Build a named list of severity thresholds for crossing scoring. Ships sensible BC fish passage defaults. Override via CSV or inline arguments for project-specific tuning.
Arguments
- csv
Path to a CSV file with columns
severity,metric,value. When provided, CSV values override in-code defaults. Usesystem.file("extdata", "thresholds_default.csv", package = "link")to see the expected format.- high
Named list of metric thresholds for high severity. Merged with CSV values (inline wins on conflict).
- moderate
Named list of metric thresholds for moderate severity.
- low
Named list of metric thresholds for low severity.
Value
A named list with elements high, moderate, low, each
containing a named list of metric thresholds (numeric values keyed by
metric name).
Details
Thresholds control how lnk_score_severity() classifies crossings. The
default values reflect BC provincial fish passage assessment criteria:
- High severity
outlet_drop >= 0.6m or slope_length >= 120 — impassable to most species at most flows
- Moderate severity
outlet_drop >= 0.3m or slope_length >= 60 — flow-dependent, potentially passable at migration flows
- Low severity
everything else with a crossing present
System-agnostic: metric names are user-defined strings, not hardcoded
to any provincial data system. A New Zealand user might define
high = list(perch_height = 0.5, pipe_gradient = 0.05).
Merge order: code defaults < CSV values < inline arguments. This lets you ship a project CSV but still tweak one threshold inline.
Examples
# Default BC thresholds — zero config
th <- lnk_thresholds()
th$high$outlet_drop
#> [1] 0.6
# [1] 0.6
# Override from bundled CSV (same result, shows the format)
csv_path <- system.file("extdata", "thresholds_default.csv", package = "link")
th_csv <- lnk_thresholds(csv = csv_path)
identical(th, th_csv)
#> [1] TRUE
# Project-specific: bull trout tolerate higher drops
th_bt <- lnk_thresholds(high = list(outlet_drop = 0.8))
th_bt$high$outlet_drop
#> [1] 0.8
# [1] 0.8 — inline override wins
# How thresholds plug into scoring (the integration point)
if (FALSE) { # \dontrun{
conn <- lnk_db_conn()
lnk_score_severity(conn, "working.crossings",
thresholds = lnk_thresholds(high = list(outlet_drop = 0.8)))
} # }