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Stream Network Habitat Interpretation

An interpretation layer between field/modelled evidence and stream-network habitat modelling. Loads override CSVs through a canonical schema, snaps points to the network, matches records across data systems, resolves per-species barrier connectivity from observations and confirmations, and orchestrates a multi-phase pipeline that produces per-segment habitat outputs. Pairs with fresh for the modelling engine. Currently reproduces bcfishpass’s fish-passage classification method on BC’s Freshwater Atlas; interpretation logic is network-agnostic by design.

Experimental — APIs and outputs change without notice as the package consolidates.

Installation 

pak::pak("NewGraphEnvironment/link")

Prerequisites

PostgreSQL with fwapg loaded (same prerequisite as fresh; see fresh’s docker/ for a local setup). Connection via lnk_db_conn() or direct DBI::dbConnect().

link sits between raw evidence — PSCIS crossings, fish observations, habitat confirmations, falls, user-defined barriers — and the habitat-modelling engine:

  1. Load override CSVs (lnk_load(), lnk_load_overrides()) with canonical-schema validation via crate.
  2. Snap points to the network (lnk_points_snap()).
  3. Match crossings across data systems by network position (lnk_match()) within a configurable in-stream distance tolerance — linking PSCIS, MoTI, operator-submitted, and provincial inventories.
  4. Resolve per-species barrier overrides from evidence (lnk_barrier_overrides()): which gradient or falls barriers to skip given upstream observations + habitat confirmations.
  5. Orchestrate the pipeline (lnk_pipeline_*(), or lnk_pipeline_run() end-to-end) that produces per-watershed-group habitat outputs reproducing bcfishpass.
  6. Compare runs across configurations (lnk_compare_*(), lnk_parity_annotate(), lnk_baseline_*()) for province-wide parity audits and reproducibility checks.

The pipeline

For a given watershed group:

load → setup → prepare → break → access → classify → connect → crossings → persist

Each phase is a callable function (lnk_pipeline_<phase>()), so a user can stop, inspect, resume, or rebuild from any phase. lnk_pipeline_run() chains them end-to-end. lnk_baseline_current() captures a known-good run as a reference for diffing future runs.

Using with fresh

fresh is the modelling engine — it segments, classifies, and aggregates on the network. link prepares fresh’s two key inputs:

  • Break sources for frs_network_segment() — per-table specs assembled via lnk_source().
  • Barrier overrides for frs_habitat_classify() — a per-species skip list produced by lnk_barrier_overrides().

The two together reproduce bcfishpass on the Freshwater Atlas.

Roadmap

link is currently FWA-grounded through its dependency on fresh. The interpretation logic — what counts as evidence of a passable barrier, how observations resolve override decisions, how cross-system crossings are matched — is network-agnostic by design. Active design work:

  • Network agnosticism inherited from fresh’s in-flight spyda topology engine (fresh#41) and configurable column names (fresh#44).
  • Crossing-connectivity scoring — lnk_score() framework for combining multiple connectivity signals into a prioritization output.
  • Province-wide parity audits — lnk_compare_*() machinery for systematic comparison of pipeline variants and reproduction of an authoritative reference run.

Ecosystem

Package Role
link Stream-network habitat interpretation (this package) — interprets evidence, drives the modelling engine
fresh Stream-network modelling engine — segment, classify, cluster, aggregate
crate Canonical schema + validation for input CSVs

License

MIT (see LICENSE). Redistributed bcfishpass override data carries its own license — see NOTICE.md and LICENSE-bcfishpass.