NewGraphEnvironment · NewGraphEnvironment · May 1, 2026 · May 1, 2026 · May 1, 2026 · May 1, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: link
 Title: Stream Network Habitat Interpretation (Experimental)
-Version: 0.21.0
+Version: 0.22.0
 Authors@R: c(
     person("Allan", "Irvine", , "airvine@newgraphenvironment.com",
            role = c("aut", "cre"),
@@ -31,7 +31,7 @@ Suggests:
     bcdata,
     digest,
     dplyr,
-    fresh (>= 0.26.0),
+    fresh (>= 0.27.5),
     lintr,
     mockery,
     sf,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,19 @@
+# link 0.22.0
+
+Wires `fresh::frs_order_child` into the pipeline as link methodology — small streams plugging directly into large rivers can be credited as rearing despite low/missing FWA channel-width estimates. Closes [fresh#158](https://github.com/NewGraphEnvironment/fresh/issues/158) on the link side.
+
+- Four new per-species columns in `dimensions.csv` (both bundles), all opt-in via `rear_stream_order_bypass: yes/no`:
+  - `rear_stream_order_parent_min` — min order at the trib BLK's mouth confluence (default 5, matches bcfp)
+  - `rear_stream_order_child_min` — lower bound on segment's own stream_order (default 1)
+  - `rear_stream_order_child_max` — upper bound on segment's own stream_order (default 1)
+  - `rear_stream_order_distance_max` — cap (m) on distance from trib mouth (empty = no cap)
+- `lnk_rules_build` emits the values into a `channel_width_min_bypass:` block on the rear stream-edge rule. `lnk_pipeline_classify` reads the block and calls `frs_order_child` per species post-classification, gated on `rear_stream_order_bypass`.
+- Both bundles ship `bypass: no` for all species — infrastructure is parametric and tested but disabled by default. Re-enable per species via `dimensions.csv`. The 4-WSG regression (HARR / HORS / LFRA / BABL) is byte-identical to the pre-#96 baseline with bypass=off, confirming the wiring is purely additive when disabled.
+- Updates `inst/extdata/configs/dimensions_columns.csv` xref doc with all four new columns and refreshes the `rear_stream_order_bypass` entry (was stale — said "currently inert").
+- Bumps fresh dep to `>= 0.27.5` for the renamed bypass YAML schema (`stream_order` → `stream_order_min` + `stream_order_max`).
+
+Related: [link#23](https://github.com/NewGraphEnvironment/link/issues/23) (CH spawning misread, closed not-a-bug). PWF for the wire-up at `planning/active/`.
+
 # link 0.21.0
 
 Closes [#87](https://github.com/NewGraphEnvironment/link/pull/94). Default-bundle SK upstream-spawn now credits any spawn-eligible segment upstream of and accessible from a qualifying rearing waterbody, dropping bcfishpass's restrictive cluster + lake-adjacency gate. bcfishpass-bundle SK keeps the gate (parity preserved).

diff --git a/R/lnk_pipeline_classify.R b/R/lnk_pipeline_classify.R
@@ -131,6 +131,43 @@ lnk_pipeline_classify <- function(conn, aoi, cfg, loaded, schema,
       verbose = FALSE)
   }
 
+  # fresh#158 stream-order bypass: post-classification, credit direct
+  # tributaries of large-order rivers as rearing even when channel
+  # width is below threshold. Mirrors bcfp's hard-coded
+  # `stream_order_parent >= 5 AND stream_order = 1` predicate in
+  # load_habitat_linear_<sp>.sql for BT/CH/CO/ST/WCT.
+  #
+  # Per-species opt-in driven by `dimensions.csv::rear_stream_order_bypass`,
+  # which `lnk_rules_build` propagates into rules.yaml as
+  # `rear[].channel_width_min_bypass = list(stream_order, stream_order_parent_min)`.
+  # We detect that field's presence on any rear rule and call
+  # `frs_order_child` with the embedded parent_order threshold.
+  for (sp in species) {
+    rear_rules <- params[[sp]][["rules"]][["rear"]]
+    bypass <- NULL
+    for (rr in rear_rules) {
+      if (!is.null(rr[["channel_width_min_bypass"]])) {
+        bypass <- rr[["channel_width_min_bypass"]]
+        break
+      }
+    }
+    if (!is.null(bypass)) {
+      pom    <- bypass[["stream_order_parent_min"]] %||% 5L
+      cs_min <- bypass[["stream_order_min"]]
+      cs_max <- bypass[["stream_order_max"]]
+      dmax   <- bypass[["distance_max"]]
+      fresh::frs_order_child(conn,
+        table   = "fresh.streams",
+        habitat = "fresh.streams_habitat",
+        species = sp,
+        parent_order_min = pom,
+        child_order_min = cs_min,
+        child_order_max = cs_max,
+        distance_max = dmax,
+        verbose = FALSE)
+    }
+  }
+
   invisible(conn)
 }
 

