diff --git a/CLAUDE.md b/CLAUDE.md index 39600cc9..d3de400e 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -60,6 +60,31 @@ To compare two code versions, prepare once and re-run classify/connect on the same schema (`data-raw/logs/habitat_thresholds_282/reclassify.R`). Issue drafted, awaiting body review. +## Status (2026-09-26, late) — observation pooling is data (#290); #284 step 5 unparked + +**Which observation species count as which model species is a bundle tracker now, not code.** +- `configs/default/species_pooling.csv` holds one dated, sourced row per decision, scoped to a region, sub-region or WSG. +- `inst/extdata/wsg_regions.csv` is package-level geography: the region is the first segment of each group's *outlet* wscode. +- `species_groups.csv` lets either side of a row be a group. +- `lnk_species_pooling()` resolves it and knows no species. +- **DV → BT pools in the Fraser, Mackenzie and Columbia/Kootenay, and in the Skeena only above Hazelton** (the sub-region `Skeena above Hazelton`: BULK, MORR, KISP, BABL, BABR, SUST, MSKE, USKE). Everything unlisted is not pooled. + - **Why the split:** interior DV is a legacy name (the DV share of char records is ~90 % before 1990 and under 15 % after 2000). Skeena DV is not: 86 % or more in every decade, and 85 % of Skeena DV streams were re-sampled and still recorded DV. The Skeena split was the operator's call, 2026-09-27. + - **The optional `obs_year_max` column** limits a row to records dated in or before a year; undated records do not qualify. It is empty in the seed. +- The state of knowledge lives in `research/species_pooling.md`, with the scenarios from `data-raw/species_pooling_evidence.R`. +- **Do not re-hard-code a species pair anywhere**; add a row. +- **`default_tuned`'s BT `rear_gradient_max` of 0.1349 hangs by a thread.** + - Under the split, the pooled P95 is 0.1309, which clears the 0.13 line that would give 0.1249 by 0.0009. + - With no Skeena pooling, or with interior pooling limited to pre-1995 records, it gives 0.1249. + - #284 step 5 scoring should test both values. + +**Facts not worth re-deriving:** +- **The region rule alone moved no #284 or #283 number** (all 55 + 59 WSGs are in pooled regions). **The Hazelton split does move them:** 852 DV records in LSKE, KLUM, LKEL and ZYMO drop out. No #284 verdict changes. +- **Where the new rule bites:** 29 BT-present WSGs in the Nass, Stikine, Taku, Yukon and the coast, which pooled before and do not now. +- **"No tracker" means no pooling in the resolver**, but the validator's list default (global DV→BT) is kept for back-compat. The driver resolves pooling **once**, from the first bundle declaring a tracker, and applies it to both bundles. +- **Two presence tables must agree, WSG by WSG**: the pooling bundle's and each scored bundle's. Both drivers stop if they do not, and the comparison is keyed by WSG, never by row position (review found the row-position version). +- **The #284 obs producer is not bit-reproducible.** A double-precision `sum(length_metre)` gives 1-ulp differences in `candidates.csv` between identical runs. This is pre-existing: #293. +- **Hand-kept `consumed_by` file:line refs drift on every edit above them.** The two new dictionaries are now test-checked with a whole-token match. + ## Status (2026-09-26) — v0.51.1: first calibrated threshold in `default_tuned` (#284; step 5 open) **`research/habitat_thresholds.md` is the staging table for tuning CH/BT numbers.** One diff --git a/NAMESPACE b/NAMESPACE index 23ff364f..aff3c132 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -53,6 +53,7 @@ export(lnk_rollup_wsg) export(lnk_rules_build) export(lnk_score) export(lnk_source) +export(lnk_species_pooling) export(lnk_stamp) export(lnk_stamp_finish) export(lnk_thresholds) diff --git a/R/lnk_habitat_validate.R b/R/lnk_habitat_validate.R index f91a3ab9..ca024916 100644 --- a/R/lnk_habitat_validate.R +++ b/R/lnk_habitat_validate.R @@ -135,10 +135,20 @@ #' matched on that key). Species and WSG codes are compared upper-cased #' and trimmed. Optional: `match_type`, `source`, `is_spawn`, `is_rear` #' (logical, 0/1 or t/true/yes), `activity_code`, `activity`, -#' `life_stage`. -#' @param species_obs Named list mapping a model species to the observation -#' species codes that count as it. Species not named map to themselves. -#' Default pools DV records with BT (`list(BT = c("BT", "DV"))`). +#' `life_stage`, and `observation_date`, which is required when +#' `species_obs` carries a year limit (`obs_year_max`). +#' @param species_obs Which observation species count as each model species. +#' Either a named list mapping a model species to observation species +#' codes, applied in every WSG (default `list(BT = c("BT", "DV"))`, which +#' pools DV records with BT), or a per-WSG data frame with +#' `watershed_group_code`, `species_code` and `obs_species`, such as +#' [lnk_species_pooling()] returns, optionally with `obs_year_max` (a +#' pooled record counts only if dated in or before that year; an undated +#' one does not). In the list form a species not named +#' maps to itself; in the data frame form a species always counts as +#' itself, and a WSG and species pair it does not list maps to itself only. +#' Either way a species is scored only where +#' `loaded$wsg_species_presence` marks it present. #' @param match_types Character vector of `match_type` classes (first #' letter) to keep, or `NULL` for no match-type filter. Default #' `c("A", "B")`. @@ -216,8 +226,6 @@ lnk_habitat_validate <- function(conn, aoi, cfg, loaded, species, schema, is.character(schema), length(schema) == 1L, !is.na(schema), grepl("^[a-z_][a-z0-9_]*$", schema), is.list(species_obs), - length(species_obs) == 0L || !is.null(names(species_obs)), - all(vapply(species_obs, is.character, logical(1))), is.null(match_types) || (is.character(match_types) && length(match_types) >= 1L && all(grepl("^[A-Z]$", match_types))), @@ -240,8 +248,7 @@ lnk_habitat_validate <- function(conn, aoi, cfg, loaded, species, schema, } aoi <- unique(aoi) species <- unique(toupper(species)) - species_obs <- lapply(species_obs, toupper) - names(species_obs) <- toupper(names(species_obs)) + species_obs <- .lnk_hv_species_obs(species_obs) .lnk_hv_check_schema(conn, schema, aoi, species) logged <- .lnk_hv_check_log(conn, schema, aoi, cfg) @@ -355,26 +362,79 @@ lnk_habitat_validate <- function(conn, aoi, cfg, loaded, species, schema, #' the model species is present. #' @noRd .lnk_hv_spec <- function(presence, aoi, species, species_obs) { + per_wsg <- is.data.frame(species_obs) rows <- lapply(aoi, function(w) { row <- presence[presence$watershed_group_code == w, , drop = FALSE] if (nrow(row) == 0L) return(NULL) present <- intersect(species, .lnk_wsg_species_present(row[1, ])) if (length(present) == 0L) return(NULL) do.call(rbind, lapply(present, function(sp) { - data.frame(watershed_group_code = w, species_code = sp, - obs_species = unique(species_obs[[sp]] %||% sp), - stringsAsFactors = FALSE) + if (per_wsg) { + k <- species_obs$watershed_group_code == w & + species_obs$species_code == sp + obs <- c(sp, species_obs$obs_species[k]) + yr <- c(NA_integer_, species_obs$obs_year_max[k]) + } else { + obs <- species_obs[[sp]] %||% sp + yr <- rep(NA_integer_, length(obs)) + } + d <- unique(data.frame(watershed_group_code = w, species_code = sp, + obs_species = obs, obs_year_max = yr, + stringsAsFactors = FALSE)) + if (anyDuplicated(d$obs_species)) { + stop("species_obs gives ", w, " ", sp, " two year limits for one ", + "observation species", call. = FALSE) + } + d })) }) out <- do.call(rbind, rows) if (is.null(out)) { out <- data.frame(watershed_group_code = character(0), species_code = character(0), - obs_species = character(0), stringsAsFactors = FALSE) + obs_species = character(0), + obs_year_max = integer(0), stringsAsFactors = FALSE) } out } +#' Normalise `species_obs`: a named list (applied in every WSG) or a per-WSG +#' data frame (`watershed_group_code`, `species_code`, `obs_species`). +#' Checked as a data frame first, because a data frame is also a list and +#' would otherwise pass the list checks and silently map nothing. +#' @noRd +.lnk_hv_species_obs <- function(species_obs) { + up <- function(x) toupper(trimws(as.character(x))) + if (is.data.frame(species_obs)) { + cols <- c("watershed_group_code", "species_code", "obs_species") + miss <- setdiff(cols, names(species_obs)) + if (length(miss) > 0L) { + stop("species_obs data frame lacks columns: ", + paste(miss, collapse = ", "), call. = FALSE) + } + out <- data.frame(lapply(species_obs[cols], up), stringsAsFactors = FALSE) + if (anyNA(out) || !all(vapply(out, function(x) all(nzchar(x)), TRUE))) { + stop("species_obs data frame has empty or NA codes", call. = FALSE) + } + # Optional record-date limit from lnk_species_pooling(); NA is no limit. + out$obs_year_max <- if ("obs_year_max" %in% names(species_obs)) { + .lnk_sp_year(species_obs[["obs_year_max"]]) + } else { + rep(NA_integer_, nrow(out)) + } + return(unique(out)) + } + if (!(length(species_obs) == 0L || !is.null(names(species_obs))) || + !all(vapply(species_obs, is.character, logical(1)))) { + stop("species_obs must be a named list of character vectors or a data ", + "frame of watershed_group_code, species_code, obs_species", + call. = FALSE) + } + out <- lapply(species_obs, up) + names(out) <- up(names(out)) + out +} + #' Spawn / rear stage from bcfishobs activity and life stage. #' #' Spawning from activity; rearing from activity or a juvenile life stage. @@ -424,7 +484,8 @@ lnk_habitat_validate <- function(conn, aoi, cfg, loaded, species, schema, cols_req <- c("species_code", "watershed_group_code", "blue_line_key", "downstream_route_measure") cols_opt <- c("observation_key", "match_type", "source", "is_spawn", - "is_rear", "activity_code", "activity", "life_stage") + "is_rear", "activity_code", "activity", "life_stage", + "observation_date") key_generated <- FALSE if (is.data.frame(observations)) { d <- as.data.frame(observations) @@ -506,6 +567,10 @@ lnk_habitat_validate <- function(conn, aoi, cfg, loaded, species, schema, DBI::dbWriteTable(conn, "lnk_vd_excl", data.frame(observation_key = as.character(keys)), temporary = TRUE, overwrite = TRUE) + if (any(!is.na(spec$obs_year_max)) && !has("observation_date")) { + stop(s$src, " has no observation_date column, which the year limits in ", + "species_obs (obs_year_max) need", call. = FALSE) + } DBI::dbWriteTable(conn, "lnk_vd_spec", spec, temporary = TRUE, overwrite = TRUE) uhc <- loaded$user_habitat_classification @@ -541,13 +606,16 @@ lnk_habitat_validate <- function(conn, aoi, cfg, loaded, species, schema, JOIN pg_temp.lnk_vd_spec sp ON sp.watershed_group_code = upper(trim(o.watershed_group_code::text)) AND sp.obs_species = upper(trim(o.species_code::text)) + -- a year-limited pooling admits only records dated within it + AND (sp.obs_year_max IS NULL + OR extract(year FROM %10$s) <= sp.obs_year_max) WHERE TRUE %8$s %9$s) o WHERE NOT EXISTS (SELECT 1 FROM pg_temp.lnk_vd_excl e WHERE e.observation_key = o.observation_key)", s$src, opt("match_type", "text"), opt("activity_code", "text"), opt("activity", "text"), opt("life_stage", "text"), opt_flag("is_spawn"), opt_flag("is_rear"), - where_match, where_source), + where_match, where_source, opt("observation_date", "date")), params = if (is.null(match_types)) NULL else list(paste0("{", paste(match_types, collapse = ","), "}"))) diff --git a/R/lnk_log.R b/R/lnk_log.R index f510e956..e4dc4b76 100644 --- a/R/lnk_log.R +++ b/R/lnk_log.R @@ -98,6 +98,20 @@ digest::digest(file = p, algo = "sha256") }, character(1), USE.NAMES = FALSE) + # A pooling tracker (#290) is scoped by the package's region lookup, which + # sits outside the bundle: a region reassignment changes what pools, so it + # enters the hash too, by a fixed name. + if (!is.null(cfg$files$species_pooling)) { + regions <- .lnk_wsg_regions_path() + paths <- c(paths, regions) + rel <- c(rel, "link:wsg_regions.csv") + digests <- c(digests, if (file.exists(regions)) { + digest::digest(file = regions, algo = "sha256") + } else { + "MISSING" + }) + } + if (length(fallback) == 1L && nzchar(fallback)) { paths <- c(paths, fallback) rel <- c(rel, "fresh:parameters_habitat_thresholds.csv") diff --git a/R/lnk_presence.R b/R/lnk_presence.R index 7c2adace..64156b61 100644 --- a/R/lnk_presence.R +++ b/R/lnk_presence.R @@ -91,8 +91,7 @@ lnk_presence <- function( call. = FALSE) } - species_cols <- setdiff(names(wsg_species_presence), - c("watershed_group_code", "notes")) + species_cols <- .lnk_presence_species_cols(wsg_species_presence) raw_present <- vapply(species_cols, function(sp) { .lnk_presence_truthy(row[[sp]]) diff --git a/R/lnk_species_pooling.R b/R/lnk_species_pooling.R new file mode 100644 index 00000000..625b980c --- /dev/null +++ b/R/lnk_species_pooling.R @@ -0,0 +1,306 @@ +#' Resolve which observation species count as each model species, per WSG +#' +#' Reads a bundle's pooling tracker (`species_pooling.csv`) and species +#' groups (`species_groups.csv`) and returns, for each watershed group in +#' `aoi` and each model species present there, the observation species +#' whose records count as evidence for it. The tool knows nothing about any +#' particular species: pooling Dolly Varden records into bull trout, or all +#' salmon together, is a row in the tracker. +#' +#' A tracker row is `species_code` (the model species or a group of them), +#' `species_obs` (the observation species or a group), `scope_level` +#' (`region`, `subregion` or `wsg`), `scope` (a name in +#' `inst/extdata/wsg_regions.csv`, or a WSG code) and `pool` (`yes` / `no`). +#' An optional `obs_year_max` limits a pooling row to records dated in or +#' before that year, for evidence whose meaning changed over time (a name +#' that was applied to another species until recording practice caught up). +#' Empty means no limit. Other columns (`confidence`, `rationale`, `source`, +#' `verified`, `issue`) are the record of why, and are not read here. +#' +#' For each WSG, target and observation species pair, the applicable rows +#' are resolved in order: +#' 1. the most specific scope wins (`wsg` over `subregion` over `region`); +#' 2. at equal scope, the row naming fewer groups wins (a species-to-species +#' row beats one that names a group); +#' 3. rows still tied must agree on `pool` and `obs_year_max`, or the call +#' errors. +#' +#' Anything no row covers is not pooled. A species always counts as itself, +#' and a model species yields rows only where `wsg_species_presence` marks it +#' present. +#' +#' @param loaded Named list from [lnk_load_overrides()]. Uses +#' `wsg_species_presence` (required: its species columns are also the set of +#' known species codes), `species_pooling` and `species_groups` (both +#' optional; without a tracker nothing is pooled). +#' @param aoi Character vector of watershed group codes. +#' @param species Character vector of model species codes. +#' @param regions Data frame with `watershed_group_code`, `region` and +#' `subregion`, or `NULL` (default) for the package's +#' `inst/extdata/wsg_regions.csv`. +#' +#' @return A data frame, one row per WSG x model species x observation +#' species: `watershed_group_code`, `species_code`, `obs_species`, +#' `scope_level` (`self` for the species itself, else the winning row's +#' level), `scope`, `rule` (the winning row's number in the tracker, `NA` +#' for `self`) and `obs_year_max` (the winning row's year limit, `NA` for +#' none; always `NA` for `self`). Consumers apply the year limit per record, +#' and an undated record does not meet one. Codes are upper case. +#' +#' @seealso [lnk_presence()], [lnk_habitat_validate()] +#' @export +#' +#' @examples +#' cfg <- lnk_config("default") +#' loaded <- suppressWarnings(lnk_load_overrides(cfg)) +#' +#' # Which observation species count as each model species in three groups +#' # on different drainages? +#' p <- lnk_species_pooling(loaded, aoi = c("MORR", "ELKR", "COMX"), +#' species = c("BT", "CO")) +#' p +#' +#' # The pooled rows alone, with the tracker row that decided each one +#' p[p$scope_level != "self", ] +lnk_species_pooling <- function(loaded, aoi, species, regions = NULL) { + stopifnot( + is.list(loaded), + is.character(aoi), length(aoi) > 0L, !anyNA(aoi), + is.character(species), length(species) > 0L, !anyNA(species), + is.null(regions) || is.data.frame(regions) + ) + presence <- loaded$wsg_species_presence + if (!is.data.frame(presence) || + !"watershed_group_code" %in% names(presence)) { + stop("loaded$wsg_species_presence is required", call. = FALSE) + } + norm <- function(x) toupper(trimws(as.character(x))) + aoi <- unique(norm(aoi)) + species <- unique(norm(species)) + + if (is.null(regions)) { + regions <- utils::read.csv(.lnk_wsg_regions_path(), + stringsAsFactors = FALSE, na.strings = "") + } + miss <- setdiff(c("watershed_group_code", "region", "subregion"), + names(regions)) + if (length(miss) > 0L) { + stop("regions lacks columns: ", paste(miss, collapse = ", "), + call. = FALSE) + } + regions$watershed_group_code <- norm(regions$watershed_group_code) + if (anyNA(regions$watershed_group_code) || + anyDuplicated(regions$watershed_group_code)) { + stop("regions$watershed_group_code must be unique and not NA", + call. = FALSE) + } + unknown_aoi <- setdiff(aoi, regions$watershed_group_code) + if (length(unknown_aoi) > 0L) { + stop("WSGs not in the region lookup: ", + paste(unknown_aoi, collapse = ", "), call. = FALSE) + } + + known_species <- norm(.lnk_presence_species_cols(presence)) + unknown_sp <- setdiff(species, known_species) + if (length(unknown_sp) > 0L) { + stop("species not in wsg_species_presence: ", + paste(unknown_sp, collapse = ", "), call. = FALSE) + } + groups <- .lnk_sp_groups(loaded$species_groups, known_species) + rules <- .lnk_sp_rules(loaded$species_pooling, groups, known_species, + regions) + + presence$watershed_group_code <- norm(presence$watershed_group_code) + out <- lapply(aoi, function(w) { + prow <- presence[which(presence$watershed_group_code == w), , drop = FALSE] + if (nrow(prow) == 0L) return(NULL) + if (nrow(prow) > 1L) { + stop("wsg_species_presence has ", nrow(prow), " rows for ", w, + call. = FALSE) + } + present <- intersect(species, .lnk_wsg_species_present(prow)) + if (length(present) == 0L) return(NULL) + reg <- regions[which(regions$watershed_group_code == w), , drop = FALSE] + hit <- rules[ + (rules$scope_level == "wsg" & rules$scope_key == w) | + (rules$scope_level == "subregion" & + rules$scope_key %in% norm(reg$subregion)) | + (rules$scope_level == "region" & + rules$scope_key %in% norm(reg$region)), + , drop = FALSE] + hit <- hit[hit$target %in% present, , drop = FALSE] + self <- data.frame(watershed_group_code = w, species_code = present, + obs_species = present, scope_level = "self", + scope = NA_character_, rule = NA_integer_, + obs_year_max = NA_integer_, stringsAsFactors = FALSE) + if (nrow(hit) == 0L) return(self) + won <- lapply(split(hit, paste(hit$target, hit$obs)), function(h) { + h <- h[h$scope_rank == min(h$scope_rank), , drop = FALSE] + h <- h[h$taxon_rank == min(h$taxon_rank), , drop = FALSE] + if (length(unique(paste(h$pool, h$obs_year_max))) > 1L) { + stop(sprintf( + "species_pooling conflict for %s <- %s in %s: rows %s tie at %s scope and disagree on pool or obs_year_max", + h$target[1], h$obs[1], w, paste(sort(unique(h$rule)), collapse = ", "), + h$scope_level[1]), call. = FALSE) + } + h[order(h$rule), ][1, ] + }) + won <- do.call(rbind, won) + won <- won[won$pool, , drop = FALSE] + rbind(self, data.frame(watershed_group_code = rep(w, nrow(won)), + species_code = won$target, + obs_species = won$obs, + scope_level = won$scope_level, + scope = won$scope, + rule = won$rule, + obs_year_max = won$obs_year_max, + stringsAsFactors = FALSE)) + }) + out <- do.call(rbind, out) + if (is.null(out)) { + out <- data.frame(watershed_group_code = character(0), + species_code = character(0), + obs_species = character(0), + scope_level = character(0), scope = character(0), + rule = integer(0), obs_year_max = integer(0), + stringsAsFactors = FALSE) + } + out <- out[order(out$watershed_group_code, out$species_code, + out$scope_level != "self", out$obs_species), ] + rownames(out) <- NULL + out +} + +#' Path to the package's WSG region lookup (`inst/extdata/wsg_regions.csv`). +#' One place, so the resolver and `.lnk_config_hash()` read the same file. +#' @noRd +.lnk_wsg_regions_path <- function() { + p <- system.file("extdata", "wsg_regions.csv", package = "link") + # system.file() returns "" for a missing file, and read.csv("") reads stdin + if (!nzchar(p)) stop("link's inst/extdata/wsg_regions.csv is missing", call. = FALSE) + p +} + +#' Validate species groups; named list group_code -> member species. +#' @noRd +.lnk_sp_groups <- function(species_groups, known_species) { + if (is.null(species_groups) || nrow(species_groups) == 0L) return(list()) + miss <- setdiff(c("group_code", "species_code"), names(species_groups)) + if (length(miss) > 0L) { + stop("species_groups lacks columns: ", paste(miss, collapse = ", "), + call. = FALSE) + } + g <- toupper(trimws(species_groups$group_code)) + s <- toupper(trimws(species_groups$species_code)) + if (anyNA(g) || anyNA(s) || !all(nzchar(g)) || !all(nzchar(s))) { + stop("species_groups has an empty group_code or species_code", + call. = FALSE) + } + clash <- intersect(unique(g), known_species) + if (length(clash) > 0L) { + stop("species_groups group codes that are also species codes: ", + paste(clash, collapse = ", "), call. = FALSE) + } + nested <- intersect(unique(s), unique(g)) + if (length(nested) > 0L) { + stop("species_groups may not nest groups; members that are groups: ", + paste(nested, collapse = ", "), call. = FALSE) + } + unknown <- setdiff(s, known_species) + if (length(unknown) > 0L) { + stop("species_groups members that are not known species: ", + paste(unknown, collapse = ", "), call. = FALSE) + } + lapply(split(s, g), unique) +} + +#' Parse `obs_year_max`: empty or NA is no limit; anything else a whole year. +#' @noRd +.lnk_sp_year <- function(x) { + v <- trimws(as.character(x)) + v[is.na(v)] <- "" + y <- suppressWarnings(as.numeric(v)) + bad <- which(nzchar(v) & (is.na(y) | y != round(y) | y < 1800 | y > 2100)) + if (length(bad) > 0L) { + stop(sprintf("species_pooling rows %s: obs_year_max must be a year or empty", + paste(bad, collapse = ", ")), call. = FALSE) + } + as.integer(ifelse(nzchar(v), y, NA)) +} + +#' Validate the tracker and expand groups into one row per target x obs. +#' @noRd +.lnk_sp_rules <- function(species_pooling, groups, known_species, regions) { + empty <- data.frame(target = character(0), obs = character(0), + scope_level = character(0), scope = character(0), + scope_key = character(0), pool = logical(0), + scope_rank = integer(0), taxon_rank = integer(0), + rule = integer(0), obs_year_max = integer(0), + stringsAsFactors = FALSE) + if (is.null(species_pooling) || nrow(species_pooling) == 0L) return(empty) + cols <- c("species_code", "species_obs", "scope_level", "scope", "pool") + miss <- setdiff(cols, names(species_pooling)) + if (length(miss) > 0L) { + stop("species_pooling lacks columns: ", paste(miss, collapse = ", "), + call. = FALSE) + } + p <- species_pooling + up <- function(x) toupper(trimws(as.character(x))) + for (col in cols) { + v <- trimws(as.character(p[[col]])) + bad <- which(is.na(v) | !nzchar(v)) + if (length(bad) > 0L) { + stop(sprintf("species_pooling has an empty %s in rows %s", col, + paste(bad, collapse = ", ")), call. = FALSE) + } + } + level <- tolower(trimws(p$scope_level)) + bad <- which(!level %in% c("region", "subregion", "wsg")) + if (length(bad) > 0L) { + stop(sprintf("species_pooling rows %s: scope_level must be region, subregion or wsg", + paste(bad, collapse = ", ")), call. = FALSE) + } + pool <- tolower(trimws(p$pool)) + bad <- which(!pool %in% c("yes", "no")) + if (length(bad) > 0L) { + stop(sprintf("species_pooling rows %s: pool must be yes or no", + paste(bad, collapse = ", ")), call. = FALSE) + } + key <- up(p$scope) + valid <- list( + region = unique(up(stats::na.omit(regions$region))), + subregion = unique(up(stats::na.omit(regions$subregion))), + wsg = up(regions$watershed_group_code)) + bad <- which(!mapply(function(l, k) k %in% valid[[l]], level, key)) + if (length(bad) > 0L) { + stop(sprintf("species_pooling rows %s name a scope not in the region lookup: %s", + paste(bad, collapse = ", "), + paste(unique(trimws(p$scope[bad])), collapse = ", ")), + call. = FALSE) + } + expand <- function(code) { + if (code %in% names(groups)) return(groups[[code]]) + if (code %in% known_species) return(code) + stop("species_pooling names '", code, + "', which is neither a known species nor a species_groups group", + call. = FALSE) + } + year <- .lnk_sp_year(p$obs_year_max %||% rep(NA, nrow(p))) + scope_rank <- c(wsg = 1L, subregion = 2L, region = 3L) + rows <- lapply(seq_len(nrow(p)), function(i) { + t_code <- up(p$species_code[i]) + o_code <- up(p$species_obs[i]) + grid <- expand.grid(target = expand(t_code), obs = expand(o_code), + stringsAsFactors = FALSE) + grid <- grid[grid$target != grid$obs, , drop = FALSE] + if (nrow(grid) == 0L) return(NULL) + data.frame(grid, scope_level = level[i], scope = trimws(p$scope[i]), + scope_key = key[i], pool = pool[i] == "yes", + scope_rank = scope_rank[[level[i]]], + taxon_rank = (t_code %in% names(groups)) + + (o_code %in% names(groups)), + rule = i, obs_year_max = year[i], stringsAsFactors = FALSE) + }) + out <- do.call(rbind, rows) + if (is.null(out)) empty else out +} diff --git a/R/utils.R b/R/utils.R index ada34147..6f915d76 100644 --- a/R/utils.R +++ b/R/utils.R @@ -122,6 +122,12 @@ } +# The species columns of a wsg_species_presence frame: everything but the key +# and `notes`. One definition, shared by every reader of the table (#290). +.lnk_presence_species_cols <- function(x) { + setdiff(names(x), c("watershed_group_code", "notes")) +} + #' Species codes flagged present in a wsg_species_presence row. #' #' Treats every column except `watershed_group_code` and `notes` as a @@ -133,7 +139,7 @@ #' a code edit. See link#106. #' @noRd .lnk_wsg_species_present <- function(row) { - spp_cols <- setdiff(names(row), c("watershed_group_code", "notes")) + spp_cols <- .lnk_presence_species_cols(row) present <- vapply(spp_cols, function(x) identical(row[[x]], "t"), logical(1)) toupper(spp_cols[present]) diff --git a/data-raw/habitat_validate.R b/data-raw/habitat_validate.R index 3391e918..88b90704 100644 --- a/data-raw/habitat_validate.R +++ b/data-raw/habitat_validate.R @@ -11,6 +11,14 @@ # Rscript data-raw/habitat_validate.R \ # --bundles=default:fresh_default,bcfishpass:fresh \ # [--wsgs=MORR,BULK] [--species=CH,BT] [--buffers=0,100] [--out=] +# [--pooling=] +# +# Pooling (link#290): which observation species count as each model species +# comes from one bundle's tracker (species_pooling.csv, resolved per WSG by +# lnk_species_pooling()), by default the first of --bundles that declares +# one. It is resolved once and applied to both bundles, so they are scored on +# the same observations, and stamp.txt says which tracker it was. When no +# bundle declares a tracker, lnk_habitat_validate()'s own default applies. # # Absences (optional): with LNK_KNOWLEDGE_DIR pointing at the private # `knowledge` repo, FISS data-submission sites that were sampled (effort @@ -78,6 +86,7 @@ if (anyNA(buffers) || !0 %in% buffers) { } wsgs_arg <- toupper(split_csv(opt("wsgs"))) dir_out <- opt("out", file.path("data-raw", "logs", "habitat_validate_283")) +pooling_cfg <- opt("pooling") fs::dir_create(dir_out) # Clear this script's outputs first, so a partial or one-bundle run cannot # leave an older stamp or diff beside new CSVs. @@ -204,6 +213,56 @@ absences <- fiss_absences() abs_note <- attr(absences, "reason") if (!is.null(abs_note)) absences <- NULL +# -- pooling: resolved once, from one bundle ----------------------------------- +if (is.null(pooling_cfg)) { + declares <- vapply(bundles$config, function(b) { + !is.null(lnk_config(b)$files$species_pooling) + }, logical(1)) + pooling_cfg <- if (any(declares)) bundles$config[which(declares)[1]] else NULL +} +loaded_pool <- if (is.null(pooling_cfg)) list() else + suppressWarnings(lnk_load_overrides(lnk_config(pooling_cfg))) +args_pool <- list() +pooling_note <- "no bundle declares a species_pooling tracker: lnk_habitat_validate() default" +if (!is.null(pooling_cfg) && is.null(loaded_pool$species_pooling)) { + stop("--pooling=", pooling_cfg, " declares no species_pooling tracker", + call. = FALSE) +} +if (!is.null(loaded_pool$species_pooling)) { + # The pooling table is resolved against the pooling bundle's presence, and + # each bundle is then scored against its own. If they disagree on a species + # in play, pooled records drop silently in the WSGs where they differ. + presence_flags <- function(p, w) { + p <- as.data.frame(p) + names(p) <- tolower(names(p)) + p <- p[match(w, toupper(p$watershed_group_code)), tolower(species), drop = FALSE] + vapply(p, function(x) as.character(x) %in% "t", logical(length(w))) + } + for (i in seq_len(nrow(bundles))) { + lp <- suppressWarnings(lnk_load_overrides(lnk_config(bundles$config[i]))) + w <- bundle_wsgs[[i]] + if (!identical(presence_flags(lp$wsg_species_presence, w), + presence_flags(loaded_pool$wsg_species_presence, w))) { + stop("bundle ", bundles$config[i], "'s wsg_species_presence differs ", + "from --pooling=", pooling_cfg, "'s for ", + paste(species, collapse = ", "), " in its WSGs", call. = FALSE) + } + } + args_pool$species_obs <- lnk_species_pooling( + loaded_pool, aoi = sort(unique(unlist(bundle_wsgs))), species = species) + pooled <- args_pool$species_obs[args_pool$species_obs$scope_level != "self", ] + pooling_note <- sprintf("%s species_pooling.csv (sha256 %s): %d WSG x species pairs pooled (%s)", + pooling_cfg, + substr(digest::digest( + file = lnk_config(pooling_cfg)$files$species_pooling$path, + algo = "sha256"), 1, 12), nrow(unique(pooled[c("watershed_group_code", + "species_code")])), + if (nrow(pooled) == 0L) "none" else + paste(unique(paste0(pooled$species_code, "<-", + pooled$obs_species)), + collapse = ", ")) +} + # -- validate ------------------------------------------------------------------ runs <- list() for (i in seq_len(nrow(bundles))) { @@ -214,10 +273,11 @@ for (i in seq_len(nrow(bundles))) { bundles$config[i], bundles$schema[i], length(bundle_wsgs[[i]]), b)) runs[[length(runs) + 1L]] <- c( - lnk_habitat_validate(conn, aoi = bundle_wsgs[[i]], cfg = cfg, - loaded = loaded, species = species, - schema = bundles$schema[i], buffer_m = b, - absences = absences), + do.call(lnk_habitat_validate, + c(list(conn, aoi = bundle_wsgs[[i]], cfg = cfg, + loaded = loaded, species = species, + schema = bundles$schema[i], buffer_m = b, + absences = absences), args_pool)), list(bundle = paste0(bundles$config[i], ":", bundles$schema[i]))) } } @@ -388,6 +448,7 @@ stamp <- c( log_lines, sprintf("species: %s; buffers: %s m", paste(species, collapse = ","), paste(buffers, collapse = ",")), + sprintf("pooling: %s", pooling_note), sprintf("bcfishobs.observations rows: %s", dbGetQuery(conn, "SELECT count(*) FROM bcfishobs.observations")[[1]]), if (!is.null(abs_note)) sprintf("absences: none (%s)", abs_note) else diff --git a/data-raw/logs/habitat_thresholds_284/README.md b/data-raw/logs/habitat_thresholds_284/README.md index 79c06f2a..9f57fc4a 100644 --- a/data-raw/logs/habitat_thresholds_284/README.md +++ b/data-raw/logs/habitat_thresholds_284/README.md @@ -28,8 +28,9 @@ Both are read-only against docker `fwapg` (:5432). Environment stamps are in 1 is avoided or under-sampled. - **Sets**: `CH_spawn` = activity SPL/SPM/S; `CH_rear` = activity R/REA or Fry/Parr/Juvenile. BT has no stage in bcfishobs. **`BT_any_dv` is the primary BT - evidence**: BT and DV records pooled in WSGs with BT, the way the pipeline already counts - them for access (`BT;DV`). Inland, DV are bull trout recorded under the other name, and + evidence**: BT and DV records pooled where `default`'s `species_pooling.csv` pools them (#290: + Fraser, Mackenzie, Skeena and Columbia, where BT is present; before #290, every WSG with + BT). All 55 WSGs here are in those regions, so the evidence is unchanged. Inland, DV are bull trout recorded under the other name, and on the coast the two species' habitat biology is treated as equivalent. `BT_any` (BT records only) is kept as the comparison: `candidates.csv` and `bridge_bt.csv` carry both, marked by `evidence_role` / `set`. `BT_spawn_dv` and `BT_rear_dv` are the staged DV diff --git a/data-raw/logs/habitat_thresholds_284/bridge_bt.csv b/data-raw/logs/habitat_thresholds_284/bridge_bt.csv index 3f5d01a4..5d9bd721 100644 --- a/data-raw/logs/habitat_thresholds_284/bridge_bt.csv +++ b/data-raw/logs/habitat_thresholds_284/bridge_bt.csv @@ -1,10 +1,10 @@ set,passes_predicate,rearing,accessible,n,share -BT_any_dv,FALSE,FALSE,FALSE,31,0.006073667711598746 -BT_any_dv,FALSE,FALSE,TRUE,874,0.17123824451410657 -BT_any_dv,FALSE,TRUE,TRUE,154,0.03017241379310345 -BT_any_dv,TRUE,FALSE,FALSE,7,0.001371473354231975 -BT_any_dv,TRUE,FALSE,TRUE,85,0.01665360501567398 -BT_any_dv,TRUE,TRUE,TRUE,3953,0.7744905956112853 +BT_any_dv,FALSE,FALSE,FALSE,19,0.0044444444444444444 +BT_any_dv,FALSE,FALSE,TRUE,707,0.16538011695906432 +BT_any_dv,FALSE,TRUE,TRUE,138,0.032280701754385965 +BT_any_dv,TRUE,FALSE,FALSE,4,9.356725146198831e-4 +BT_any_dv,TRUE,FALSE,TRUE,62,0.014502923976608188 +BT_any_dv,TRUE,TRUE,TRUE,3345,0.7824561403508772 BT_any,FALSE,FALSE,FALSE,11,0.004296875 