_compare_mapping_code(), lnk_compare_rollup(), lnk_compare_wsg(), lnk_mapping_code(), lnk_parity_annotate()

Examples

if (FALSE) { # \dontrun{
conn <- lnk_db_conn()
cfg <- lnk_config("bcfishpass")
loaded <- lnk_load_overrides(cfg)
pres <- lnk_presence(loaded$wsg_species_presence, "PARS")

# Post-consolidate recompute against persist (cheap; cross-WSG correct):
lnk_access(
  conn, cfg, aoi = "PARS",
  table_streams  = "fresh.streams",
  table_barriers = "fresh.barriers",
  table_to       = "fresh.streams_access",
  merge          = TRUE, presence = pres)
lnk_mapping_code(
  conn,
  table_access  = "fresh.streams_access",
  table_habitat = "fresh.streams_habitat_long_vw",
  table_streams = "fresh.streams",
  aoi           = "PARS",
  table_to      = "fresh.streams_mapping_code",
  presence      = pres)
} # }