diff --git a/R/lnk_rules_build.R b/R/lnk_rules_build.R
@@ -86,6 +86,22 @@ lnk_rules_build <- function(csv,
       tolower(trimws(dimensions$rear_stream_order_bypass)) == "yes"
   }
 
+  # Optional: per-species `stream_order_parent_min` for the bypass.
+  # Default 5L matches bcfishpass's hard-coded predicate; the column lets
+  # callers tune the threshold without editing the rules YAML by hand.
+  has_sopm <- "rear_stream_order_parent_min" %in% names(dimensions)
+
+  # Optional: per-species child-order range for the bypass. Both default to
+  # 1L (matches bcfp). `_min` and `_max` map to fresh's frs_order_child
+  # `child_order_min` and `child_order_max` arguments.
+  has_csmin <- "rear_stream_order_child_min" %in% names(dimensions)
+  has_csmax <- "rear_stream_order_child_max" %in% names(dimensions)
+
+  # Optional: per-species `distance_max` for the bypass — caps the bypass
+  # to the lower N metres of each direct-trib BLK (segment's
+  # downstream_route_measure <= distance_max). Empty → no cap (whole BLK).
+  has_sodm <- "rear_stream_order_distance_max" %in% names(dimensions)
+
   # Optional: requires_connected columns (value is the habitat type, not yes/no)
   has_spawn_rc <- "spawn_requires_connected" %in% names(dimensions)
   has_rear_rc <- "rear_requires_connected" %in% names(dimensions)
@@ -266,10 +282,35 @@ lnk_rules_build <- function(csv,
       if (!is.na(rlhm)) lake_rule$lake_ha_min <- rlhm
       rear_rules[[1]] <- add_rc(lake_rule, rear_rc, rear_cdm)
     } else {
-      # Stream order bypass: first-order streams with parent order >= 5
-      # bypass rearing channel_width_min
+      # Stream order bypass: first-order streams with parent order
+      # >= stream_order_parent_min bypass rearing channel_width_min.
+      # Threshold defaults to 5L (bcfishpass parity); per-species
+      # `rear_stream_order_parent_min` column overrides when present
+      # and numeric.
       soe_bypass <- if (has_soe && d$rear_stream_order_bypass) {
-        list(stream_order = 1L, stream_order_parent_min = 5L)
+        # Helper: read a positive integer column with default fallback
+        read_pos_int <- function(raw, default) {
+          if (is.null(raw) || is.na(raw) ||
+              nchar(trimws(as.character(raw))) == 0L) return(default)
+          n <- suppressWarnings(as.integer(raw))
+          if (is.na(n) || n < 1L) return(default)
+          n
+        }
+        pom    <- read_pos_int(if (has_sopm)  d$rear_stream_order_parent_min else NULL, 5L)
+        cs_min <- read_pos_int(if (has_csmin) d$rear_stream_order_child_min  else NULL, 1L)
+        cs_max <- read_pos_int(if (has_csmax) d$rear_stream_order_child_max  else NULL, 1L)
+        out <- list(stream_order_min = cs_min,
+                    stream_order_max = cs_max,
+                    stream_order_parent_min = pom)
+        if (has_sodm) {
+          raw_dm <- d$rear_stream_order_distance_max
+          if (!is.null(raw_dm) && !is.na(raw_dm) &&
+              nchar(trimws(as.character(raw_dm))) > 0) {
+            dm <- suppressWarnings(as.numeric(raw_dm))
+            if (!is.na(dm) && dm > 0) out$distance_max <- dm
+          }
+        }
+        out
       } else {
         NULL
       }