BT_any,FALSE,FALSE,TRUE,351,0.137109375 BT_any,FALSE,TRUE,TRUE,50,0.01953125 diff --git a/data-raw/logs/habitat_thresholds_284/candidates.csv b/data-raw/logs/habitat_thresholds_284/candidates.csv index c841834f..ba7fce65 100644 --- a/data-raw/logs/habitat_thresholds_284/candidates.csv +++ b/data-raw/logs/habitat_thresholds_284/candidates.csv @@ -3,17 +3,17 @@ CH,spawn_gradient_max,CH_spawn,primary,0.0449,226,0.044275,0.0449,0.458114788836 CH,rear_gradient_max,CH_rear,primary,0.0549,497,0.059559999999999995,0.054900000000000004,0.5132900582683886,keep,,,,, CH,spawn_channel_width_min,CH_spawn,primary,4,67,6.6370000000000005,6.6,,change,,,,, CH,rear_channel_width_min,CH_rear,primary,1.5,215,1.714,1.7,,keep,,,,, -BT,spawn_gradient_max,BT_spawn_dv,primary,0.0549,76,0.19642500000000002,0.1949,1.3243211974618845,change,,,,, -BT,rear_gradient_max,BT_any_dv,primary,0.1049,4764,0.13482499999999972,0.1349,0.7234104861018281,change,,,,, +BT,spawn_gradient_max,BT_spawn_dv,primary,0.0549,59,0.19538999999999995,0.1949,1.137270180871223,change,,,,, +BT,rear_gradient_max,BT_any_dv,primary,0.1049,3988,0.1308949999999999,0.1349,0.691339529747063,change,,,,, BT,rear_gradient_max,BT_any,comparison: BT records only,0.1049,2443,0.12533000000000008,0.1249,0.594507121781058,change,,,,, -BT,spawn_channel_width_min,BT_spawn_dv,primary,2,53,1.16,1.2,,change,,,,, -BT,rear_channel_width_min,BT_any_dv,primary,1.5,3035,1.48,1.5,,keep,,,,, +BT,spawn_channel_width_min,BT_spawn_dv,primary,2,40,1.1235,1.1,,change,,,,, +BT,rear_channel_width_min,BT_any_dv,primary,1.5,2533,1.47,1.5,,keep,,,,, BT,rear_channel_width_min,BT_any,comparison: BT records only,1.5,1469,1.9120000000000001,1.9,,keep,,,,, -CH,spawn_gradient_min,CH_spawn,primary,0,226,,,,keep,0.001,0.35398230088495575,0.11325447588492017,3.125548002576457, +CH,spawn_gradient_min,CH_spawn,primary,0,226,,,,keep,0.001,0.35398230088495575,0.11325447588492016,3.125548002576457, CH,spawn_gradient_min,CH_spawn,primary,0,226,,,,keep,0.0025,0.41150442477876104,0.14603458433984534,2.8178559663724987, -CH,spawn_gradient_min,CH_spawn,primary,0,226,,,,keep,0.005,0.4911504424778761,0.19031838731696,2.580677828358773, -BT,spawn_gradient_min,BT_spawn_dv,primary,0,76,,,,keep,0.001,0.13157894736842105,0.06124296573643084,2.1484744539428844, -BT,spawn_gradient_min,BT_spawn_dv,primary,0,76,,,,keep,0.0025,0.18421052631578946,0.08162888627134028,2.2566830778930442, -BT,spawn_gradient_min,BT_spawn_dv,primary,0,76,,,,keep,0.005,0.18421052631578946,0.11064730346196426,1.6648442442983986, -BT,cluster_bridge_gradient,BT_any_dv,primary,0.05,5104,,,,keep,,,,,0.01665360501567398 +CH,spawn_gradient_min,CH_spawn,primary,0,226,,,,keep,0.005,0.4911504424778761,0.19031838731695996,2.5806778283587732, +BT,spawn_gradient_min,BT_spawn_dv,primary,0,59,,,,keep,0.001,0.11864406779661017,0.06124296573643084,1.9372684906739233, +BT,spawn_gradient_min,BT_spawn_dv,primary,0,59,,,,keep,0.0025,0.1694915254237288,0.08162888627134028,2.0763669966086122, +BT,spawn_gradient_min,BT_spawn_dv,primary,0,59,,,,keep,0.005,0.1694915254237288,0.11064730346196426,1.531817948749132, +BT,cluster_bridge_gradient,BT_any_dv,primary,0.05,4275,,,,keep,,,,,0.014502923976608188 BT,cluster_bridge_gradient,BT_any,comparison: BT records only,0.05,2560,,,,keep,,,,,0.012109375 diff --git a/data-raw/logs/habitat_thresholds_284/fig_selection_gradient.png b/data-raw/logs/habitat_thresholds_284/fig_selection_gradient.png index 4ac28d4d..3fbf5363 100644 Binary files a/data-raw/logs/habitat_thresholds_284/fig_selection_gradient.png and b/data-raw/logs/habitat_thresholds_284/fig_selection_gradient.png differ diff --git a/data-raw/logs/habitat_thresholds_284/fig_selection_width.png b/data-raw/logs/habitat_thresholds_284/fig_selection_width.png index 945527a0..f190b602 100644 Binary files a/data-raw/logs/habitat_thresholds_284/fig_selection_width.png and b/data-raw/logs/habitat_thresholds_284/fig_selection_width.png differ diff --git a/data-raw/logs/habitat_thresholds_284/obs_ledger.csv b/data-raw/logs/habitat_thresholds_284/obs_ledger.csv index 43052d28..c6f3baf9 100644 --- a/data-raw/logs/habitat_thresholds_284/obs_ledger.csv +++ b/data-raw/logs/habitat_thresholds_284/obs_ledger.csv @@ -8,18 +8,18 @@ step,obs_species,n 2 minus Releases Database,BT,11247 2 minus Releases Database,CH,9002 2 minus Releases Database,DV,13090 -3 DV kept only where WSG has BT (pooled with BT),BT,11247 -3 DV kept only where WSG has BT (pooled with BT),CH,9002 -3 DV kept only where WSG has BT (pooled with BT),DV,8888 +3 pooled species kept only where species_pooling.csv pools them into a present model species,BT,11247 +3 pooled species kept only where species_pooling.csv pools them into a present model species,CH,9002 +3 pooled species kept only where species_pooling.csv pools them into a present model species,DV,4880 4 in fresh_default WSGs where species present,BT,4844 4 in fresh_default WSGs where species present,CH,3544 -4 in fresh_default WSGs where species present,DV,3981 +4 in fresh_default WSGs where species present,DV,2723 5 joined to a segment,BT,4844 5 joined to a segment,CH,3544 -5 joined to a segment,DV,3981 +5 joined to a segment,DV,2723 "6 match type A/B (stream, within 100 m)",BT,3297 "6 match type A/B (stream, within 100 m)",CH,2971 -"6 match type A/B (stream, within 100 m)",DV,3457 +"6 match type A/B (stream, within 100 m)",DV,2327 7 deduplicated to one per species x blue_line_key x metre,BT,2560 7 deduplicated to one per species x blue_line_key x metre,CH,1745 -7 deduplicated to one per species x blue_line_key x metre,DV,2822 +7 deduplicated to one per species x blue_line_key x metre,DV,1970 diff --git a/data-raw/logs/habitat_thresholds_284/obs_segments.csv b/data-raw/logs/habitat_thresholds_284/obs_segments.csv index 4d60dd85..8c1ddf69 100644 --- a/data-raw/logs/habitat_thresholds_284/obs_segments.csv +++ b/data-raw/logs/habitat_thresholds_284/obs_segments.csv @@ -5195,33 +5195,20 @@ e564a4cb8e,DV,BT,TOOD,359572999,32108,A,FALSE,FALSE,1,200,45744,1,0.0013,0.0196, 3bfb4663fd,DV,BT,NATR,359573116,1709,A,FALSE,FALSE,1,200,34980,1,0.0024,0.0103,0.008829084484043506,10.97,MODELLED,1000,5,,stream,TRUE,TRUE,TRUE 4a296e494e,DV,BT,MSKE,360213317,978,A,FALSE,FALSE,1,400,14,1,0,0,,,,1100,1,,stream,TRUE,FALSE,FALSE b625d0dca8,DV,BT,MORR,360216143,117,B,FALSE,TRUE,1,400,83,1,0,0,0,58.49,MODELLED,1100,4,W,wetland,TRUE,FALSE,TRUE -964c2cfaaf,DV,BT,LSKE,360216959,831,B,FALSE,FALSE,1,400,357,1,0,0,0,188.95,MODELLED,1350,2,R,river_poly,TRUE,TRUE,TRUE -e842f1356e,DV,BT,KLUM,360217417,74,A,FALSE,FALSE,1,400,20,1,0.0013,0.0013,9.722881809635453e-4,59.57,MODELLED,1350,4,R,river_poly,TRUE,TRUE,TRUE -1dde3fb3fb,DV,BT,ZYMO,360220816,647,A,FALSE,FALSE,1,400,37,1,0.0134,0.005,0.010660639559447418,54.23,MODELLED,1100,3,,stream,TRUE,TRUE,TRUE -c188995499,DV,BT,LSKE,360223771,375,B,FALSE,FALSE,1,400,773,1,9e-4,0.0038,0.001358926418107629,182.93,MODELLED,1350,5,R,river_poly,TRUE,TRUE,TRUE -662f9a31c1,DV,BT,ZYMO,360225985,1208,B,FALSE,TRUE,1,400,92,1,0,0,0.002557080297185337,,,1100,1,,stream,TRUE,FALSE,FALSE -91017d77d6,DV,BT,KLUM,360228652,1907,B,FALSE,FALSE,1,400,264,1,0,0,1.0119666055516063e-4,50.66,MODELLED,1100,2,,stream,TRUE,TRUE,TRUE 3d954f469a,DV,BT,MORR,360228910,196,B,FALSE,TRUE,1,400,276,1,0.0284,0.0214,0.032330549217286945,,,1100,1,,stream,TRUE,FALSE,FALSE aaf8745565,DV,BT,MORR,360230530,1821,A,FALSE,FALSE,1,400,295,1,0.0127,0.0243,0.017036982204112972,,,1100,1,,stream,TRUE,FALSE,FALSE 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-916cea80f8,DV,BT,LSKE,360887108,9447,B,FALSE,TRUE,1,400,36720,1,0.0191,0.0266,0.01740517855363578,62.86,FWA_RIVERS_POLY,1250,4,R,river_poly,TRUE,TRUE,TRUE -3e0339f134,DV,BT,LSKE,360887108,9459,B,FALSE,TRUE,6,400,36721,1,0.0191,0.0191,0.017006378077352904,62.86,FWA_RIVERS_POLY,1250,4,R,river_poly,TRUE,TRUE,TRUE 268fa3f91e,DV,BT,KISP,360887129,560,A,FALSE,FALSE,1,400,30575,1,0.0489,0.0496,0.04426008896002486,5.34,MODELLED,1000,4,,stream,TRUE,TRUE,TRUE a4d89e8c5f,DV,BT,MORR,360887227,3332,A,FALSE,TRUE,1,400,29051,1,0.0946,0.0841,0.15118442433558926,3.02,FIELD_MEASURMENT,1000,3,,stream,TRUE,FALSE,TRUE 09a5719be6,DV,BT,KISP,360887278,269912,A,FALSE,FALSE,1,400,30685,1,0.0018,0.0018,0.0017507321899100248,191.82,FWA_RIVERS_POLY,1250,8,R,river_poly,TRUE,TRUE,TRUE @@ -7105,7 +6257,6 @@ a4d89e8c5f,DV,BT,MORR,360887227,3332,A,FALSE,TRUE,1,400,29051,1,0.0946,0.0841,0. 608ccf7e39,DV,BT,MSKE,360887278,372249,A,FALSE,FALSE,1,400,29655,1,0,2e-4,1.5285758287518546e-4,123.68,FWA_RIVERS_POLY,1250,8,R,river_poly,TRUE,TRUE,TRUE b39cf361ee,DV,BT,MSKE,360887278,390220,A,FALSE,FALSE,1,400,29695,1,0.0028,4e-4,0.002139294754395564,67.31,FWA_RIVERS_POLY,1250,8,R,river_poly,TRUE,TRUE,TRUE 0b68591c1f,DV,BT,MSKE,360887278,399230,A,FALSE,FALSE,1,400,29723,1,0.0015,9e-4,0.0021423687213734865,74.2,FWA_RIVERS_POLY,1250,8,R,river_poly,TRUE,TRUE,TRUE -31bca8042c,DV,BT,LSKE,360887278,43535,A,FALSE,FALSE,1,400,36942,1,0,0,0,457.47,FWA_RIVERS_POLY,1250,9,R,river_poly,TRUE,TRUE,TRUE b84c77bc55,DV,BT,MSKE,360887278,474060,A,FALSE,FALSE,1,400,29890,1,0.0075,0.0075,0.007475927261488095,86.05,FWA_RIVERS_POLY,1250,8,R,river_poly,TRUE,TRUE,TRUE 5cbd7d0006,DV,BT,MSKE,360887278,474108,B,FALSE,FALSE,1,400,29891,1,0.0075,0.0075,0.006547412940818731,86.05,FWA_RIVERS_POLY,1250,8,R,river_poly,TRUE,TRUE,TRUE c35bf3a7f8,DV,BT,USKE,360887278,545748,A,FALSE,FALSE,1,400,26193,1,0,0.0034,0,64.69,FWA_RIVERS_POLY,1250,7,R,river_poly,TRUE,TRUE,TRUE @@ -7119,9 +6270,6 @@ cf3f201260,DV,BT,BULK,360887296,17570,A,FALSE,FALSE,1,400,42742,1,0.0156,0.0313, dadc2e9034,DV,BT,BULK,360887296,30897,A,FALSE,TRUE,1,400,42775,1,0.0975,0.1048,0.0932356804878168,2.34,MODELLED,1000,3,,stream,TRUE,FALSE,FALSE ea5f0217bd,DV,BT,BULK,360887296,31004,A,FALSE,TRUE,1,400,42777,1,0.0816,0.0841,0.08268558475538612,1.7,FIELD_MEASURMENT,1000,3,,stream,TRUE,FALSE,FALSE f6b7e4804c,DV,BT,KISP,360887384,1355,A,FALSE,TRUE,1,400,30862,1,0.0281,0.0177,0.03000067180057272,4.23,FIELD_MEASURMENT,1000,3,,stream,TRUE,TRUE,TRUE -91dd5c5de8,DV,BT,LSKE,360887399,17085,A,FALSE,FALSE,1,400,37402,1,0,0,0,49.09,FWA_RIVERS_POLY,1250,5,R,river_poly,TRUE,TRUE,TRUE -12451b7fc9,DV,BT,LSKE,360887399,23613,A,FALSE,FALSE,1,400,37438,1,0,0,0,38.29,FWA_RIVERS_POLY,1250,5,R,river_poly,TRUE,TRUE,TRUE -7012d6dbfe,DV,BT,LSKE,360887399,6135,A,FALSE,FALSE,1,400,37364,1,0,0,0,77.43,FWA_RIVERS_POLY,1250,6,R,river_poly,TRUE,TRUE,TRUE 54188ece3d,DV,BT,CHWK,380887781,41084,A,TRUE,FALSE,1,100,8725,1,0.0189,0.0139,0.018819189448170164,22.62,FWA_RIVERS_POLY,1250,5,R,river_poly,TRUE,TRUE,TRUE 5bd69cdced,DV,BT,CHWK,380887781,47063,B,FALSE,FALSE,1,100,8745,1,0.0092,0.0285,0.015255541845954212,20.55,FWA_RIVERS_POLY,1250,5,R,river_poly,TRUE,TRUE,TRUE a87134b631,DV,BT,CHWK,380887781,48508,A,FALSE,FALSE,1,100,8754,1,0,0,0,14.9,MODELLED,1200,5,L,lake,TRUE,FALSE,FALSE diff --git a/data-raw/logs/habitat_thresholds_284/obs_status.csv b/data-raw/logs/habitat_thresholds_284/obs_status.csv index 8061f75c..33b22026 100644 --- a/data-raw/logs/habitat_thresholds_284/obs_status.csv +++ b/data-raw/logs/habitat_thresholds_284/obs_status.csv @@ -85,55 +85,55 @@ BT_any,rear,waterbody_rule,FALSE,50 BT_any,rear,waterbody_rule,TRUE,50 BT_any,rear,width_null,FALSE,35 BT_any,rear,width_null_river_poly,FALSE,30 -BT_any_dv,spawn,fails_gradient,FALSE,1270 -BT_any_dv,spawn,fails_width,FALSE,136 -BT_any_dv,spawn,not_tested_lake,FALSE,135 +BT_any_dv,spawn,fails_gradient,FALSE,1008 +BT_any_dv,spawn,fails_width,FALSE,112 +BT_any_dv,spawn,not_tested_lake,FALSE,118 BT_any_dv,spawn,not_tested_other_edge,FALSE,3 BT_any_dv,spawn,not_tested_other_waterbody,FALSE,1 -BT_any_dv,spawn,not_tested_wetland,FALSE,163 +BT_any_dv,spawn,not_tested_wetland,FALSE,142 BT_any_dv,spawn,passes,FALSE,2 -BT_any_dv,spawn,passes,TRUE,1817 -BT_any_dv,spawn,passes_river_poly,TRUE,1470 -BT_any_dv,spawn,width_null,FALSE,76 +BT_any_dv,spawn,passes,TRUE,1545 +BT_any_dv,spawn,passes_river_poly,TRUE,1254 +BT_any_dv,spawn,width_null,FALSE,59 BT_any_dv,spawn,width_null_river_poly,FALSE,31 -BT_any_dv,rear,fails_gradient,FALSE,479 -BT_any_dv,rear,fails_width,FALSE,122 +BT_any_dv,rear,fails_gradient,FALSE,373 +BT_any_dv,rear,fails_width,FALSE,101 BT_any_dv,rear,not_tested_other_edge,FALSE,3 BT_any_dv,rear,not_tested_other_waterbody,FALSE,1 -BT_any_dv,rear,passes,FALSE,91 -BT_any_dv,rear,passes,TRUE,2455 +BT_any_dv,rear,passes,FALSE,65 +BT_any_dv,rear,passes,TRUE,2073 BT_any_dv,rear,passes_river_poly,FALSE,1 -BT_any_dv,rear,passes_river_poly,TRUE,1498 -BT_any_dv,rear,waterbody_rule,FALSE,144 -BT_any_dv,rear,waterbody_rule,TRUE,154 -BT_any_dv,rear,width_null,FALSE,124 +BT_any_dv,rear,passes_river_poly,TRUE,1272 +BT_any_dv,rear,waterbody_rule,FALSE,122 +BT_any_dv,rear,waterbody_rule,TRUE,138 +BT_any_dv,rear,width_null,FALSE,94 BT_any_dv,rear,width_null_river_poly,FALSE,32 -BT_spawn_dv,spawn,fails_gradient,FALSE,28 +BT_spawn_dv,spawn,fails_gradient,FALSE,22 BT_spawn_dv,spawn,fails_width,FALSE,5 BT_spawn_dv,spawn,not_tested_lake,FALSE,2 BT_spawn_dv,spawn,not_tested_wetland,FALSE,4 -BT_spawn_dv,spawn,passes,TRUE,21 -BT_spawn_dv,spawn,passes_river_poly,TRUE,17 -BT_spawn_dv,spawn,width_null,FALSE,5 -BT_spawn_dv,rear,fails_gradient,FALSE,12 +BT_spawn_dv,spawn,passes,TRUE,14 +BT_spawn_dv,spawn,passes_river_poly,TRUE,15 +BT_spawn_dv,spawn,width_null,FALSE,3 +BT_spawn_dv,rear,fails_gradient,FALSE,9 BT_spawn_dv,rear,fails_width,FALSE,5 -BT_spawn_dv,rear,passes,TRUE,36 -BT_spawn_dv,rear,passes_river_poly,TRUE,18 +BT_spawn_dv,rear,passes,TRUE,26 +BT_spawn_dv,rear,passes_river_poly,TRUE,16 BT_spawn_dv,rear,waterbody_rule,FALSE,2 BT_spawn_dv,rear,waterbody_rule,TRUE,4 -BT_spawn_dv,rear,width_null,FALSE,5 -BT_rear_dv,spawn,fails_gradient,FALSE,430 -BT_rear_dv,spawn,fails_width,FALSE,70 -BT_rear_dv,spawn,not_tested_lake,FALSE,15 -BT_rear_dv,spawn,not_tested_wetland,FALSE,36 -BT_rear_dv,spawn,passes,TRUE,377 -BT_rear_dv,spawn,passes_river_poly,TRUE,90 -BT_rear_dv,spawn,width_null,FALSE,35 -BT_rear_dv,rear,fails_gradient,FALSE,173 -BT_rear_dv,rear,fails_width,FALSE,60 -BT_rear_dv,rear,passes,FALSE,43 -BT_rear_dv,rear,passes,TRUE,567 -BT_rear_dv,rear,passes_river_poly,TRUE,99 -BT_rear_dv,rear,waterbody_rule,FALSE,23 -BT_rear_dv,rear,waterbody_rule,TRUE,28 -BT_rear_dv,rear,width_null,FALSE,60 +BT_spawn_dv,rear,width_null,FALSE,3 +BT_rear_dv,spawn,fails_gradient,FALSE,253 +BT_rear_dv,spawn,fails_width,FALSE,49 +BT_rear_dv,spawn,not_tested_lake,FALSE,12 +BT_rear_dv,spawn,not_tested_wetland,FALSE,23 +BT_rear_dv,spawn,passes,TRUE,233 +BT_rear_dv,spawn,passes_river_poly,TRUE,35 +BT_rear_dv,spawn,width_null,FALSE,23 +BT_rear_dv,rear,fails_gradient,FALSE,98 +BT_rear_dv,rear,fails_width,FALSE,41 +BT_rear_dv,rear,passes,FALSE,25 +BT_rear_dv,rear,passes,TRUE,354 +BT_rear_dv,rear,passes_river_poly,TRUE,38 +BT_rear_dv,rear,waterbody_rule,FALSE,15 +BT_rear_dv,rear,waterbody_rule,TRUE,20 +BT_rear_dv,rear,width_null,FALSE,37 diff --git a/data-raw/logs/habitat_thresholds_284/projects.csv b/data-raw/logs/habitat_thresholds_284/projects.csv index ea20d69d..1a7c8162 100644 --- a/data-raw/logs/habitat_thresholds_284/projects.csv +++ b/data-raw/logs/habitat_thresholds_284/projects.csv @@ -19,13 +19,13 @@ CH,"01-JAN-74 An assessment of the effects of the system E flood control proposa CH,01-SEP-99 SUSTUT AND BULKLEY RIVERS JUVENILE STEELHEAD SURVEYS,27,0.015472779369627506 CH,Project ID/Name: 11918/Sarahs Fish Sampling Project - 2004,25,0.014326647564469915 CH,Project ID/Name: 25416/Fraser River Gravel Removal EIA - 2009,24,0.013753581661891117 -DV,,515,0.1824946846208363 -DV,01-JUL-99 1998 STREAM INVENTORY REPORT GOSNELL CREEK WATERSHED WSC: 460-600600-50800-00500,105,0.03720765414599575 -DV,01-MAR-93 FISHERIES RESOURCES AND ENHANCEMENT POTENTIALS OF SELECTED TRIBUTARIES OF THE WILLISTON RESERVOIR VOLUME II,92,0.03260099220411056 -DV,01-JUN-98 RECONNAISANCE LEVEL FISH AND FISH HABITAT INVENTORY IN THE BULKLEY T.S.A. (WORKING UNIT #11 - ZYMOETZ),80,0.028348688873139617 -DV,Project ID/Name: 71/6-TritonWhole,64,0.022678951098511695 -DV,01-OCT-97 STREAM INVENTORY THAUTIL RIVER WATERSHED 1996,61,0.02161587526576896 -DV,01-JUN-98 RECONNAISANCE LEVEL FISH AND FISH HABITAT INVENTORY IN THE BULKLEY T.S.A. (WORKING UNIT #13 TELKWA),45,0.015946137491141033 -DV,01-JUN-98 RECONNAISANCE LEVEL FISH AND FISH HABITAT INVENTORY IN THE BULKLEY T.S.A. (WORKING UNIT #6 - BLUNT),43,0.015237420269312544 -DV,Project ID/Name: 73/6-TritonZ1,36,0.012756909992912827 -DV," AQUATICS BIOPHYSICAL MAPS - 1:50000. MAPS-BC, VICTORIA, B.C.",32,0.011339475549255847 +DV,,382,0.19390862944162437 +DV,01-JUL-99 1998 STREAM INVENTORY REPORT GOSNELL CREEK WATERSHED WSC: 460-600600-50800-00500,105,0.0532994923857868 +DV,01-MAR-93 FISHERIES RESOURCES AND ENHANCEMENT POTENTIALS OF SELECTED TRIBUTARIES OF THE WILLISTON RESERVOIR VOLUME II,92,0.046700507614213196 +DV,01-OCT-97 STREAM INVENTORY THAUTIL RIVER WATERSHED 