diff --git a/data-raw/maps/_lnk_map_compare.R b/data-raw/maps/_lnk_map_compare.R
@@ -140,7 +140,10 @@ lnk_map_compare <- function(wsg, species, habitat,
     function() {
       c <- conn_local(); on.exit(DBI::dbDisconnect(c))
       sf::st_read(c, query = sprintf("
-        SELECT linear_feature_id, blue_line_key, edge_type, geom
+        SELECT linear_feature_id, blue_line_key,
+               downstream_route_measure, edge_type,
+               stream_order, gradient,
+               gnis_name, geom
         FROM whse_basemapping.fwa_stream_networks_sp
         WHERE watershed_group_code = '%s'", wsg))
     })
@@ -201,19 +204,23 @@ lnk_map_compare <- function(wsg, species, habitat,
         " | ", round(length_metre), "m"))
   }
 
-  axis_combined <- dplyr::bind_rows(
-    bcfp_axis |> dplyr::filter(category == "bcfp_only") |> mk_label("bcfp-only"),
-    link_axis |> dplyr::filter(category == "link_only") |> mk_label("link-only"),
-    link_axis |> dplyr::filter(category == "both")      |> mk_label("both"))
+  # Split axis layers per category so each is independently toggleable
+  # in the layers control (link_only / bcfp_only / both).
+  axis_bcfp_only <- bcfp_axis |>
+    dplyr::filter(category == "bcfp_only") |> mk_label("bcfp-only")
+  axis_link_only <- link_axis |>
+    dplyr::filter(category == "link_only") |> mk_label("link-only")
+  axis_both <- link_axis |>
+    dplyr::filter(category == "both") |> mk_label("both")
 
   other_label <- if (habitat == "rearing") "spawning" else "rearing"
-  other_combined <- dplyr::bind_rows(
-    bcfp_other |> mk_label(paste("bcfp", other_label)),
-    link_other |> mk_label(paste("link", other_label)))
+  other_bcfp <- bcfp_other |> mk_label(paste("bcfp", other_label))
+  other_link <- link_other |> mk_label(paste("link", other_label))
 
   # ---- bbox: full WSG (let user zoom) ------------------------------------
 
-  fb <- sf::st_bbox(dplyr::bind_rows(bcfp_axis, link_axis, bcfp_other, link_other))
+  fb <- sf::st_bbox(dplyr::bind_rows(
+    axis_bcfp_only, axis_link_only, axis_both, other_bcfp, other_link))
   pad <- 0.02
   dx <- fb["xmax"] - fb["xmin"]; dy <- fb["ymax"] - fb["ymin"]
   view_bbox <- sf::st_bbox(c(
@@ -223,10 +230,11 @@ lnk_map_compare <- function(wsg, species, habitat,
 
   # ---- mapgl --------------------------------------------------------------
 
-  pal_values <- c("bcfp_only", "link_only", "both")
-  pal_colors <- c("#1f78b4",  "#e31a1c",   "#6a3d9a")
-  pal_labels <- c("bcfp only (link missing)", "link only (extra)", "both")
-  other_color <- "#33a02c"
+  col_bcfp_only <- "#1f78b4"
+  col_link_only <- "#e31a1c"
+  col_both      <- "#6a3d9a"
+  col_other_bcfp <- "#33a02c"  # green (bcfp side of "other" habitat context)
+  col_other_link <- "#b15928"  # brown (link side)
 
   legend_title <- sprintf("%s %s %s — link vs bcfishpass",
     wsg, species, habitat)
@@ -237,21 +245,56 @@ lnk_map_compare <- function(wsg, species, habitat,
       fill_color = "#a6cee3", fill_opacity = 0.4, popup = "gnis_name")
 
   if (underlay) {
+    streams_under <- streams_under |>
+      dplyr::mutate(under_label = paste0(
+        "fwa | lfid ", linear_feature_id,
+        " | blkey ", blue_line_key,
+        " | DRM ", round(downstream_route_measure %||% NA),
+        " | edge ", edge_type,
+        " | order ", stream_order,
+        " | grad ", formatC(gradient, format = "f", digits = 4),
+        ifelse(is.na(gnis_name) | gnis_name == "", "", paste0(" | ", gnis_name))))
     m <- m |> mapgl::add_line_layer(
       id = "streams_all", source = streams_under,
-      line_color = "#cccccc", line_width = 0.4, line_opacity = 0.6)
+      line_color = "#cccccc", line_width = 0.4, line_opacity = 0.6,
+      popup = "under_label")
   }
 
-  m <- m |>
-    mapgl::add_line_layer(
-      id = other_label, source = other_combined,
-      line_color = other_color, line_width = 1.5, line_opacity = 0.85,
-      popup = "label") |>
-    mapgl::add_line_layer(
-      id = habitat, source = axis_combined,
-      line_color = mapgl::match_expr("category",
-        values = pal_values, stops = pal_colors, default = "#999999"),
-      line_width = 3, line_opacity = 0.9, popup = "label")
+  # Spawn / rear context layers (the OTHER habitat) — split per side so
+  # the user can isolate "where does bcfp see spawn?" independently of
+  # link's spawn picture.
+  if (nrow(other_bcfp) > 0) {
+    m <- m |> mapgl::add_line_layer(
+      id = sprintf("%s_bcfp", other_label), source = other_bcfp,
+      line_color = col_other_bcfp, line_width = 1.5, line_opacity = 0.85,
+      popup = "label")
+  }
+  if (nrow(other_link) > 0) {
+    m <- m |> mapgl::add_line_layer(
+      id = sprintf("%s_link", other_label), source = other_link,
+      line_color = col_other_link, line_width = 1.5, line_opacity = 0.85,
+      popup = "label")
+  }
+
+  # Axis (target habitat) layers — three independent toggles.
+  if (nrow(axis_both) > 0) {
+    m <- m |> mapgl::add_line_layer(
+      id = sprintf("%s_both", habitat), source = axis_both,
+      line_color = col_both, line_width = 3, line_opacity = 0.9,
+      popup = "label")
+  }
+  if (nrow(axis_bcfp_only) > 0) {
+    m <- m |> mapgl::add_line_layer(
+      id = sprintf("%s_bcfp_only", habitat), source = axis_bcfp_only,
+      line_color = col_bcfp_only, line_width = 3, line_opacity = 0.9,
+      popup = "label")
+  }
+  if (nrow(axis_link_only) > 0) {
+    m <- m |> mapgl::add_line_layer(
+      id = sprintf("%s_link_only", habitat), source = axis_link_only,
+      line_color = col_link_only, line_width = 3, line_opacity = 0.9,
+      popup = "label")
+  }
 
   for (lyr in extra_layers) {
     m <- m |> mapgl::add_line_layer(
@@ -265,8 +308,14 @@ lnk_map_compare <- function(wsg, species, habitat,
   m <- m |>
     mapgl::add_legend(
       legend_title,
-      values = c(pal_labels, paste(other_label, "(either)")),
-      colors = c(pal_colors, other_color),
+      values = c(
+        "bcfp only (link missing)",
+        "link only (extra)",
+        "both",
+        sprintf("%s (bcfp)", other_label),
+        sprintf("%s (link)", other_label)),
+      colors = c(col_bcfp_only, col_link_only, col_both,
+                 col_other_bcfp, col_other_link),
       type = "categorical", position = "top-right") |>
     mapgl::add_layers_control(collapsible = TRUE, position = "top-left")
 

diff --git a/inst/extdata/configs/bcfishpass/dimensions.csv b/inst/extdata/configs/bcfishpass/dimensions.csv
@@ -1,9 +1,9 @@
-"species","spawn_lake","spawn_stream","spawn_stream_in_waterbody","rear_lake","rear_lake_only","rear_lake_area_only","rear_no_fw","rear_stream","rear_stream_in_waterbody","rear_wetland","rear_wetland_polygon","rear_wetland_area_only","rear_all_edges","river_skip_cw_min","rear_stream_order_bypass","spawn_requires_connected","spawn_connected_distance_max","spawn_connected_direction","spawn_connected_gradient_max","spawn_connected_cw_min","spawn_connected_edge_types","spawn_connected_lake_adjacent","rear_requires_connected","rear_connected_distance_max","notes"
-"BT","no","yes","no","no","no","no","no","yes","no","no","no","no","yes","yes","no","",,"",,,,"",,,"bcfishpass: rear_all_edges=yes means no edge_type filter for rearing."
-"CH","no","yes","no","no","no","no","no","yes","no","no","no","no","no","yes","no","",,"",,,,"",,,"bcfishpass: stream order bypass handled in compare script Step 7b."
-"CM","no","yes","no","no","no","no","yes","no","no","no","no","no","no","yes","no","",,"",,,,"",,,"bcfishpass: no freshwater rearing."
-"CO","no","yes","no","no","no","no","no","yes","yes","yes","no","no","no","yes","no","",,"",,,,"",,,"bcfishpass: wetland-flow carve-out (1050/1150 no thresholds); polygon=no excludes the W-polygon rule."
-"PK","no","yes","no","no","no","no","yes","no","no","no","no","no","no","yes","no","",,"",,,,"",,,"bcfishpass: no freshwater rearing."
-"SK","no","yes","no","yes","yes","no","no","no","no","no","no","no","no","yes","no","rearing",3000,"downstream",0.05,0,,"yes",,,"bcfishpass: lake-only rearing. Spawning within 3km ds of rearing lake."
-"ST","no","yes","no","no","no","no","no","yes","yes","no","no","no","no","yes","no","",,"",,,,"",,,"bcfishpass: stream order bypass handled in compare script Step 7b."
-"WCT","no","yes","no","no","no","no","no","yes","no","no","no","no","no","yes","no","",,"",,,,"",,,"bcfishpass: stream order bypass handled in compare script Step 7b."
+"species","spawn_lake","spawn_stream","spawn_stream_in_waterbody","rear_lake","rear_lake_only","rear_lake_area_only","rear_no_fw","rear_stream","rear_stream_in_waterbody","rear_wetland","rear_wetland_polygon","rear_wetland_area_only","rear_all_edges","river_skip_cw_min","rear_stream_order_bypass","rear_stream_order_parent_min","rear_stream_order_child_min","rear_stream_order_child_max","rear_stream_order_distance_max","spawn_requires_connected","spawn_connected_distance_max","spawn_connected_direction","spawn_connected_gradient_max","spawn_connected_cw_min","spawn_connected_edge_types","spawn_connected_lake_adjacent","rear_requires_connected","rear_connected_distance_max","notes"
+"BT","no","yes","no","no","no","no","no","yes","no","no","no","no","yes","yes","no","","","","","",,"",,,,"",,,"bcfishpass: rear_all_edges=yes means no edge_type filter for rearing."
+"CH","no","yes","no","no","no","no","no","yes","no","no","no","no","no","yes","no","","","","","",,"",,,,"",,,"bcfishpass: stream order bypass handled in compare script Step 7b."
+"CM","no","yes","no","no","no","no","yes","no","no","no","no","no","no","yes","no",,,,,"",,"",,,,"",,,"bcfishpass: no freshwater rearing."
+"CO","no","yes","no","no","no","no","no","yes","yes","yes","no","no","no","yes","no","","","","","",,"",,,,"",,,"bcfishpass: wetland-flow carve-out (1050/1150 no thresholds); polygon=no excludes the W-polygon rule."
+"PK","no","yes","no","no","no","no","yes","no","no","no","no","no","no","yes","no",,,,,"",,"",,,,"",,,"bcfishpass: no freshwater rearing."
+"SK","no","yes","no","yes","yes","no","no","no","no","no","no","no","no","yes","no",,,,,"rearing",3000,"downstream",0.05,0,,"yes",,,"bcfishpass: lake-only rearing. Spawning within 3km ds of rearing lake."
+"ST","no","yes","no","no","no","no","no","yes","yes","no","no","no","no","yes","no","","","","","",,"",,,,"",,,"bcfishpass: stream order bypass handled in compare script Step 7b."
+"WCT","no","yes","no","no","no","no","no","yes","no","no","no","no","no","yes","no","","","","","",,"",,,,"",,,"bcfishpass: stream order bypass handled in compare script Step 7b."