1996,61,0.030964467005076143 +DV,Project ID/Name: 71/6-TritonWhole,49,0.024873096446700507 +DV,01-JUN-98 RECONNAISANCE LEVEL FISH AND FISH HABITAT INVENTORY IN THE BULKLEY T.S.A. (WORKING UNIT #13 TELKWA),45,0.02284263959390863 +DV,01-JUN-98 RECONNAISANCE LEVEL FISH AND FISH HABITAT INVENTORY IN THE BULKLEY T.S.A. (WORKING UNIT #6 - BLUNT),43,0.02182741116751269 +DV,01-JAN-95 Kemess South Gold-copper project 1994 fisheries studies,32,0.016243654822335026 +DV,01-NOV-96 STREAM INVENTORY AND CLASSIFICATION IN THE KISPIOX FOREST DISTRICT,31,0.015736040609137057 +DV," AquaticS BIOPHYSICAL MAPS - 1:50000. MAPS-BC, VICTORIA, B.C.",30,0.015228426395939087 diff --git a/data-raw/logs/habitat_thresholds_284/quantiles.csv b/data-raw/logs/habitat_thresholds_284/quantiles.csv index 2c3eabc1..0f500bfc 100644 --- a/data-raw/logs/habitat_thresholds_284/quantiles.csv +++ b/data-raw/logs/habitat_thresholds_284/quantiles.csv @@ -91,11 +91,11 @@ BT_any,400,gradient_w100,stream+river_poly,155,0,0.0074859933653492585,0.0155475 BT_any,400,channel_width,"stream, any source",106,2.15,2.875,4.84,7.4,11.6,15.715,17.965,22.5665 BT_any,400,channel_width,"stream, field measured",59,2.3819999999999997,3.5000000000000004,5.085,8.65,11.735,16.808000000000007,22.049999999999997,25.48060000000001 BT_any,400,channel_width,"stream, modelled",47,1.8560000000000003,2.468,3.84,6.42,10.82,15.148,15.756999999999998,17.0734 -BT_any_dv,all,gradient,stream+river_poly,4764,0,0,0.0061,0.0238,0.0566,0.1023,0.13482499999999972,0.28898799999999863 -BT_any_dv,all,gradient_w100,stream+river_poly,4756,0,2.9327521459094897e-5,0.007097641165015886,0.023950322775936284,0.05626745619065218,0.10726806606321745,0.1491883077237918,0.27538772152378427 -BT_any_dv,all,channel_width,"stream, any source",3035,1.48,2,3.61,7,10.645,15.43,18.779999999999973,30 -BT_any_dv,all,channel_width,"stream, field measured",1454,1.3465000000000003,1.8220000000000005,3.5,6.98,10.785,17.555000000000007,22,38.51270000000001 -BT_any_dv,all,channel_width,"stream, modelled",1581,1.6,2.15,3.71,7.18,10.58,14.39,16.15,22.400000000000045 +BT_any_dv,all,gradient,stream+river_poly,3988,0,0,0.0052,0.0214,0.0541,0.09956000000000004,0.1308949999999999,0.27893400000000024 +BT_any_dv,all,gradient_w100,stream+river_poly,3981,0,0,0.0061867430302254434,0.022056848643577497,0.0540445980582308,0.10167137491242556,0.1448891079376085,0.2636056770595346 +BT_any_dv,all,channel_width,"stream, any source",2533,1.47,2,3.6,6.9,10.5,15,18.092,28.78239999999989 +BT_any_dv,all,channel_width,"stream, field measured",1191,1.3,1.8,3.365,6.72,10.56,16.67,21.25,30.20799999999999 +BT_any_dv,all,channel_width,"stream, modelled",1342,1.6215000000000002,2.161,3.7525,7.025,10.37,14.149000000000001,16.535500000000003,22.093099999999993 BT_any_dv,100,gradient,stream+river_poly,906,0,3e-4,0.0105,0.02855,0.062075000000000005,0.10275,0.132625,0.31097000000000263 BT_any_dv,100,gradient_w100,stream+river_poly,905,0,0.001004904346028559,0.011524339230080614,0.030550691887348193,0.0639727720184078,0.10538865784735163,0.14086799883947915,0.23287247013965878 BT_any_dv,100,channel_width,"stream, any source",649,1.45,2.184,3.65,7.27,11.36,17.532000000000018,21.25,29.42159999999999 @@ -111,11 +111,11 @@ BT_any_dv,300,gradient_w100,stream+river_poly,428,0,0.0013994365176378098,0.0126 BT_any_dv,300,channel_width,"stream, any source",321,1.5,4.24,6.68,9.7,11.76,15.6,18.22,22.04 BT_any_dv,300,channel_width,"stream, field measured",151,0.425,1.55,5.984999999999999,8.9,11.96,17.3,18.8,23.634999999999998 BT_any_dv,300,channel_width,"stream, modelled",170,4.24,5.839,7.1975,9.84,11.405000000000001,14.701,17.7155,20.225300000000004 -BT_any_dv,400,gradient,stream+river_poly,1861,0,0.0014,0.0132,0.0338,0.0722,0.1158,0.1547,0.32662000000000047 -BT_any_dv,400,gradient_w100,stream+river_poly,1857,0,0.002391666890150077,0.01365070329377147,0.034413370323210304,0.07141006290623068,0.12824989717957197,0.16816187880179834,0.27335846958684384 -BT_any_dv,400,channel_width,"stream, any source",1297,1.4,1.73,2.85,5.62,10.05,15.128000000000014,18,34.17 -BT_any_dv,400,channel_width,"stream, field measured",708,1.3,1.721,2.9875,5.734999999999999,10.5,16.769000000000023,22.545499999999997,38.87799999999997 -BT_any_dv,400,channel_width,"stream, modelled",589,1.5,1.738,2.7,5.41,9.63,14.432000000000002,15.442,18.365600000000004 +BT_any_dv,400,gradient,stream+river_poly,1085,0,0.0022,0.0123,0.0328,0.0768,0.11690000000000002,0.1519999999999999,0.2811240000000004 +BT_any_dv,400,gradient_w100,stream+river_poly,1082,0,0.0025296635941318766,0.013065588556443438,0.03452310129517116,0.0728968106209669,0.12916642291958125,0.16762076770283663,0.23656234891327677 +BT_any_dv,400,channel_width,"stream, any source",795,1.3,1.69,2.4,4.7,8.73,13,16.51,25 +BT_any_dv,400,channel_width,"stream, field measured",445,1.2,1.658,2.6,5,9.32,13.98,17.939999999999987,29.28 +BT_any_dv,400,channel_width,"stream, modelled",350,1.44,1.699,2.3525,4.505,8.002500000000001,11.466000000000006,14.873000000000001,17.7963 BT_any_dv,900,gradient,stream+river_poly,9,0,0,0,0,0.0052,0.005879999999999999,0.006039999999999999,0.006167999999999999 BT_any_dv,900,gradient_w100,stream+river_poly,9,0,0,0,4.101278352787485e-4,0.005248530809797778,0.0066415608446068935,0.008320780422303447,0.00966415608446069 BT_any_dv,900,channel_width,"stream, any source",6,3.1675,3.505,4.6075,6.635,8.7225,10.190000000000001,10.700000000000001,11.108000000000002 @@ -125,11 +125,11 @@ BT_any_dv,970,gradient,stream+river_poly,2,6.850000000000006e-4,0.00137000000000 BT_any_dv,970,gradient_w100,stream+river_poly,2,7.421711600169167e-4,0.0014843423200338335,0.0037108558000845805,0.007421711600169161,0.011132567400253741,0.013359080880304488,0.014101252040321406,0.014694988968334939 BT_any_dv,970,channel_width,"stream, any source",2,3.8945,3.939,4.0725,4.295,4.5175,4.651000000000001,4.6955,4.7311000000000005 BT_any_dv,970,channel_width,"stream, modelled",2,3.8945,3.939,4.0725,4.295,4.5175,4.651000000000001,4.6955,4.7311000000000005 -BT_spawn_dv,all,gradient,stream+river_poly,76,0,0,0.0115,0.03145,0.08045,0.12290000000000001,0.19642500000000002,0.2117 -BT_spawn_dv,all,gradient_w100,stream+river_poly,75,8.913598560354787e-6,0.0013396214117121588,0.013234615681944888,0.03162156218677865,0.08087446594816469,0.12270061189505899,0.193534188331334,0.2139879398629587 -BT_spawn_dv,all,channel_width,"stream, any source",53,1.16,1.328,2.03,4,6.18,9.768,13.481999999999998,49.621599999999816 -BT_spawn_dv,all,channel_width,"stream, field measured",32,1.4274999999999998,1.8,2.4,3.855,5.6,6.48,14.880999999999991,61.88980000000007 -BT_spawn_dv,all,channel_width,"stream, modelled",21,1.13,1.3,1.73,4.2,7.06,12.33,12.55,14.414000000000001 +BT_spawn_dv,all,gradient,stream+river_poly,59,0,0,0.011300000000000001,0.0322,0.0809,0.12862,0.19538999999999995,0.213876 +BT_spawn_dv,all,gradient_w100,stream+river_poly,58,1.2995497294724602e-5,0.0013954157665726115,0.014611423153330635,0.03601613174816407,0.08233534025143627,0.13316552669140672,0.19343559362280732,0.21638116978543617 +BT_spawn_dv,all,channel_width,"stream, any source",40,1.1235,1.2880000000000003,1.8,3.3,5.5625,8.010000000000007,13.001499999999975,57.216199999999965 +BT_spawn_dv,all,channel_width,"stream, field measured",23,1.225,1.664,2,3.3,4.1850000000000005,6.300000000000001,20.071999999999978,67.14760000000007 +BT_spawn_dv,all,channel_width,"stream, modelled",17,1.1039999999999999,1.232,1.44,4.2,6.39,9.450000000000003,12.374,12.5148 BT_spawn_dv,100,gradient,stream+river_poly,11,0,0,9.5e-4,0.0148,0.0355,0.0535,0.0953,0.12874000000000005 BT_spawn_dv,100,gradient_w100,stream+river_poly,10,5.730170503085218e-6,1.1460341006170437e-5,0.0013117242342819326,0.018897381678546595,0.02929515869815475,0.05505721013869193,0.11002717075464975,0.15400313924741624 BT_spawn_dv,100,channel_width,"stream, any source",5,2.8099999999999996,3.9899999999999998,7.53,12.33,12.55,17.967999999999996,19.773999999999997,21.218799999999998 @@ -140,16 +140,16 @@ BT_spawn_dv,200,gradient_w100,stream+river_poly,7,0.003660237083270829,0.0051429 BT_spawn_dv,200,channel_width,"stream, any source",3,1.7450000000000006,2.1899999999999995,3.525,5.75,42.875,65.14999999999999,72.575,78.515 BT_spawn_dv,200,channel_width,"stream, field measured",1,80,80,80,80,80,80,80,80 BT_spawn_dv,200,channel_width,"stream, modelled",2,1.5225000000000002,1.7450000000000006,2.4125,3.525,4.6375,5.305,5.5275,5.7055 -BT_spawn_dv,400,gradient,stream+river_poly,58,0,0,0.01345,0.0372,0.09467500000000001,0.1419200000000002,0.2022,0.21400399999999997 -BT_spawn_dv,400,gradient_w100,stream+river_poly,58,1.1085440460362863e-5,0.002372038836063439,0.016737549325538836,0.05103656312027653,0.0854456412693422,0.13750656579993284,0.19465163040308164,0.21638116978543617 -BT_spawn_dv,400,channel_width,"stream, any source",45,1.14,1.356,2.03,3.6,5.5,6.4559999999999995,8.931999999999993,12.671200000000011 -BT_spawn_dv,400,channel_width,"stream, field measured",29,1.4280000000000002,1.8,2.5,3.71,4.9,6.3,6.42,8.587999999999997 -BT_spawn_dv,400,channel_width,"stream, modelled",16,1.0975,1.2149999999999999,1.6574999999999998,3.01,6.2325,8.459999999999999,11.115,14.126999999999999 -BT_rear_dv,all,gradient,stream+river_poly,991,0.00245,0.0089,0.0223,0.045,0.08685000000000001,0.1217,0.15765,0.4452100000000001 -BT_rear_dv,all,gradient_w100,stream+river_poly,989,0.004725065700857386,0.009427165022444343,0.021960304077431374,0.04506163042029357,0.08739432402128955,0.141840561545503,0.17743440386341253,0.3653146255554057 -BT_rear_dv,all,channel_width,"stream, any source",804,1.34,1.5730000000000002,2.3475,4.705,9.085,14.89,18,29.78470000000004 -BT_rear_dv,all,channel_width,"stream, field measured",494,1.3,1.6150000000000002,2.4,4.91,8.995000000000001,16.51,21.25,34.30999999999999 -BT_rear_dv,all,channel_width,"stream, modelled",310,1.35,1.499,2.1625,4.26,9.43,12.09100000000001,15.344500000000002,17.992500000000017 +BT_spawn_dv,400,gradient,stream+river_poly,41,0,0.0011,0.0139,0.054,0.095,0.1779,0.2016,0.21618 +BT_spawn_dv,400,gradient_w100,stream+river_poly,41,8.590309810074359e-5,0.009815801317121214,0.018290248242601594,0.05856247354566335,0.09053850771636462,0.16711147814171112,0.1939942969711251,0.21877439970791376 +BT_spawn_dv,400,channel_width,"stream, any source",32,1.0715,1.1919999999999997,1.8,3.14,4.242500000000001,6.112000000000001,6.4395,6.8864 +BT_spawn_dv,400,channel_width,"stream, field measured",20,1.1535000000000002,1.7380000000000004,2,3.2,4,4.906000000000001,5.550000000000001,6.309999999999999 +BT_spawn_dv,400,channel_width,"stream, modelled",12,1.0715,1.147,1.405,3.01,5.1675,6.369,6.6915,6.9863 +BT_rear_dv,all,gradient,stream+river_poly,587,0.0037600000000000003,0.00822,0.021249999999999998,0.043,0.0873,0.11964,0.1536199999999997,0.3630859999999987 +BT_rear_dv,all,gradient_w100,stream+river_poly,586,0.004885063414273958,0.00958427646495636,0.021940501115661558,0.04367671213805352,0.08686008251302667,0.1308892680086876,0.17078064364619905,0.243543476008304 +BT_rear_dv,all,channel_width,"stream, any source",497,1.296,1.486,2.03,3.59,6.2,10.170000000000003,16.872,22.81800000000001 +BT_rear_dv,all,channel_width,"stream, field measured",302,1.3020000000000003,1.581,2.1,3.6,6.5,11.103000000000023,17.437499999999996,24.982500000000016 +BT_rear_dv,all,channel_width,"stream, modelled",195,1.264,1.394,1.99,3.45,5.75,9.276,11.359999999999971,18.3086 BT_rear_dv,100,gradient,stream+river_poly,110,3.600000000000002e-4,0.0068800000000000016,0.019299999999999998,0.036199999999999996,0.05695,0.09809000000000004,0.11180999999999999,0.15646899999999989 BT_rear_dv,100,gradient_w100,stream+river_poly,110,0.0029277394556513634,0.008094242625162118,0.01651207967660838,0.0321939757066292,0.060448923338459505,0.09962224782621798,0.11925140387161638,0.16745611817271205 BT_rear_dv,100,channel_width,"stream, any source",99,1.247,1.35,1.665,3.08,6.76,17.130000000000003,21.25,21.391399999999972 @@ -160,8 +160,8 @@ BT_rear_dv,200,gradient_w100,stream+river_poly,76,0.0030221363148831416,0.006490 BT_rear_dv,200,channel_width,"stream, any source",53,2.212,2.428,3.68,5.75,8.39,9.920000000000002,10.17,13.465999999999983 BT_rear_dv,200,channel_width,"stream, field measured",6,1.98,1.98,2.04,2.31,8.2725,13.265,14.782500000000002,15.996500000000001 BT_rear_dv,200,channel_width,"stream, modelled",47,2.729,3.182,4.14,5.75,7.785,9.56,10.094000000000001,10.518799999999999 -BT_rear_dv,400,gradient,stream+river_poly,805,0.0039,0.0108,0.0255,0.0518,0.0925,0.13260000000000002,0.1721,0.44959600000000016 -BT_rear_dv,400,gradient_w100,stream+river_poly,803,0.005393480003954658,0.01125475478937483,0.024209883494836645,0.05113032713064627,0.09193288485512255,0.14949098143748418,0.19322622009638998,0.3976047095960674 -BT_rear_dv,400,channel_width,"stream, any source",652,1.3220000000000003,1.6,2.4,4.9,9.46,14.89,17.62049999999995,32.29830000000003 -BT_rear_dv,400,channel_width,"stream, field measured",439,1.3,1.65,2.625,5.1,9,16.51,20.27099999999999,35.41000000000001 -BT_rear_dv,400,channel_width,"stream, modelled",213,1.388,1.582,2.15,4.2,9.46,14.3,15.315999999999995,17.969999999999995 +BT_rear_dv,400,gradient,stream+river_poly,401,0.0055,0.0119,0.0276,0.0601,0.095,0.1328,0.1669,0.4447 +BT_rear_dv,400,gradient_w100,stream+river_poly,400,0.00736407485558621,0.012333602680473519,0.027054844345107656,0.05555888886060984,0.09708303494707167,0.15120631961068912,0.1879278924725746,0.34170037318527813 +BT_rear_dv,400,channel_width,"stream, any source",345,1.284,1.552,2.01,3.44,5.9,9.820000000000004,13.76000000000001,23.052 +BT_rear_dv,400,channel_width,"stream, field measured",247,1.312,1.6,2.175,3.6,6.5,10.411999999999999,13.985,24.194999999999986 +BT_rear_dv,400,channel_width,"stream, modelled",98,1.2269999999999999,1.4610000000000003,1.7925,2.95,5.03,7.053,9.123999999999992,18.308899999999998 diff --git a/data-raw/logs/habitat_thresholds_284/selection.csv b/data-raw/logs/habitat_thresholds_284/selection.csv index 20e9a7d5..3b6fee74 100644 --- a/data-raw/logs/habitat_thresholds_284/selection.csv +++ b/data-raw/logs/habitat_thresholds_284/selection.csv @@ -135,105 +135,105 @@ BT_any,channel_width,"(20,30]",50,631.6206904755269,0.03263707571801567,0.003774 BT_any,channel_width,"(30,50]",6,193.84369691778377,0.0039164490861618795,0.0011582725937765391,3.3812844292484954 BT_any,channel_width,"(50,Inf]",4,83.63546497186009,0.0026109660574412533,4.997462826235228e-4,5.224583249993256 BT_any,channel_width,NULL,63,81777.47487097817,0.041122715404699736,0.48864425017377855,0.08415675696598313 -BT_any_dv,gradient,"[-Inf,0.0025]",882,15203.432890146798,0.18513853904282115,0.08297709160124513,2.2312006298379714 -BT_any_dv,gradient,"(0.0025,0.005]",224,5282.777017886785,0.047019311502938706,0.028832269375572046,1.6307877430826 -BT_any_dv,gradient,"(0.005,0.01]",385,9384.679838760569,0.0808144416456759,0.05121957943681726,1.5778036941003366 -BT_any_dv,gradient,"(0.01,0.02]",700,18312.718564830928,0.14693534844668346,0.09994690914882752,1.470133991116094 -BT_any_dv,gradient,"(0.02,0.03]",496,16629.928306633497,0.10411418975650713,0.09076259910457259,1.1471045428806137 -BT_any_dv,gradient,"(0.03,0.04]",410,14811.249229338853,0.08606213266162889,0.08083663689062101,1.0646426666423348 -BT_any_dv,gradient,"(0.04,0.045]",168,6717.629834049128,0.03526448362720403,0.036663389782474944,0.9618446040158679 -BT_any_dv,gradient,"(0.045,0.05]",156,6247.85733838253,0.0327455919395466,0.03409947177222506,0.9602961640660593 -BT_any_dv,gradient,"(0.05,0.055]",110,5816.431635134531,0.023089840470193114,0.031744842370023306,0.7273572254999408 -BT_any_dv,gradient,"(0.055,0.06]",104,5461.322019122153,0.0218303946263644,0.029806729882583795,0.7323981769338608 -BT_any_dv,gradient,"(0.06,0.07]",195,9933.047870514969,0.04093198992443325,0.05421245510712516,0.7550292611458126 -BT_any_dv,gradient,"(0.07,0.08]",169,8694.320344496466,0.03547439126784215,0.047451744671652675,0.7475887665102922 -BT_any_dv,gradient,"(0.08,0.09]",144,7586.718368410069,0.030226700251889168,0.041406689499474805,0.7299955784263448 -BT_any_dv,gradient,"(0.09,0.1]",120,6444.019182851476,0.02518891687657431,0.035170081249359525,0.7162029765578952 -BT_any_dv,gradient,"(0.1,0.105]",55,2895.318584445264,0.011544920235096557,0.01580203083949564,0.7305972474272833 -BT_any_dv,gradient,"(0.105,0.12]",140,7443.118547250665,0.02938706968933669,0.04062295232640591,0.7234104861018281 -BT_any_dv,gradient,"(0.12,0.15]",126,11650.1131453007,0.02644836272040302,0.06358383087605106,0.4159605100227586 -BT_any_dv,gradient,"(0.15,0.2]",83,12064.684519007404,0.017422334172963894,0.06584647294510702,0.26459024141639353 -BT_any_dv,gradient,"(0.2,0.25]",34,4615.139212930478,0.007136859781696054,0.025188444740793868,0.2833386441735156 -BT_any_dv,gradient,"(0.25, Inf]",63,8029.9546247564995,0.01322418136020151,0.043825778379571516,0.3017443579819153 -BT_any_dv,channel_width,"[0,1.5]",159,20354.12304816135,0.04927176944530524,0.12162181836141915,0.40512278231925547 -BT_any_dv,channel_width,"(1.5,2]",152,12413.948506707824,0.04710257204834211,0.07417696094586669,0.6350027211645528 -BT_any_dv,channel_width,"(2,3]",269,16179.235565736924,0.08335915711186861,0.09667564869027466,0.8622559893953352 -BT_any_dv,channel_width,"(3,4]",283,9508.485151266355,0.08769755190579485,0.05681597046570044,1.5435369876985117 -BT_any_dv,channel_width,"(4,5]",207,6262.25757545213,0.0641462658816238,0.03741881443734616,1.7142784143797478 -BT_any_dv,channel_width,"(5,6]",243,4382.137303780023,0.07530213820886272,0.02618454776627074,2.8758235154957354 -BT_any_dv,channel_width,"(6,8]",410,5917.241295300836,0.1270529903935544,0.035357241592522286,3.5934078754725274 -BT_any_dv,channel_width,"(8,10]",396,3755.4971372677733,0.12271459559962813,0.02244019010815946,5.468518537862475 -BT_any_dv,channel_width,"(10,15]",593,4557.118845365355,0.1837620080570189,0.027230113483690078,6.748484840765947 -BT_any_dv,channel_width,"(15,20]",198,1339.232966813817,0.06135729779981407,0.008002307357976201,7.667450780762244 -BT_any_dv,channel_width,"(20,30]",96,631.6206904755269,0.029748992872637124,0.0037741177405954595,7.882370110674791 -BT_any_dv,channel_width,"(30,50]",20,193.84369691778377,0.006197706848466067,0.0011582725937765391,5.35081886748135 -BT_any_dv,channel_width,"(50,Inf]",9,83.63546497186009,0.0027889680818097306,4.997462826235228e-4,5.580768039270764 -BT_any_dv,channel_width,NULL,192,81777.47487097817,0.05949798574527425,0.48864425017377855,0.12176135444981648 -BT_spawn_dv,gradient,"[-Inf,0.0025]",14,15203.432890146798,0.18421052631578946,0.08297709160124514,2.220016666781139 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+BT_rear_dv,gradient,"(0.045,0.05]",22,6247.85733838253,0.03747870528109029,0.03409947177222506,1.099099291960813 +BT_rear_dv,gradient,"(0.05,0.055]",17,5816.431635134531,0.028960817717206135,0.031744842370023306,0.9122999377232338 +BT_rear_dv,gradient,"(0.055,0.06]",15,5461.322019122153,0.02555366269165247,0.029806729882583795,0.857311848442106 +BT_rear_dv,gradient,"(0.06,0.07]",33,9933.047870514969,0.056218057921635436,0.05421245510712516,1.0369952404949592 +BT_rear_dv,gradient,"(0.07,0.08]",30,8694.320344496466,0.05110732538330494,0.047451744671652675,1.0770378568153276 +BT_rear_dv,gradient,"(0.08,0.09]",31,7586.718368410069,0.05281090289608177,0.041406689499474805,1.2754195888263806 +BT_rear_dv,gradient,"(0.09,0.1]",33,6444.019182851476,0.056218057921635436,0.035170081249359525,1.5984625546652445 +BT_rear_dv,gradient,"(0.1,0.105]",13,2895.318584445264,0.022146507666098807,0.01580203083949564,1.4014975600949824 +BT_rear_dv,gradient,"(0.105,0.12]",34,7443.118547250665,0.05792163543441227,0.04062295232640591,1.4258352019570422 +BT_rear_dv,gradient,"(0.12,0.15]",27,11650.1131453007,0.04599659284497445,0.06358383087605106,0.7234007799032934 +BT_rear_dv,gradient,"(0.15,0.2]",19,12064.684519007404,0.03236797274275979,0.06584647294510702,0.4915672973060134 +BT_rear_dv,gradient,"(0.2,0.25]",4,4615.139212930478,0.0068143100511073255,0.025188444740793868,0.2705331798462027 +BT_rear_dv,gradient,"(0.25, Inf]",8,8029.9546247564995,0.013628620102214651,0.043825778379571516,0.31097268790478233 +BT_rear_dv,channel_width,"[0,1.5]",53,20354.12304816135,0.0965391621129326,0.12162181836141915,0.7937651600147161 +BT_rear_dv,channel_width,"(1.5,2]",68,12413.948506707824,0.12386156648451731,0.07417696094586669,1.669811824387221 +BT_rear_dv,channel_width,"(2,3]",81,16179.235565736924,0.14754098360655737,0.09667564869027466,1.5261442318245302 +BT_rear_dv,channel_width,"(3,4]",71,9508.485151266355,0.12932604735883424,0.05681597046570044,2.2762270238243634 +BT_rear_dv,channel_width,"(4,5]",40,6262.25757545213,0.07285974499089254,0.03741881443734616,1.9471419949151103 +BT_rear_dv,channel_width,"(5,6]",57,4382.137303780023,0.10382513661202186,0.02618454776627074,3.965130027785424 +BT_rear_dv,channel_width,"(6,8]",46,5917.241295300836,0.08378870673952642,0.035357241592522286,2.3697749871202314 +BT_rear_dv,channel_width,"(8,10]",27,3755.4971372677733,0.04918032786885246,0.02244019010815946,2.19161814725313 +BT_rear_dv,channel_width,"(10,15]",22,4557.118845365355,0.04007285974499089,0.027230113483690078,1.4716376326890148 +BT_rear_dv,channel_width,"(15,20]",19,1339.232966813817,0.03460837887067395,0.008002307357976201,4.324800001111989 +BT_rear_dv,channel_width,"(20,30]",11,631.6206904755269,0.020036429872495445,0.0037741177405954595,5.308904292247705 +BT_rear_dv,channel_width,"(30,50]",2,193.84369691778377,0.0036429872495446266,0.0011582725937765391,3.145189888044138 +BT_rear_dv,channel_width,"(50,Inf]",0,83.63546497186009,0,4.997462826235228e-4,0 +BT_rear_dv,channel_width,NULL,52,81777.47487097817,0.0947176684881603,0.48864425017377855,0.19383768141030097 diff --git a/data-raw/logs/habitat_thresholds_284/stamp.txt b/data-raw/logs/habitat_thresholds_284/stamp.txt index bdaa4884..d31db2b5 100644 --- a/data-raw/logs/habitat_thresholds_284/stamp.txt +++ b/data-raw/logs/habitat_thresholds_284/stamp.txt @@ -1,8 +1,9 @@ -date: 2026-09-26 10:03 PDT -link: 0.51.0 @ 267fd71 +date: 2026-09-27 07:48 PDT +link: 0.52.0 @ 773672e fresh installed: 0.34.0 @ no recorded sha db: docker fwapg localhost:5432 schema: fresh_default (55 WSGs persisted; 4 run-log rows, 2026-08-06 to 2026-08-27, built with fresh 0.32.0@NA, 0.33.0@NA; the other WSGs predate the log) bcfishobs.observations rows: 373050 thresholds: inst/extdata/configs/default/parameters_habitat_thresholds.csv -retained observations with 2+ candidate segments (upstream chosen): 45 +pooling: default species_pooling.csv; BT<-DV +retained observations with 2+ candidate segments (upstream chosen): 38 diff --git a/data-raw/logs/habitat_validate_283/diff.csv b/data-raw/logs/habitat_validate_283/diff.csv index f2af53a1..2e9fb136 100644 --- a/data-raw/logs/habitat_validate_283/diff.csv +++ b/data-raw/logs/habitat_validate_283/diff.csv @@ -16,15 +16,15 @@ 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"default:fresh_default","bcfishpass:fresh","KISP","BT","any",0,195,192,122,159,162,0.984615384615385,0.625641025641026,0.815384615384615,0.830769230769231,0.625641025641026,0.830769230769231,4529.14,1258.71,1894.95,195,187,120,161,161,0.958974358974359,0.615384615384615,0.825641025641026,0.825641025641026,0.615384615384615,0.825641025641026,4475.39,1261.15,1962.71,-5,-2,2,-1,-0.0256410256410257,-0.0102564102564102,0.0102564102564102,-0.00512820512820522,-0.0102564102564102,-0.00512820512820522,-53.75,2.44000000000005,67.76 -"default:fresh_default","bcfishpass:fresh","KLUM","BT","any",0,314,302,194,243,244,0.961783439490446,0.617834394904459,0.773885350318471,0.777070063694268,0.617834394904459,0.777070063694268,2173.93,929.96,1229.04,314,275,183,232,232,0.875796178343949,0.582802547770701,0.738853503184713,0.738853503184713,0.582802547770701,0.738853503184713,1930.45,894.45,1189.16,-27,-11,-11,-12,-0.0859872611464968,-0.035031847133758,-0.0350318471337581,-0.0382165605095542,-0.035031847133758,-0.0382165605095542,-243.48,-35.51,-39.8799999999999 +"default:fresh_default","bcfishpass:fresh","KLUM","BT","any",0,30,29,21,25,25,0.966666666666667,0.7,0.833333333333333,0.833333333333333,0.7,0.833333333333333,2173.93,929.96,1229.04,30,29,21,25,25,0.966666666666667,0.7,0.833333333333333,0.833333333333333,0.7,0.833333333333333,1930.45,894.45,1189.16,0,0,0,0,0,0,0,0,0,0,-243.48,-35.51,-39.8799999999999 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-"default:fresh_default","bcfishpass:fresh","LKEL","BT","any",0,63,63,36,45,48,1,0.571428571428571,0.714285714285714,0.761904761904762,0.571428571428571,0.761904761904762,405.16,144.67,218.77,63,63,36,48,48,1,0.571428571428571,0.761904761904762,0.761904761904762,0.571428571428571,0.761904761904762,401.02,144.74,222.78,0,0,3,0,0,0,0.0476190476190476,0,0,0,-4.14000000000004,0.0700000000000216,4.00999999999999 +"default:fresh_default","bcfishpass:fresh","LKEL","BT","any",0,1,1,0,0,0,1,0,0,0,0,0,405.16,144.67,218.77,1,1,0,0,0,1,0,0,0,0,0,401.02,144.74,222.78,0,0,0,0,0,0,0,0,0,0,-4.14000000000004,0.0700000000000216,4.00999999999999 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"default:fresh_default","bcfishpass:fresh","MESI","BT","any",0,64,64,50,60,60,1,0.78125,0.9375,0.9375,0.78125,0.9375,2825.32,691.09,1077.07,64,64,50,60,60,1,0.78125,0.9375,0.9375,0.78125,0.9375,2767.09,685.99,1126.99,0,0,0,0,0,0,0,0,0,0,-58.23,-5.10000000000002,49.9200000000001 "default:fresh_default","bcfishpass:fresh","MFRA","BT","any",0,0,0,0,0,0,,,,,,,,,,0,0,0,0,0,,,,,,,,,,0,0,0,0,,,,,,,,, "default:fresh_default","bcfishpass:fresh","MORK","BT","any",0,79,79,70,72,73,1,0.886075949367089,0.911392405063291,0.924050632911392,0.886075949367089,0.924050632911392,7202.59,2148.8,3077.39,79,79,70,73,73,1,0.886075949367089,0.924050632911392,0.924050632911392,0.886075949367089,0.924050632911392,8075.86,2434.23,3397.59,0,0,1,0,0,0,0.0126582278481013,0,0,0,873.27,285.43,320.2 @@ -49,7 +49,7 @@ "default:fresh_default","bcfishpass:fresh","UPCE","BT","any",0,153,152,138,138,138,0.993464052287582,0.901960784313726,0.901960784313726,0.901960784313726,0.901960784313726,0.901960784313726,5689.87,1682.32,2340.3,153,152,138,139,139,0.993464052287582,0.901960784313726,0.908496732026144,0.908496732026144,0.901960784313726,0.908496732026144,5261.16,1657.29,2320.94,0,0,1,1,0,0,0.00653594771241828,0.00653594771241828,0,0.00653594771241828,-428.71,-25.03,-19.3600000000001 "default:fresh_default","bcfishpass:fresh","USKE","BT","any",0,32,32,28,31,31,1,0.875,0.96875,0.96875,0.875,0.96875,2969.07,739.68,1264.94,32,32,28,31,31,1,0.875,0.96875,0.96875,0.875,0.96875,3451.92,878.03,1438.52,0,0,0,0,0,0,0,0,0,0,482.85,138.35,173.58 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"default:fresh_default","bcfishpass:fresh","MESI","BT","spawn",0,0,0,0,0,0,,,,,,,2825.32,691.09,1077.07,0,0,0,0,0,,,,,,,2767.09,685.99,1126.99,0,0,0,0,,,,,,,-58.23,-5.10000000000002,49.9200000000001 "default:fresh_default","bcfishpass:fresh","MFRA","BT","spawn",0,0,0,0,0,0,,,,,,,,,,0,0,0,0,0,,,,,,,,,,0,0,0,0,,,,,,,,, "default:fresh_default","bcfishpass:fresh","MORK","BT","spawn",0,0,0,0,0,0,,,,,,,7202.59,2148.8,3077.39,0,0,0,0,0,,,,,,,8075.86,2434.23,3397.59,0,0,0,0,,,,,,,873.27,285.43,320.2 @@ -151,7 +151,7 @@ "default:fresh_default","bcfishpass:fresh","UPCE","BT","spawn",0,1,1,1,1,1,1,1,1,1,1,1,5689.87,1682.32,2340.3,1,1,1,1,1,1,1,1,1,1,1,5261.16,1657.29,2320.94,0,0,0,0,0,0,0,0,0,0,-428.71,-25.03,-19.3600000000001 "default:fresh_default","bcfishpass:fresh","USKE","BT","spawn",0,0,0,0,0,0,,,,,,,2969.07,739.68,1264.94,0,0,0,0,0,,,,,,,3451.92,878.03,1438.52,0,0,0,0,,,,,,,482.85,138.35,173.58 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"default:fresh_default","bcfishpass:fresh","LSAL","BT","spawn",100,0,0,0,0,0,,,,,,,,,,0,0,0,0,0,,,,,,,,,,0,0,0,0,,,,,,,,, -"default:fresh_default","bcfishpass:fresh","LSKE","BT","spawn",100,3,3,2,2,2,1,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,3075.25,1326.45,1709.47,3,3,2,2,2,1,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,2884.31,1315.64,1751.5,0,0,0,0,0,0,0,0,0,0,-190.94,-10.8099999999999,42.03 +"default:fresh_default","bcfishpass:fresh","LSKE","BT","spawn",100,0,0,0,0,0,,,,,,,3075.25,1326.45,1709.47,0,0,0,0,0,,,,,,,2884.31,1315.64,1751.5,0,0,0,0,,,,,,,-190.94,-10.8099999999999,42.03 "default:fresh_default","bcfishpass:fresh","MESI","BT","spawn",100,0,0,0,0,0,,,,,,,2825.32,691.09,1077.07,0,0,0,0,0,,,,,,,2767.09,685.99,1126.99,0,0,0,0,,,,,,,-58.23,-5.10000000000002,49.9200000000001 "default:fresh_default","bcfishpass:fresh","MFRA","BT","spawn",100,0,0,0,0,0,,,,,,,,,,0,0,0,0,0,,,,,,,,,,0,0,0,0,,,,,,,,, "default:fresh_default","bcfishpass:fresh","MORK","BT","spawn",100,0,0,0,0,0,,,,,,,7202.59,2148.8,3077.39,0,0,0,0,0,,,,,,,8075.86,2434.23,3397.59,0,0,0,0,,,,,,,873.27,285.43,320.2 @@ -457,7 +457,7 @@ "default:fresh_default","bcfishpass:fresh","UPCE","BT","spawn",100,1,1,1,1,1,1,1,1,1,1,1,5689.87,1682.32,2340.3,1,1,1,1,1,1,1,1,1,1,1,5261.16,1657.29,2320.94,0,0,0,0,0,0,0,0,0,0,-428.71,-25.03,-19.3600000000001 "default:fresh_default","bcfishpass:fresh","USKE","BT","spawn",100,0,0,0,0,0,,,,,,,2969.07,739.68,1264.94,0,0,0,0,0,,,,,,,3451.92,878.03,1438.52,0,0,0,0,,,,,,,482.85,138.35,173.58 "default:fresh_default","bcfishpass:fresh","WILL","BT","spawn",100,0,0,0,0,0,,,,,,,4562.41,1055.35,1720.76,0,0,0,0,0,,,,,,,4515.45,1052.18,1690.35,0,0,0,0,,,,,,,-46.96,-3.16999999999985,-30.4100000000001 -"default:fresh_default","bcfishpass:fresh","ZYMO","BT","spawn",100,14,14,7,11,11,1,0.5,0.785714285714286,0.785714285714286,0.5,0.785714285714286,2058.68,594.73,897.89,14,12,7,9,9,0.857142857142857,0.5,0.642857142857143,0.642857142857143,0.5,0.642857142857143,1840.06,575.42,863.2,-2,0,-2,-2,-0.142857142857143,0,-0.142857142857143,-0.142857142857143,0,-0.142857142857143,-218.62,-19.3100000000001,-34.6899999999999 +"default:fresh_default","bcfishpass:fresh","ZYMO","BT","spawn",100,0,0,0,0,0,,,,,,,2058.68,594.73,897.89,0,0,0,0,0,,,,,,,1840.06,575.42,863.2,0,0,0,0,,,,,,,-218.62,-19.3100000000001,-34.6899999999999 "default:fresh_default","bcfishpass:fresh","BBAR","CH","any",100,5,3,1,1,1,0.6,0.2,0.2,0.2,0.2,0.2,275.36,160.2,169.06,5,3,1,1,1,0.6,0.2,0.2,0.2,0.2,0.2,269.11,160.2,167.83,0,0,0,0,0,0,0,0,0,0,-6.25,0,-1.22999999999999 "default:fresh_default","bcfishpass:fresh","BULK","CH","any",100,110,110,105,108,108,1,0.954545454545455,0.981818181818182,0.981818181818182,0.945054945054945,0.981818181818182,5178.19,1264.07,2038.12,110,110,105,108,108,1,0.954545454545455,0.981818181818182,0.981818181818182,0.945054945054945,0.981818181818182,5089.63,1260.25,1730.12,0,0,0,0,0,0,0,0,0,0,-88.5599999999995,-3.81999999999994,-308 "default:fresh_default","bcfishpass:fresh","CARP","CH","any",100,0,0,0,0,0,,,,,,,,,,0,0,0,0,0,,,,,,,,,,0,0,0,0,,,,,,,,, diff --git a/data-raw/logs/habitat_validate_283/misses.csv b/data-raw/logs/habitat_validate_283/misses.csv index 4136ee86..9bd5d5e7 100644 --- a/data-raw/logs/habitat_validate_283/misses.csv +++ b/data-raw/logs/habitat_validate_283/misses.csv @@ -1,89 +1,89 @@ "bundle","stage","species_code","reason","n" -"default:fresh_default","any","BT","captured",4207 -"default:fresh_default","rear","BT","captured",700 -"default:fresh_default","spawn","BT","captured",38 +"default:fresh_default","any","BT","captured",3571 +"default:fresh_default","rear","BT","captured",415 +"default:fresh_default","spawn","BT","captured",29 "default:fresh_default","any","CH","captured",1577 "default:fresh_default","rear","CH","captured",434 "default:fresh_default","spawn","CH","captured",246 -"default:fresh_default","any","BT","fails_gradient",344 -"default:fresh_default","rear","BT","fails_gradient",123 -"default:fresh_default","spawn","BT","fails_gradient",21 +"default:fresh_default","any","BT","fails_gradient",268 +"default:fresh_default","rear","BT","fails_gradient",66 +"default:fresh_default","spawn","BT","fails_gradient",15 "default:fresh_default","any","CH","fails_gradient",51 "default:fresh_default","rear","CH","fails_gradient",25 "default:fresh_default","spawn","CH","fails_gradient",1 -"default:fresh_default","any","BT","fails_gradient_and_width",100 -"default:fresh_default","rear","BT","fails_gradient_and_width",37 +"default:fresh_default","any","BT","fails_gradient_and_width",83 +"default:fresh_default","rear","BT","fails_gradient_and_width",25 "default:fresh_default","spawn","BT","fails_gradient_and_width",6 "default:fresh_default","any","CH","fails_gradient_and_width",8 "default:fresh_default","rear","CH","fails_gradient_and_width",7 -"default:fresh_default","any","BT","fails_width",126 -"default:fresh_default","rear","BT","fails_width",61 +"default:fresh_default","any","BT","fails_width",103 +"default:fresh_default","rear","BT","fails_width",42 "default:fresh_default","spawn","BT","fails_width",5 "default:fresh_default","any","CH","fails_width",10 "default:fresh_default","rear","CH","fails_width",5 -"default:fresh_default","any","BT","not_accessible",42 -"default:fresh_default","rear","BT","not_accessible",13 +"default:fresh_default","any","BT","not_accessible",26 +"default:fresh_default","rear","BT","not_accessible",7 "default:fresh_default","spawn","BT","not_accessible",1 "default:fresh_default","any","CH","not_accessible",27 "default:fresh_default","rear","CH","not_accessible",10 "default:fresh_default","spawn","CH","not_accessible",1 -"default:fresh_default","any","BT","post_predicate",89 -"default:fresh_default","rear","BT","post_predicate",47 +"default:fresh_default","any","BT","post_predicate",63 +"default:fresh_default","rear","BT","post_predicate",26 "default:fresh_default","any","CH","post_predicate",14 "default:fresh_default","rear","CH","post_predicate",6 -"default:fresh_default","any","BT","rule_excludes",36 -"default:fresh_default","rear","BT","rule_excludes",11 +"default:fresh_default","any","BT","rule_excludes",31 +"default:fresh_default","rear","BT","rule_excludes",9 "default:fresh_default","spawn","BT","rule_excludes",6 "default:fresh_default","any","CH","rule_excludes",11 "default:fresh_default","rear","CH","rule_excludes",2 "default:fresh_default","spawn","CH","rule_excludes",1 -"default:fresh_default","any","BT","width_null",160 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+"bcfishpass:fresh","any","BT","fails_gradient",226 +"bcfishpass:fresh","rear","BT","fails_gradient",63 +"bcfishpass:fresh","spawn","BT","fails_gradient",14 "bcfishpass:fresh","any","CH","fails_gradient",75 "bcfishpass:fresh","rear","CH","fails_gradient",28 "bcfishpass:fresh","spawn","CH","fails_gradient",11 -"bcfishpass:fresh","any","BT","fails_gradient_and_width",74 -"bcfishpass:fresh","rear","BT","fails_gradient_and_width",28 +"bcfishpass:fresh","any","BT","fails_gradient_and_width",61 +"bcfishpass:fresh","rear","BT","fails_gradient_and_width",19 "bcfishpass:fresh","spawn","BT","fails_gradient_and_width",5 "bcfishpass:fresh","any","CH","fails_gradient_and_width",8 "bcfishpass:fresh","rear","CH","fails_gradient_and_width",7 "bcfishpass:fresh","spawn","CH","fails_gradient_and_width",1 -"bcfishpass:fresh","any","BT","fails_width",131 -"bcfishpass:fresh","rear","BT","fails_width",62 +"bcfishpass:fresh","any","BT","fails_width",104 +"bcfishpass:fresh","rear","BT","fails_width",39 "bcfishpass:fresh","spawn","BT","fails_width",5 "bcfishpass:fresh","any","CH","fails_width",12 "bcfishpass:fresh","rear","CH","fails_width",6 "bcfishpass:fresh","spawn","CH","fails_width",2 -"bcfishpass:fresh","any","BT","not_accessible",181 -"bcfishpass:fresh","rear","BT","not_accessible",89 -"bcfishpass:fresh","spawn","BT","not_accessible",6 +"bcfishpass:fresh","any","BT","not_accessible",95 +"bcfishpass:fresh","rear","BT","not_accessible",36 +"bcfishpass:fresh","spawn","BT","not_accessible",4 "bcfishpass:fresh","any","CH","not_accessible",48 "bcfishpass:fresh","rear","CH","not_accessible",15 "bcfishpass:fresh","spawn","CH","not_accessible",7 -"bcfishpass:fresh","any","BT","post_predicate",71 -"bcfishpass:fresh","rear","BT","post_predicate",38 +"bcfishpass:fresh","any","BT","post_predicate",54 +"bcfishpass:fresh","rear","BT","post_predicate",23 "bcfishpass:fresh","any","CH","post_predicate",16 "bcfishpass:fresh","rear","CH","post_predicate",7 "bcfishpass:fresh","spawn","BT","rule_excludes",6 "bcfishpass:fresh","any","CH","rule_excludes",66 "bcfishpass:fresh","rear","CH","rule_excludes",7 "bcfishpass:fresh","spawn","CH","rule_excludes",25 -"bcfishpass:fresh","any","BT","width_null",189 -"bcfishpass:fresh","rear","BT","width_null",64 -"bcfishpass:fresh","spawn","BT","width_null",5 +"bcfishpass:fresh","any","BT","width_null",159 +"bcfishpass:fresh","rear","BT","width_null",42 +"bcfishpass:fresh","spawn","BT","width_null",3 "bcfishpass:fresh","any","CH","width_null",52 "bcfishpass:fresh","rear","CH","width_null",26 "bcfishpass:fresh","spawn","CH","width_null",2 diff --git a/data-raw/logs/habitat_validate_283/misses_binned.csv b/data-raw/logs/habitat_validate_283/misses_binned.csv index 59b5958d..3bed74a6 100644 --- a/data-raw/logs/habitat_validate_283/misses_binned.csv +++ b/data-raw/logs/habitat_validate_283/misses_binned.csv @@ -1,5 +1,5 @@ "bundle","stage","species_code","reason","gradient_bin","width_bin","n" -"default:fresh_default","any","BT","fails_width","(-Inf,0.0025]","[0,1.5)",7 +"default:fresh_default","any","BT","fails_width","(-Inf,0.0025]","[0,1.5)",5 "default:fresh_default","rear","BT","fails_width","(-Inf,0.0025]","[0,1.5)",3 "default:fresh_default","any","CH","fails_width","(-Inf,0.0025]","[0,1.5)",4 "default:fresh_default","rear","CH","fails_width","(-Inf,0.0025]","[0,1.5)",1 @@ -7,40 +7,36 @@ "default:fresh_default","any","BT","fails_width","(0.0025,0.01]","[0,1.5)",2 "default:fresh_default","any","CH","fails_width","(0.0025,0.01]","[0,1.5)",1 "default:fresh_default","rear","CH","fails_width","(0.0025,0.01]","[0,1.5)",1 -"default:fresh_default","any","BT","post_predicate","(0.0025,0.01]","[0,1.5)",1 -"default:fresh_default","rear","BT","post_predicate","(0.0025,0.01]","[0,1.5)",1 -"default:fresh_default","any","BT","fails_width","(0.01,0.02]","[0,1.5)",12 -"default:fresh_default","rear","BT","fails_width","(0.01,0.02]","[0,1.5)",5 +"default:fresh_default","any","BT","fails_width","(0.01,0.02]","[0,1.5)",10 +"default:fresh_default","rear","BT","fails_width","(0.01,0.02]","[0,1.5)",3 "default:fresh_default","spawn","BT","fails_width","(0.01,0.02]","[0,1.5)",1 "default:fresh_default","any","CH","fails_width","(0.01,0.02]","[0,1.5)",3 "default:fresh_default","rear","CH","fails_width","(0.01,0.02]","[0,1.5)",1 -"default:fresh_default","any","BT","post_predicate","(0.01,0.02]","[0,1.5)",1 -"default:fresh_default","rear","BT","post_predicate","(0.01,0.02]","[0,1.5)",1 -"default:fresh_default","any","BT","fails_width","(0.02,0.03]","[0,1.5)",15 -"default:fresh_default","rear","BT","fails_width","(0.02,0.03]","[0,1.5)",5 +"default:fresh_default","any","BT","fails_width","(0.02,0.03]","[0,1.5)",12 +"default:fresh_default","rear","BT","fails_width","(0.02,0.03]","[0,1.5)",2 "default:fresh_default","any","CH","fails_width","(0.02,0.03]","[0,1.5)",1 "default:fresh_default","rear","CH","fails_width","(0.02,0.03]","[0,1.5)",1 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"default:fresh_default","spawn","BT","fails_gradient_and_width","(0.055,0.07]","[0,1.5)",1 "default:fresh_default","any","CH","fails_gradient_and_width","(0.055,0.07]","[0,1.5)",2 "default:fresh_default","rear","CH","fails_gradient_and_width","(0.055,0.07]","[0,1.5)",2 -"default:fresh_default","any","BT","fails_width","(0.055,0.07]","[0,1.5)",15 +"default:fresh_default","any","BT","fails_width","(0.055,0.07]","[0,1.5)",14 "default:fresh_default","rear","BT","fails_width","(0.055,0.07]","[0,1.5)",4 "default:fresh_default","spawn","BT","fails_gradient_and_width","(0.07,0.105]","[0,1.5)",2 "default:fresh_default","any","CH","fails_gradient_and_width","(0.07,0.105]","[0,1.5)",1 "default:fresh_default","rear","CH","fails_gradient_and_width","(0.07,0.105]","[0,1.5)",1 -"default:fresh_default","any","BT","fails_width","(0.07,0.105]","[0,1.5)",34 -"default:fresh_default","rear","BT","fails_width","(0.07,0.105]","[0,1.5)",19 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-"bcfishpass:fresh","rear","BT","fails_gradient_and_width","(0.15,0.2]","NULL",3 +"bcfishpass:fresh","any","BT","fails_gradient_and_width","(0.15,0.2]","NULL",3 "bcfishpass:fresh","any","BT","not_accessible","(0.15,0.2]","NULL",2 "bcfishpass:fresh","rear","BT","not_accessible","(0.15,0.2]","NULL",1 -"bcfishpass:fresh","any","BT","fails_gradient_and_width","(0.2,0.25]","NULL",5 -"bcfishpass:fresh","rear","BT","fails_gradient_and_width","(0.2,0.25]","NULL",2 +"bcfishpass:fresh","any","BT","fails_gradient_and_width","(0.2,0.25]","NULL",4 +"bcfishpass:fresh","rear","BT","fails_gradient_and_width","(0.2,0.25]","NULL",1 "bcfishpass:fresh","any","BT","not_accessible","(0.2,0.25]","NULL",1 "bcfishpass:fresh","rear","BT","not_accessible","(0.2,0.25]","NULL",1 "bcfishpass:fresh","any","CH","not_accessible","(0.2,0.25]","NULL",1 "bcfishpass:fresh","spawn","CH","not_accessible","(0.2,0.25]","NULL",1 -"bcfishpass:fresh","any","BT","fails_gradient_and_width","(0.25, Inf]","NULL",12 -"bcfishpass:fresh","rear","BT","fails_gradient_and_width","(0.25, Inf]","NULL",3 -"bcfishpass:fresh","any","BT","not_accessible","(0.25, Inf]","NULL",13 -"bcfishpass:fresh","rear","BT","not_accessible","(0.25, Inf]","NULL",9 +"bcfishpass:fresh","any","BT","fails_gradient_and_width","(0.25, Inf]","NULL",9 +"bcfishpass:fresh","rear","BT","fails_gradient_and_width","(0.25, Inf]","NULL",1 +"bcfishpass:fresh","any","BT","not_accessible","(0.25, Inf]","NULL",7 +"bcfishpass:fresh","rear","BT","not_accessible","(0.25, Inf]","NULL",4 "bcfishpass:fresh","any","CH","not_accessible","(0.25, Inf]","NULL",1 diff --git a/data-raw/logs/habitat_validate_283/stamp.txt b/data-raw/logs/habitat_validate_283/stamp.txt index 94129d1c..919ff892 100644 --- a/data-raw/logs/habitat_validate_283/stamp.txt +++ b/data-raw/logs/habitat_validate_283/stamp.txt @@ -1,9 +1,10 @@ -date: 2026-09-26 13:39 PDT -link: 0.51.1 @ 0c19e0a +date: 2026-09-27 07:58 PDT +link: 0.52.0 @ 911bed3 fresh installed (builds the miss-reason predicates): 0.34.0 @ no recorded sha db: docker fwapg localhost:5432 bundle default:fresh_default — 55 WSGs scored; 4 with a run-log row (fresh 0.32.0, 0.33.0, 2026-08-06 to 2026-08-27); the rest predate the log bundle bcfishpass:fresh — 59 WSGs scored; 39 with a run-log row (fresh 0.33.0, 2026-08-31 to 2026-09-26); the rest predate the log species: CH,BT; buffers: 0,100 m +pooling: default species_pooling.csv (sha256 9c42964e0469): 56 WSG x species pairs pooled (BT<-DV) bcfishobs.observations rows: 373050 absences: 4174 sampled FISS sites snapped within the snapshot WSGs (COTR,LNTH,PINE,UNTH,UPCE); usable as absences, before presence: CH 1906, BT 1535; other WSGs report NA; knowledge @ 508bf44 diff --git a/data-raw/logs/habitat_validate_283/summary.csv b/data-raw/logs/habitat_validate_283/summary.csv index abae60e1..08038cac 100644 --- a/data-raw/logs/habitat_validate_283/summary.csv +++ b/data-raw/logs/habitat_validate_283/summary.csv @@ -107,9 +107,9 @@ "fresh_default","default",0,TRUE,"KISP","CH","any",89,0,89,0,82,76,79,83,1,0.921348314606742,0.853932584269663,0.887640449438202,0.932584269662921,37,0,52,45,89,79,0.865384615384615,0.887640449438202,2841.44,862.28,1178.83,,,,,,FALSE "fresh_default","default",0,TRUE,"KISP","CH","spawn",30,0,30,0,30,25,26,30,1,1,0.833333333333333,0.866666666666667,1,30,0,0,0,30,26,,0.866666666666667,2841.44,862.28,1178.83,,,,,,FALSE "fresh_default","default",0,TRUE,"KISP","CH","rear",12,0,12,0,10,10,10,10,1,0.833333333333333,0.833333333333333,0.833333333333333,0.833333333333333,1,0,11,9,12,10,0.818181818181818,0.833333333333333,2841.44,862.28,1178.83,,,,,,FALSE -"fresh_default","default",0,TRUE,"KLUM","BT","any",314,0,302,12,194,243,244,244,0.961783439490446,0.617834394904459,0.773885350318471,0.777070063694268,0.777070063694268,0,0,314,194,314,244,0.617834394904459,0.777070063694268,2173.93,929.96,1229.04,,,,,,FALSE +"fresh_default","default",0,TRUE,"KLUM","BT","any",30,0,29,1,21,25,25,25,0.966666666666667,0.7,0.833333333333333,0.833333333333333,0.833333333333333,0,0,30,21,30,25,0.7,0.833333333333333,2173.93,929.96,1229.04,,,,,,FALSE "fresh_default","default",0,TRUE,"KLUM","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2173.93,929.96,1229.04,,,,,,FALSE -"fresh_default","default",0,TRUE,"KLUM","BT","rear",141,0,137,4,66,95,96,96,0.971631205673759,0.468085106382979,0.673758865248227,0.680851063829787,0.680851063829787,0,0,141,66,141,96,0.468085106382979,0.680851063829787,2173.93,929.96,1229.04,,,,,,FALSE +"fresh_default","default",0,TRUE,"KLUM","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2173.93,929.96,1229.04,,,,,,FALSE "fresh_default","default",0,TRUE,"KLUM","CH","any",104,0,99,5,87,88,90,91,0.951923076923077,0.836538461538462,0.846153846153846,0.865384615384615,0.875,28,0,76,59,104,90,0.776315789473684,0.865384615384615,1523.16,708.12,905.48,,,,,,FALSE "fresh_default","default",0,TRUE,"KLUM","CH","spawn",20,0,19,1,20,18,19,20,0.95,1,0.9,0.95,1,20,0,0,0,20,19,,0.95,1523.16,708.12,905.48,,,,,,FALSE "fresh_default","default",0,TRUE,"KLUM","CH","rear",19,0,19,0,14,16,16,16,1,0.736842105263158,0.842105263157895,0.842105263157895,0.842105263157895,4,0,15,10,19,16,0.666666666666667,0.842105263157895,1523.16,708.12,905.48,,,,,,FALSE @@ -143,9 +143,9 @@ "fresh_default","default",0,TRUE,"LFRA","CH","any",165,0,161,4,105,132,133,133,0.975757575757576,0.636363636363636,0.8,0.806060606060606,0.806060606060606,19,0,146,86,165,133,0.589041095890411,0.806060606060606,3074.38,826.28,1254.99,,,,,,FALSE "fresh_default","default",0,TRUE,"LFRA","CH","spawn",10,0,10,0,10,10,10,10,1,1,1,1,1,10,0,0,0,10,10,,1,3074.38,826.28,1254.99,,,,,,FALSE "fresh_default","default",0,TRUE,"LFRA","CH","rear",66,0,65,1,39,54,54,54,0.984848484848485,0.590909090909091,0.818181818181818,0.818181818181818,0.818181818181818,6,0,60,33,66,54,0.55,0.818181818181818,3074.38,826.28,1254.99,,,,,,FALSE -"fresh_default","default",0,TRUE,"LKEL","BT","any",63,0,63,0,36,45,48,48,1,0.571428571428571,0.714285714285714,0.761904761904762,0.761904761904762,0,0,63,36,63,48,0.571428571428571,0.761904761904762,405.16,144.67,218.77,,,,,,FALSE +"fresh_default","default",0,TRUE,"LKEL","BT","any",1,0,1,0,0,0,0,0,1,0,0,0,0,0,0,1,0,1,0,0,0,405.16,144.67,218.77,,,,,,FALSE "fresh_default","default",0,TRUE,"LKEL","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,405.16,144.67,218.77,,,,,,FALSE -"fresh_default","default",0,TRUE,"LKEL","BT","rear",26,0,26,0,11,16,16,16,1,0.423076923076923,0.615384615384615,0.615384615384615,0.615384615384615,0,0,26,11,26,16,0.423076923076923,0.615384615384615,405.16,144.67,218.77,,,,,,FALSE +"fresh_default","default",0,TRUE,"LKEL","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,405.16,144.67,218.77,,,,,,FALSE "fresh_default","default",0,TRUE,"LKEL","CH","any",14,0,14,0,12,11,12,14,1,0.857142857142857,0.785714285714286,0.857142857142857,1,5,0,9,7,14,12,0.777777777777778,0.857142857142857,332.18,106.7,162.87,,,,,,FALSE "fresh_default","default",0,TRUE,"LKEL","CH","spawn",3,0,3,0,3,2,2,3,1,1,0.666666666666667,0.666666666666667,1,3,0,0,0,3,2,,0.666666666666667,332.18,106.7,162.87,,,,,,FALSE "fresh_default","default",0,TRUE,"LKEL","CH","rear",2,0,2,0,1,2,2,2,1,0.5,1,1,1,0,0,2,1,2,2,0.5,1,332.18,106.7,162.87,,,,,,FALSE @@ -167,9 +167,9 @@ "fresh_default","default",0,TRUE,"LSAL","CH","any",17,0,17,0,17,17,17,17,1,1,1,1,1,6,0,11,11,17,17,1,1,3029.07,317.62,1060.92,,,,,,FALSE "fresh_default","default",0,TRUE,"LSAL","CH","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,3029.07,317.62,1060.92,,,,,,FALSE "fresh_default","default",0,TRUE,"LSAL","CH","rear",4,0,4,0,4,4,4,4,1,1,1,1,1,2,0,2,2,4,4,1,1,3029.07,317.62,1060.92,,,,,,FALSE -"fresh_default","default",0,TRUE,"LSKE","BT","any",230,0,227,3,168,193,193,193,0.98695652173913,0.730434782608696,0.839130434782609,0.839130434782609,0.839130434782609,0,0,230,168,230,193,0.730434782608696,0.839130434782609,3075.25,1326.45,1709.47,,,,,,FALSE -"fresh_default","default",0,TRUE,"LSKE","BT","spawn",3,0,3,0,2,2,2,2,1,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,0,0,3,2,3,2,0.666666666666667,0.666666666666667,3075.25,1326.45,1709.47,,,,,,FALSE -"fresh_default","default",0,TRUE,"LSKE","BT","rear",111,0,109,2,69,85,85,85,0.981981981981982,0.621621621621622,0.765765765765766,0.765765765765766,0.765765765765766,0,0,111,69,111,85,0.621621621621622,0.765765765765766,3075.25,1326.45,1709.47,,,,,,FALSE +"fresh_default","default",0,TRUE,"LSKE","BT","any",8,0,8,0,7,8,8,8,1,0.875,1,1,1,0,0,8,7,8,8,0.875,1,3075.25,1326.45,1709.47,,,,,,FALSE +"fresh_default","default",0,TRUE,"LSKE","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,3075.25,1326.45,1709.47,,,,,,FALSE +"fresh_default","default",0,TRUE,"LSKE","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,3075.25,1326.45,1709.47,,,,,,FALSE "fresh_default","default",0,TRUE,"LSKE","CH","any",122,0,119,3,106,106,106,111,0.975409836065574,0.868852459016393,0.868852459016393,0.868852459016393,0.90983606557377,40,0,82,66,122,106,0.804878048780488,0.868852459016393,2101.75,1052.46,1308.55,,,,,,FALSE "fresh_default","default",0,TRUE,"LSKE","CH","spawn",24,0,23,1,24,22,22,24,0.958333333333333,1,0.916666666666667,0.916666666666667,1,24,0,0,0,24,22,,0.916666666666667,2101.75,1052.46,1308.55,,,,,,FALSE "fresh_default","default",0,TRUE,"LSKE","CH","rear",35,0,35,0,26,29,29,30,1,0.742857142857143,0.828571428571429,0.828571428571429,0.857142857142857,3,0,32,23,35,29,0.71875,0.828571428571429,2101.75,1052.46,1308.55,,,,,,FALSE @@ -323,9 +323,9 @@ "fresh_default","default",0,TRUE,"WILL","CH","any",58,0,58,0,53,53,53,54,1,0.913793103448276,0.913793103448276,0.913793103448276,0.931034482758621,40,0,18,13,58,53,0.722222222222222,0.913793103448276,3601.38,640.69,1364.26,,,,,,FALSE "fresh_default","default",0,TRUE,"WILL","CH","spawn",3,0,3,0,3,2,2,3,1,1,0.666666666666667,0.666666666666667,1,3,0,0,0,3,2,,0.666666666666667,3601.38,640.69,1364.26,,,,,,FALSE "fresh_default","default",0,TRUE,"WILL","CH","rear",42,0,42,0,38,39,39,39,1,0.904761904761905,0.928571428571429,0.928571428571429,0.928571428571429,30,0,12,8,42,39,0.666666666666667,0.928571428571429,3601.38,640.69,1364.26,,,,,,FALSE -"fresh_default","default",0,TRUE,"ZYMO","BT","any",280,0,276,4,129,188,196,196,0.985714285714286,0.460714285714286,0.671428571428571,0.7,0.7,0,0,280,129,280,196,0.460714285714286,0.7,2058.68,594.73,897.89,,,,,,FALSE -"fresh_default","default",0,TRUE,"ZYMO","BT","spawn",14,0,14,0,7,10,10,10,1,0.5,0.714285714285714,0.714285714285714,0.714285714285714,0,0,14,7,14,10,0.5,0.714285714285714,2058.68,594.73,897.89,,,,,,FALSE -"fresh_default","default",0,TRUE,"ZYMO","BT","rear",147,0,147,0,53,86,88,88,1,0.360544217687075,0.585034013605442,0.598639455782313,0.598639455782313,0,0,147,53,147,88,0.360544217687075,0.598639455782313,2058.68,594.73,897.89,,,,,,FALSE +"fresh_default","default",0,TRUE,"ZYMO","BT","any",19,0,18,1,11,12,12,12,0.947368421052632,0.578947368421053,0.631578947368421,0.631578947368421,0.631578947368421,0,0,19,11,19,12,0.578947368421053,0.631578947368421,2058.68,594.73,897.89,,,,,,FALSE +"fresh_default","default",0,TRUE,"ZYMO","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2058.68,594.73,897.89,,,,,,FALSE +"fresh_default","default",0,TRUE,"ZYMO","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2058.68,594.73,897.89,,,,,,FALSE "fresh_default","default",0,TRUE,"ZYMO","CH","any",21,0,19,2,14,16,16,17,0.904761904761905,0.666666666666667,0.761904761904762,0.761904761904762,0.80952380952381,8,0,13,6,21,16,0.461538461538462,0.761904761904762,1211.06,463.12,602.24,,,,,,FALSE "fresh_default","default",0,TRUE,"ZYMO","CH","spawn",8,0,7,1,8,7,7,8,0.875,1,0.875,0.875,1,8,0,0,0,8,7,,0.875,1211.06,463.12,602.24,,,,,,FALSE "fresh_default","default",0,TRUE,"ZYMO","CH","rear",5,0,4,1,0,1,1,1,0.8,0,0.2,0.2,0.2,0,0,5,0,5,1,0,0.2,1211.06,463.12,602.24,,,,,,FALSE @@ -437,9 +437,9 @@ "fresh_default","default",100,TRUE,"KISP","CH","any",89,0,89,0,84,78,81,85,1,0.943820224719101,0.876404494382023,0.910112359550562,0.955056179775281,38,0,51,46,89,81,0.901960784313726,0.910112359550562,2841.44,862.28,1178.83,,,,,,FALSE "fresh_default","default",100,TRUE,"KISP","CH","spawn",30,0,30,0,30,25,26,30,1,1,0.833333333333333,0.866666666666667,1,30,0,0,0,30,26,,0.866666666666667,2841.44,862.28,1178.83,,,,,,FALSE "fresh_default","default",100,TRUE,"KISP","CH","rear",12,0,12,0,10,10,10,10,1,0.833333333333333,0.833333333333333,0.833333333333333,0.833333333333333,1,0,11,9,12,10,0.818181818181818,0.833333333333333,2841.44,862.28,1178.83,,,,,,FALSE -"fresh_default","default",100,TRUE,"KLUM","BT","any",314,0,302,12,203,248,248,248,0.961783439490446,0.646496815286624,0.789808917197452,0.789808917197452,0.789808917197452,0,0,314,203,314,248,0.646496815286624,0.789808917197452,2173.93,929.96,1229.04,,,,,,FALSE 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"fresh_default","default",100,TRUE,"KLUM","CH","spawn",20,0,19,1,20,18,19,20,0.95,1,0.9,0.95,1,20,0,0,0,20,19,,0.95,1523.16,708.12,905.48,,,,,,FALSE "fresh_default","default",100,TRUE,"KLUM","CH","rear",19,0,19,0,14,16,16,16,1,0.736842105263158,0.842105263157895,0.842105263157895,0.842105263157895,4,0,15,10,19,16,0.666666666666667,0.842105263157895,1523.16,708.12,905.48,,,,,,FALSE @@ -473,9 +473,9 @@ "fresh_default","default",100,TRUE,"LFRA","CH","any",165,0,161,4,108,135,136,136,0.975757575757576,0.654545454545455,0.818181818181818,0.824242424242424,0.824242424242424,19,0,146,89,165,136,0.60958904109589,0.824242424242424,3074.38,826.28,1254.99,,,,,,FALSE "fresh_default","default",100,TRUE,"LFRA","CH","spawn",10,0,10,0,10,10,10,10,1,1,1,1,1,10,0,0,0,10,10,,1,3074.38,826.28,1254.99,,,,,,FALSE 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"fresh","bcfishpass",0,FALSE,"ZYMO","CH","any",21,0,19,2,13,16,16,16,0.904761904761905,0.619047619047619,0.761904761904762,0.761904761904762,0.761904761904762,8,0,13,6,21,16,0.461538461538462,0.761904761904762,1200.73,462.91,539.94,,,,,,TRUE "fresh","bcfishpass",0,FALSE,"ZYMO","CH","spawn",8,0,7,1,7,7,7,7,0.875,0.875,0.875,0.875,0.875,8,0,0,0,8,7,,0.875,1200.73,462.91,539.94,,,,,,TRUE "fresh","bcfishpass",0,FALSE,"ZYMO","CH","rear",5,0,4,1,0,1,1,1,0.8,0,0.2,0.2,0.2,0,0,5,0,5,1,0,0.2,1200.73,462.91,539.94,,,,,,TRUE @@ -1127,9 +1127,9 @@ "fresh","bcfishpass",100,FALSE,"KISP","CH","any",89,0,89,0,77,78,78,78,1,0.865168539325843,0.876404494382023,0.876404494382023,0.876404494382023,38,0,51,46,89,78,0.901960784313726,0.876404494382023,2786.73,860.45,1050.59,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"KISP","CH","spawn",30,0,30,0,25,25,25,25,1,0.833333333333333,0.833333333333333,0.833333333333333,0.833333333333333,30,0,0,0,30,25,,0.833333333333333,2786.73,860.45,1050.59,,,,,,TRUE 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-"fresh","bcfishpass",100,FALSE,"KLUM","BT","rear",141,0,121,20,66,92,92,92,0.858156028368794,0.468085106382979,0.652482269503546,0.652482269503546,0.652482269503546,0,0,141,66,141,92,0.468085106382979,0.652482269503546,1930.45,894.45,1189.16,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"KLUM","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,1930.45,894.45,1189.16,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"KLUM","CH","any",104,0,99,5,85,87,87,87,0.951923076923077,0.817307692307692,0.836538461538462,0.836538461538462,0.836538461538462,28,0,76,60,104,87,0.789473684210526,0.836538461538462,1481.08,707.93,830.68,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"KLUM","CH","spawn",20,0,19,1,17,18,18,18,0.95,0.85,0.9,0.9,0.9,20,0,0,0,20,18,,0.9,1481.08,707.93,830.68,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"KLUM","CH","rear",19,0,19,0,14,15,15,15,1,0.736842105263158,0.789473684210526,0.789473684210526,0.789473684210526,4,0,15,10,19,15,0.666666666666667,0.789473684210526,1481.08,707.93,830.68,,,,,,TRUE @@ -1157,9 +1157,9 @@ "fresh","bcfishpass",100,FALSE,"LFRA","CH","any",165,0,159,6,107,135,135,135,0.963636363636364,0.648484848484848,0.818181818181818,0.818181818181818,0.818181818181818,19,0,146,89,165,135,0.60958904109589,0.818181818181818,2754.05,820.43,1176.68,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LFRA","CH","spawn",10,0,10,0,9,10,10,10,1,0.9,1,1,1,10,0,0,0,10,10,,1,2754.05,820.43,1176.68,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LFRA","CH","rear",66,0,63,3,40,55,55,55,0.954545454545455,0.606060606060606,0.833333333333333,0.833333333333333,0.833333333333333,6,0,60,34,66,55,0.566666666666667,0.833333333333333,2754.05,820.43,1176.68,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"LKEL","BT","any",63,0,63,0,37,49,49,49,1,0.587301587301587,0.777777777777778,0.777777777777778,0.777777777777778,0,0,63,37,63,49,0.587301587301587,0.777777777777778,401.02,144.74,222.78,,,,,,FALSE +"fresh","bcfishpass",100,FALSE,"LKEL","BT","any",1,0,1,0,0,0,0,0,1,0,0,0,0,0,0,1,0,1,0,0,0,401.02,144.74,222.78,,,,,,FALSE "fresh","bcfishpass",100,FALSE,"LKEL","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,401.02,144.74,222.78,,,,,,FALSE -"fresh","bcfishpass",100,FALSE,"LKEL","BT","rear",26,0,26,0,12,17,17,17,1,0.461538461538462,0.653846153846154,0.653846153846154,0.653846153846154,0,0,26,12,26,17,0.461538461538462,0.653846153846154,401.02,144.74,222.78,,,,,,FALSE +"fresh","bcfishpass",100,FALSE,"LKEL","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,401.02,144.74,222.78,,,,,,FALSE "fresh","bcfishpass",100,FALSE,"LKEL","CH","any",14,0,14,0,11,11,11,11,1,0.785714285714286,0.785714285714286,0.785714285714286,0.785714285714286,5,0,9,8,14,11,0.888888888888889,0.785714285714286,328.21,106.49,123.85,,,,,,FALSE "fresh","bcfishpass",100,FALSE,"LKEL","CH","spawn",3,0,3,0,2,2,2,2,1,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,3,0,0,0,3,2,,0.666666666666667,328.21,106.49,123.85,,,,,,FALSE "fresh","bcfishpass",100,FALSE,"LKEL","CH","rear",2,0,2,0,2,2,2,2,1,1,1,1,1,0,0,2,2,2,2,1,1,328.21,106.49,123.85,,,,,,FALSE @@ -1187,9 +1187,9 @@ "fresh","bcfishpass",100,FALSE,"LSAL","CH","any",17,0,17,0,17,17,17,17,1,1,1,1,1,6,0,11,11,17,17,1,1,2968.08,312.6,617.6,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LSAL","CH","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2968.08,312.6,617.6,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LSAL","CH","rear",4,0,4,0,4,4,4,4,1,1,1,1,1,2,0,2,2,4,4,1,1,2968.08,312.6,617.6,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"LSKE","BT","any",230,0,216,14,171,187,187,187,0.939130434782609,0.743478260869565,0.81304347826087,0.81304347826087,0.81304347826087,0,0,230,171,230,187,0.743478260869565,0.81304347826087,2884.31,1315.64,1751.5,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"LSKE","BT","spawn",3,0,3,0,2,2,2,2,1,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,0,0,3,2,3,2,0.666666666666667,0.666666666666667,2884.31,1315.64,1751.5,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"LSKE","BT","rear",111,0,102,9,70,82,82,82,0.918918918918919,0.630630630630631,0.738738738738739,0.738738738738739,0.738738738738739,0,0,111,70,111,82,0.630630630630631,0.738738738738739,2884.31,1315.64,1751.5,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"LSKE","BT","any",8,0,8,0,8,8,8,8,1,1,1,1,1,0,0,8,8,8,8,1,1,2884.31,1315.64,1751.5,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"LSKE","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2884.31,1315.64,1751.5,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"LSKE","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,2884.31,1315.64,1751.5,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LSKE","CH","any",122,0,119,3,103,110,110,110,0.975409836065574,0.844262295081967,0.901639344262295,0.901639344262295,0.901639344262295,41,0,81,68,122,110,0.839506172839506,0.901639344262295,2086.32,1049.22,1167.34,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LSKE","CH","spawn",24,0,23,1,21,22,22,22,0.958333333333333,0.875,0.916666666666667,0.916666666666667,0.916666666666667,24,0,0,0,24,22,,0.916666666666667,2086.32,1049.22,1167.34,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"LSKE","CH","rear",35,0,35,0,26,30,30,30,1,0.742857142857143,0.857142857142857,0.857142857142857,0.857142857142857,3,0,32,24,35,30,0.75,0.857142857142857,2086.32,1049.22,1167.34,,,,,,TRUE @@ -1361,9 +1361,9 @@ "fresh","bcfishpass",100,FALSE,"WILL","CH","any",58,0,58,0,54,55,55,55,1,0.931034482758621,0.948275862068966,0.948275862068966,0.948275862068966,40,0,18,15,58,55,0.833333333333333,0.948275862068966,3537.67,630.48,1029.73,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"WILL","CH","spawn",3,0,3,0,2,2,2,2,1,0.666666666666667,0.666666666666667,0.666666666666667,0.666666666666667,3,0,0,0,3,2,,0.666666666666667,3537.67,630.48,1029.73,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"WILL","CH","rear",42,0,42,0,40,41,41,41,1,0.952380952380952,0.976190476190476,0.976190476190476,0.976190476190476,30,0,12,10,42,41,0.833333333333333,0.976190476190476,3537.67,630.48,1029.73,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"ZYMO","BT","any",280,0,244,36,128,188,188,188,0.871428571428571,0.457142857142857,0.671428571428571,0.671428571428571,0.671428571428571,0,0,280,128,280,188,0.457142857142857,0.671428571428571,1840.06,575.42,863.2,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"ZYMO","BT","spawn",14,0,12,2,7,9,9,9,0.857142857142857,0.5,0.642857142857143,0.642857142857143,0.642857142857143,0,0,14,7,14,9,0.5,0.642857142857143,1840.06,575.42,863.2,,,,,,TRUE -"fresh","bcfishpass",100,FALSE,"ZYMO","BT","rear",147,0,123,24,49,79,79,79,0.836734693877551,0.333333333333333,0.537414965986395,0.537414965986395,0.537414965986395,0,0,147,49,147,79,0.333333333333333,0.537414965986395,1840.06,575.42,863.2,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"ZYMO","BT","any",19,0,18,1,11,13,13,13,0.947368421052632,0.578947368421053,0.68421052631579,0.68421052631579,0.68421052631579,0,0,19,11,19,13,0.578947368421053,0.68421052631579,1840.06,575.42,863.2,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"ZYMO","BT","spawn",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,1840.06,575.42,863.2,,,,,,TRUE +"fresh","bcfishpass",100,FALSE,"ZYMO","BT","rear",0,0,0,0,0,0,0,0,,,,,,0,0,0,0,0,0,,,1840.06,575.42,863.2,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"ZYMO","CH","any",21,0,19,2,14,16,16,16,0.904761904761905,0.666666666666667,0.761904761904762,0.761904761904762,0.761904761904762,8,0,13,7,21,16,0.538461538461538,0.761904761904762,1200.73,462.91,539.94,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"ZYMO","CH","spawn",8,0,7,1,7,7,7,7,0.875,0.875,0.875,0.875,0.875,8,0,0,0,8,7,,0.875,1200.73,462.91,539.94,,,,,,TRUE "fresh","bcfishpass",100,FALSE,"ZYMO","CH","rear",5,0,4,1,0,1,1,1,0.8,0,0.2,0.2,0.2,0,0,5,0,5,1,0,0.2,1200.73,462.91,539.94,,,,,,TRUE diff --git a/data-raw/logs/habitat_validate_283/totals.csv b/data-raw/logs/habitat_validate_283/totals.csv index cc8f42f6..bff04895 100644 --- a/data-raw/logs/habitat_validate_283/totals.csv +++ b/data-raw/logs/habitat_validate_283/totals.csv @@ -1,25 +1,25 @@ "schema","config_name","buffer_m","species_code","stage","n_obs","n_unattached","n_accessible","n_inaccessible","n_spawning","n_rearing","n_rearing_any","n_habitat","n_in_uhc_spawn","n_in_uhc_rear","n_obs_outside_uhc_spawn","n_spawning_outside_uhc","n_obs_outside_uhc_rear","n_rearing_any_outside_uhc","n_absence","n_absence_accessible","n_absence_spawning","n_absence_rearing","n_absence_rearing_any","accessible_km","spawning_km","rearing_km","n_wsg","n_wsg_logged","share_accessible","share_spawning","share_rearing","share_rearing_any","share_habitat","share_spawning_outside_uhc","share_rearing_any_outside_uhc" -"fresh","bcfishpass",0,"BT","any",5708,0,5526,182,3847,4784,4784,4786,0,0,5708,3847,5708,4784,1218,1017,704,831,831,219264.85,52856.04,86470.4,59,39,0.968114926419061,0.673966362999299,0.83812193412754,0.83812193412754,0.838472319551507,0.673966362999299,0.83812193412754 -"fresh","bcfishpass",0,"BT","rear",1052,0,963,89,442,670,670,670,0,0,1052,442,1052,670,1218,1017,704,831,831,219264.85,52856.04,86470.4,59,39,0.915399239543726,0.420152091254753,0.636882129277566,0.636882129277566,0.636882129277566,0.420152091254753,0.636882129277566 -"fresh","bcfishpass",0,"BT","spawn",86,0,80,6,41,61,61,61,0,0,86,41,86,61,1218,1017,704,831,831,219264.85,52856.04,86470.4,59,39,0.930232558139535,0.476744186046512,0.709302325581395,0.709302325581395,0.709302325581395,0.476744186046512,0.709302325581395 +"fresh","bcfishpass",0,"BT","any",4879,0,4784,95,3382,4178,4178,4180,0,0,4879,3382,4879,4178,1218,1017,704,831,831,219264.85,52856.04,86470.4,59,39,0.980528796884607,0.693174830907973,0.856323017011683,0.856323017011683,0.85673293707727,0.693174830907973,0.856323017011683 +"fresh","bcfishpass",0,"BT","rear",627,0,591,36,257,405,405,405,0,0,627,257,627,405,1218,1017,704,831,831,219264.85,52856.04,86470.4,59,39,0.942583732057416,0.409888357256778,0.645933014354067,0.645933014354067,0.645933014354067,0.409888357256778,0.645933014354067 +"fresh","bcfishpass",0,"BT","spawn",69,0,65,4,32,50,50,50,0,0,69,32,69,50,1218,1017,704,831,831,219264.85,52856.04,86470.4,59,39,0.942028985507246,0.463768115942029,0.72463768115942,0.72463768115942,0.72463768115942,0.463768115942029,0.72463768115942 "fresh","bcfishpass",0,"CH","any",1999,0,1950,49,1637,1722,1722,1722,750,0,1249,951,1999,1722,481,249,147,165,165,78257.18,18104.08,24659.63,59,39,0.975487743871936,0.818909454727364,0.861430715357679,0.861430715357679,0.861430715357679,0.761409127301842,0.861430715357679 "fresh","bcfishpass",0,"CH","rear",615,0,600,15,479,519,519,519,213,0,402,272,615,519,481,249,147,165,165,78257.18,18104.08,24659.63,59,39,0.975609756097561,0.778861788617886,0.84390243902439,0.84390243902439,0.84390243902439,0.676616915422886,0.84390243902439 "fresh","bcfishpass",0,"CH","spawn",322,0,315,7,274,279,279,279,314,0,8,4,322,279,481,249,147,165,165,78257.18,18104.08,24659.63,59,39,0.978260869565217,0.850931677018634,0.866459627329193,0.866459627329193,0.866459627329193,0.5,0.866459627329193 -"fresh","bcfishpass",100,"BT","any",5708,0,5526,182,3996,4825,4825,4827,0,0,5708,3996,5708,4825,1218,1017,713,833,833,219264.85,52856.04,86470.4,59,39,0.968114926419061,0.700070077084793,0.845304835318851,0.845304835318851,0.845655220742817,0.700070077084793,0.845304835318851 -"fresh","bcfishpass",100,"BT","rear",1052,0,963,89,469,679,679,679,0,0,1052,469,1052,679,1218,1017,713,833,833,219264.85,52856.04,86470.4,59,39,0.915399239543726,0.445817490494297,0.645437262357414,0.645437262357414,0.645437262357414,0.445817490494297,0.645437262357414 -"fresh","bcfishpass",100,"BT","spawn",86,0,80,6,43,61,61,61,0,0,86,43,86,61,1218,1017,713,833,833,219264.85,52856.04,86470.4,59,39,0.930232558139535,0.5,0.709302325581395,0.709302325581395,0.709302325581395,0.5,0.709302325581395 +"fresh","bcfishpass",100,"BT","any",4879,0,4784,95,3510,4212,4212,4214,0,0,4879,3510,4879,4212,1218,1017,713,833,833,219264.85,52856.04,86470.4,59,39,0.980528796884607,0.719409715105554,0.863291658126665,0.863291658126665,0.863701578192252,0.719409715105554,0.863291658126665 +"fresh","bcfishpass",100,"BT","rear",627,0,591,36,272,409,409,409,0,0,627,272,627,409,1218,1017,713,833,833,219264.85,52856.04,86470.4,59,39,0.942583732057416,0.433811802232855,0.652312599681021,0.652312599681021,0.652312599681021,0.433811802232855,0.652312599681021 +"fresh","bcfishpass",100,"BT","spawn",69,0,65,4,34,50,50,50,0,0,69,34,69,50,1218,1017,713,833,833,219264.85,52856.04,86470.4,59,39,0.942028985507246,0.492753623188406,0.72463768115942,0.72463768115942,0.72463768115942,0.492753623188406,0.72463768115942 "fresh","bcfishpass",100,"CH","any",1999,0,1950,49,1672,1753,1753,1753,775,0,1224,958,1999,1753,481,249,149,167,167,78257.18,18104.08,24659.63,59,39,0.975487743871936,0.836418209104552,0.876938469234617,0.876938469234617,0.876938469234617,0.782679738562091,0.876938469234617 "fresh","bcfishpass",100,"CH","rear",615,0,600,15,487,528,528,528,222,0,393,273,615,528,481,249,149,167,167,78257.18,18104.08,24659.63,59,39,0.975609756097561,0.791869918699187,0.858536585365854,0.858536585365854,0.858536585365854,0.694656488549618,0.858536585365854 "fresh","bcfishpass",100,"CH","spawn",322,0,315,7,281,285,285,285,314,0,8,5,322,285,481,249,149,167,167,78257.18,18104.08,24659.63,59,39,0.978260869565217,0.872670807453416,0.885093167701863,0.885093167701863,0.885093167701863,0.625,0.885093167701863 -"fresh_default","default",0,"BT","any",5104,0,5061,43,3287,4107,4207,4207,0,0,5104,3287,5104,4207,858,814,587,635,686,219134.6,49453.94,78825.1,55,4,0.991575235109718,0.644004702194357,0.804663009404389,0.824255485893417,0.824255485893417,0.644004702194357,0.824255485893417 -"fresh_default","default",0,"BT","rear",1053,0,1040,13,467,694,700,700,0,0,1053,467,1053,700,858,814,587,635,686,219134.6,49453.94,78825.1,55,4,0.987654320987654,0.44349477682811,0.659069325735992,0.664767331433998,0.664767331433998,0.44349477682811,0.664767331433998 -"fresh_default","default",0,"BT","spawn",82,0,81,1,38,58,60,60,0,0,82,38,82,60,858,814,587,635,686,219134.6,49453.94,78825.1,55,4,0.98780487804878,0.463414634146341,0.707317073170732,0.731707317073171,0.731707317073171,0.463414634146341,0.731707317073171 +"fresh_default","default",0,"BT","any",4275,0,4249,26,2799,3483,3571,3571,0,0,4275,2799,4275,3571,858,814,587,635,686,219134.6,49453.94,78825.1,55,4,0.993918128654971,0.654736842105263,0.814736842105263,0.835321637426901,0.835321637426901,0.654736842105263,0.835321637426901 +"fresh_default","default",0,"BT","rear",628,0,621,7,268,412,415,415,0,0,628,268,628,415,858,814,587,635,686,219134.6,49453.94,78825.1,55,4,0.988853503184713,0.426751592356688,0.656050955414013,0.660828025477707,0.660828025477707,0.426751592356688,0.660828025477707 +"fresh_default","default",0,"BT","spawn",65,0,64,1,29,46,48,48,0,0,65,29,65,48,858,814,587,635,686,219134.6,49453.94,78825.1,55,4,0.984615384615385,0.446153846153846,0.707692307692308,0.738461538461539,0.738461538461539,0.446153846153846,0.738461538461539 "fresh_default","default",0,"CH","any",1745,0,1712,33,1487,1528,1549,1577,636,0,1109,852,1745,1549,68,25,11,13,15,74890.81,16236.35,27953.21,55,4,0.9810888252149,0.85214899713467,0.875644699140401,0.887679083094556,0.903724928366762,0.768259693417493,0.887679083094556 "fresh_default","default",0,"CH","rear",512,0,502,10,397,434,434,439,176,0,336,221,512,434,68,25,11,13,15,74890.81,16236.35,27953.21,55,4,0.98046875,0.775390625,0.84765625,0.84765625,0.857421875,0.657738095238095,0.84765625 "fresh_default","default",0,"CH","spawn",250,0,244,6,246,220,229,247,242,0,8,4,250,229,68,25,11,13,15,74890.81,16236.35,27953.21,55,4,0.976,0.984,0.88,0.916,0.988,0.5,0.916 -"fresh_default","default",100,"BT","any",5104,0,5061,43,3427,4191,4264,4264,0,0,5104,3427,5104,4264,858,814,591,637,687,219134.6,49453.94,78825.1,55,4,0.991575235109718,0.671434169278997,0.821120689655172,0.835423197492163,0.835423197492163,0.671434169278997,0.835423197492163 -"fresh_default","default",100,"BT","rear",1053,0,1040,13,496,711,715,715,0,0,1053,496,1053,715,858,814,591,637,687,219134.6,49453.94,78825.1,55,4,0.987654320987654,0.471035137701804,0.675213675213675,0.679012345679012,0.679012345679012,0.471035137701804,0.679012345679012 -"fresh_default","default",100,"BT","spawn",82,0,81,1,40,59,61,61,0,0,82,40,82,61,858,814,591,637,687,219134.6,49453.94,78825.1,55,4,0.98780487804878,0.48780487804878,0.719512195121951,0.74390243902439,0.74390243902439,0.48780487804878,0.74390243902439 +"fresh_default","default",100,"BT","any",4275,0,4249,26,2916,3553,3617,3617,0,0,4275,2916,4275,3617,858,814,591,637,687,219134.6,49453.94,78825.1,55,4,0.993918128654971,0.682105263157895,0.831111111111111,0.846081871345029,0.846081871345029,0.682105263157895,0.846081871345029 +"fresh_default","default",100,"BT","rear",628,0,621,7,283,420,422,422,0,0,628,283,628,422,858,814,591,637,687,219134.6,49453.94,78825.1,55,4,0.988853503184713,0.450636942675159,0.668789808917197,0.671974522292994,0.671974522292994,0.450636942675159,0.671974522292994 +"fresh_default","default",100,"BT","spawn",65,0,64,1,31,46,48,48,0,0,65,31,65,48,858,814,591,637,687,219134.6,49453.94,78825.1,55,4,0.984615384615385,0.476923076923077,0.707692307692308,0.738461538461539,0.738461538461539,0.476923076923077,0.738461538461539 "fresh_default","default",100,"CH","any",1745,0,1712,33,1513,1551,1571,1596,654,0,1091,862,1745,1571,68,25,11,13,15,74890.81,16236.35,27953.21,55,4,0.9810888252149,0.867048710601719,0.888825214899713,0.900286532951289,0.914613180515759,0.790100824931256,0.900286532951289 "fresh_default","default",100,"CH","rear",512,0,502,10,407,441,441,445,182,0,330,225,512,441,68,25,11,13,15,74890.81,16236.35,27953.21,55,4,0.98046875,0.794921875,0.861328125,0.861328125,0.869140625,0.681818181818182,0.861328125 "fresh_default","default",100,"CH","spawn",250,0,244,6,247,223,232,248,242,0,8,5,250,232,68,25,11,13,15,74890.81,16236.35,27953.21,55,4,0.976,0.988,0.892,0.928,0.992,0.625,0.928 diff --git a/data-raw/logs/habitat_validate_283/totals_shared.csv b/data-raw/logs/habitat_validate_283/totals_shared.csv index 7cf617e4..66e2cd01 100644 --- a/data-raw/logs/habitat_validate_283/totals_shared.csv +++ b/data-raw/logs/habitat_validate_283/totals_shared.csv @@ -1,25 +1,25 @@ "schema","config_name","buffer_m","species_code","stage","n_obs","n_unattached","n_accessible","n_inaccessible","n_spawning","n_rearing","n_rearing_any","n_habitat","n_in_uhc_spawn","n_in_uhc_rear","n_obs_outside_uhc_spawn","n_spawning_outside_uhc","n_obs_outside_uhc_rear","n_rearing_any_outside_uhc","n_absence","n_absence_accessible","n_absence_spawning","n_absence_rearing","n_absence_rearing_any","accessible_km","spawning_km","rearing_km","n_wsg","n_wsg_logged","share_accessible","share_spawning","share_rearing","share_rearing_any","share_habitat","share_spawning_outside_uhc","share_rearing_any_outside_uhc" -"fresh","bcfishpass",0,"BT","any",4600,0,4438,162,2966,3759,3759,3761,0,0,4600,2966,4600,3759,858,812,587,678,678,197434.02,46511.57,76872.29,51,33,0.964782608695652,0.644782608695652,0.817173913043478,0.817173913043478,0.817608695652174,0.644782608695652,0.817173913043478 -"fresh","bcfishpass",0,"BT","rear",1047,0,958,89,438,666,666,666,0,0,1047,438,1047,666,858,812,587,678,678,197434.02,46511.57,76872.29,51,33,0.914995224450812,0.418338108882521,0.636103151862464,0.636103151862464,0.636103151862464,0.418338108882521,0.636103151862464 -"fresh","bcfishpass",0,"BT","spawn",81,0,76,5,37,57,57,57,0,0,81,37,81,57,858,812,587,678,678,197434.02,46511.57,76872.29,51,33,0.938271604938272,0.45679012345679,0.703703703703704,0.703703703703704,0.703703703703704,0.45679012345679,0.703703703703704 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"fresh","bcfishpass",0,"CH","rear",510,0,498,12,390,429,429,429,175,0,335,220,510,429,68,25,11,12,12,70816.66,15640.34,21570.26,51,33,0.976470588235294,0.764705882352941,0.841176470588235,0.841176470588235,0.841176470588235,0.656716417910448,0.841176470588235 "fresh","bcfishpass",0,"CH","spawn",245,0,239,6,207,212,212,212,237,0,8,4,245,212,68,25,11,12,12,70816.66,15640.34,21570.26,51,33,0.975510204081633,0.844897959183673,0.86530612244898,0.86530612244898,0.86530612244898,0.5,0.86530612244898 -"fresh","bcfishpass",100,"BT","any",4600,0,4438,162,3084,3792,3792,3794,0,0,4600,3084,4600,3792,858,812,591,678,678,197434.02,46511.57,76872.29,51,33,0.964782608695652,0.670434782608696,0.824347826086957,0.824347826086957,0.824782608695652,0.670434782608696,0.824347826086957 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"fresh","bcfishpass",100,"CH","spawn",245,0,239,6,213,216,216,216,237,0,8,5,245,216,68,25,11,12,12,70816.66,15640.34,21570.26,51,33,0.975510204081633,0.869387755102041,0.881632653061225,0.881632653061225,0.881632653061225,0.625,0.881632653061225 -"fresh_default","default",0,"BT","any",4600,0,4564,36,3009,3729,3809,3809,0,0,4600,3009,4600,3809,858,814,587,635,686,210822,47098.83,75280.2,51,1,0.992173913043478,0.654130434782609,0.810652173913043,0.82804347826087,0.82804347826087,0.654130434782609,0.82804347826087 -"fresh_default","default",0,"BT","rear",1047,0,1034,13,464,690,696,696,0,0,1047,464,1047,696,858,814,587,635,686,210822,47098.83,75280.2,51,1,0.987583572110793,0.443170964660936,0.659025787965616,0.664756446991404,0.664756446991404,0.443170964660936,0.664756446991404 -"fresh_default","default",0,"BT","spawn",81,0,80,1,37,57,59,59,0,0,81,37,81,59,858,814,587,635,686,210822,47098.83,75280.2,51,1,0.987654320987654,0.45679012345679,0.703703703703704,0.728395061728395,0.728395061728395,0.45679012345679,0.728395061728395 +"fresh_default","default",0,"BT","any",3771,0,3752,19,2521,3105,3173,3173,0,0,3771,2521,3771,3173,858,814,587,635,686,210822,47098.83,75280.2,51,1,0.994961548660833,0.668522938212676,0.823389021479714,0.841421373640944,0.841421373640944,0.668522938212676,0.841421373640944 +"fresh_default","default",0,"BT","rear",622,0,615,7,265,408,411,411,0,0,622,265,622,411,858,814,587,635,686,210822,47098.83,75280.2,51,1,0.988745980707395,0.42604501607717,0.655948553054662,0.660771704180064,0.660771704180064,0.42604501607717,0.660771704180064 +"fresh_default","default",0,"BT","spawn",64,0,63,1,28,45,47,47,0,0,64,28,64,47,858,814,587,635,686,210822,47098.83,75280.2,51,1,0.984375,0.4375,0.703125,0.734375,0.734375,0.4375,0.734375 "fresh_default","default",0,"CH","any",1734,0,1701,33,1478,1520,1539,1567,629,0,1105,850,1734,1539,68,25,11,13,15,74048.75,15958.82,27601.52,51,1,0.980968858131488,0.852364475201845,0.876585928489043,0.887543252595156,0.903690888119954,0.769230769230769,0.887543252595156 "fresh_default","default",0,"CH","rear",510,0,500,10,395,432,432,437,175,0,335,220,510,432,68,25,11,13,15,74048.75,15958.82,27601.52,51,1,0.980392156862745,0.774509803921569,0.847058823529412,0.847058823529412,0.856862745098039,0.656716417910448,0.847058823529412 "fresh_default","default",0,"CH","spawn",245,0,239,6,241,216,224,242,237,0,8,4,245,224,68,25,11,13,15,74048.75,15958.82,27601.52,51,1,0.975510204081633,0.983673469387755,0.881632653061225,0.914285714285714,0.987755102040816,0.5,0.914285714285714 -"fresh_default","default",100,"BT","any",4600,0,4564,36,3129,3798,3855,3855,0,0,4600,3129,4600,3855,858,814,591,637,687,210822,47098.83,75280.2,51,1,0.992173913043478,0.680217391304348,0.825652173913043,0.83804347826087,0.83804347826087,0.680217391304348,0.83804347826087 -"fresh_default","default",100,"BT","rear",1047,0,1034,13,493,707,711,711,0,0,1047,493,1047,711,858,814,591,637,687,210822,47098.83,75280.2,51,1,0.987583572110793,0.470869149952244,0.675262655205349,0.679083094555874,0.679083094555874,0.470869149952244,0.679083094555874 -"fresh_default","default",100,"BT","spawn",81,0,80,1,39,58,60,60,0,0,81,39,81,60,858,814,591,637,687,210822,47098.83,75280.2,51,1,0.987654320987654,0.481481481481481,0.716049382716049,0.740740740740741,0.740740740740741,0.481481481481481,0.740740740740741 +"fresh_default","default",100,"BT","any",3771,0,3752,19,2618,3160,3208,3208,0,0,3771,2618,3771,3208,858,814,591,637,687,210822,47098.83,75280.2,51,1,0.994961548660833,0.694245558207372,0.837974012198356,0.850702731370989,0.850702731370989,0.694245558207372,0.850702731370989 +"fresh_default","default",100,"BT","rear",622,0,615,7,280,416,418,418,0,0,622,280,622,418,858,814,591,637,687,210822,47098.83,75280.2,51,1,0.988745980707395,0.45016077170418,0.668810289389068,0.672025723472669,0.672025723472669,0.45016077170418,0.672025723472669 +"fresh_default","default",100,"BT","spawn",64,0,63,1,30,45,47,47,0,0,64,30,64,47,858,814,591,637,687,210822,47098.83,75280.2,51,1,0.984375,0.46875,0.703125,0.734375,0.734375,0.46875,0.734375 "fresh_default","default",100,"CH","any",1734,0,1701,33,1503,1542,1561,1586,647,0,1087,859,1734,1561,68,25,11,13,15,74048.75,15958.82,27601.52,51,1,0.980968858131488,0.866782006920415,0.889273356401384,0.900230680507497,0.914648212226067,0.790248390064397,0.900230680507497 "fresh_default","default",100,"CH","rear",510,0,500,10,405,439,439,443,181,0,329,224,510,439,68,25,11,13,15,74048.75,15958.82,27601.52,51,1,0.980392156862745,0.794117647058823,0.86078431372549,0.86078431372549,0.868627450980392,0.680851063829787,0.86078431372549 "fresh_default","default",100,"CH","spawn",245,0,239,6,242,219,227,243,237,0,8,5,245,227,68,25,11,13,15,74048.75,15958.82,27601.52,51,1,0.975510204081633,0.987755102040816,0.893877551020408,0.926530612244898,0.991836734693878,0.625,0.926530612244898 diff --git a/data-raw/logs/species_pooling_290/README.md b/data-raw/logs/species_pooling_290/README.md new file mode 100644 index 00000000..b87fb929 --- /dev/null +++ b/data-raw/logs/species_pooling_290/README.md @@ -0,0 +1,17 @@ +# species_pooling_290: DV and BT naming, and the pooling sensitivity (link#290) + +Produced by `data-raw/species_pooling_evidence.R --validate` on local docker fwapg (bcfishobs 373,050 rows). The write-up is [`research/species_pooling.md`](../../../../research/species_pooling.md). + +| File | What it holds | +|---|---| +| `decade_region.csv` | BT and DV records (releases removed) by region x decade | +| `dv_streams_resampled.csv` | Streams with a DV record, and what happened to each: later recorded as BT, not sampled after 1995, or sampled after 1995 with DV only | +| `wsg_dv_share.csv` | BT and DV records per WSG, before 1995 and from 1995 on | +| `scenarios.csv` | The #284 BT thresholds under S0 (current tracker), S1 (Skeena above Hazelton only), S2 (no Skeena), S3 (interior, pre-1995 DV only) and BT records only | +| `scenarios_dropped.csv` | DV evidence rows each scenario drops, by WSG | +| `validate_scenarios.csv` | BT capture under S0 (the committed #283 baseline), S1 and S2 | +| `fig_*.png` | The figures and maps used in the research doc and the walkthrough page | + +S0–S2 run through `query_habitat_thresholds_obs.R` with scratch bundles. S3 is computed from the S0 evidence by the same rule, and the script stops unless that computation reproduces the producer for S0–S2. + +The run's `stamp.txt` records link @ `eb7ae12`: the script and these outputs were committed together in the next commit (`e929a96`), so the tree it ran on was eb7ae12 plus this script. diff --git a/data-raw/logs/species_pooling_290/decade_region.csv b/data-raw/logs/species_pooling_290/decade_region.csv new file mode 100644 index 00000000..28b1eafa --- /dev/null +++ b/data-raw/logs/species_pooling_290/decade_region.csv @@ -0,0 +1,36 @@ +grp,decade,DV,BT,n,dv_share +Coast and north,1960,56,0,56,1 +Coast and north,1970,553,1,554,0.9981949458483754 +Coast and north,1980,761,3,764,0.9960732984293194 +Coast and north,1990,2147,100,2247,0.9554962171784601 +Coast and north,2000,912,118,1030,0.8854368932038835 +Coast and north,2010,2042,419,2461,0.8297440065014222 +Coast and north,2020,150,0,150,1 +Columbia,1960,32,4,36,0.8888888888888888 +Columbia,1970,413,61,474,0.8713080168776371 +Columbia,1980,118,59,177,0.6666666666666666 +Columbia,1990,8,1376,1384,0.005780346820809248 +Columbia,2000,0,743,743,0 +Columbia,2010,0,1631,1631,0 +Columbia,2020,0,36,36,0 +Fraser,1960,43,3,46,0.9347826086956522 +Fraser,1970,267,43,310,0.8612903225806452 +Fraser,1980,426,52,478,0.891213389121339 +Fraser,1990,403,686,1089,0.37006427915518825 +Fraser,2000,86,519,605,0.14214876033057852 +Fraser,2010,49,1032,1081,0.045328399629972246 +Fraser,2020,1,274,275,0.0036363636363636364 +Mackenzie,1960,15,1,16,0.9375 +Mackenzie,1970,334,119,453,0.7373068432671082 +Mackenzie,1980,199,149,348,0.5718390804597702 +Mackenzie,1990,237,779,1016,0.23326771653543307 +Mackenzie,2000,129,1327,1456,0.0885989010989011 +Mackenzie,2010,117,1445,1562,0.07490396927016646 +Mackenzie,2020,0,11,11,0 +Skeena,1960,24,0,24,1 +Skeena,1970,346,0,346,1 +Skeena,1980,141,0,141,1 +Skeena,1990,1582,160,1742,0.9081515499425947 +Skeena,2000,387,63,450,0.86 +Skeena,2010,439,8,447,0.9821029082774049 +Skeena,2020,6,0,6,1 diff --git a/data-raw/logs/species_pooling_290/dv_streams_resampled.csv b/data-raw/logs/species_pooling_290/dv_streams_resampled.csv new file mode 100644 index 00000000..e275a1ce --- /dev/null +++ b/data-raw/logs/species_pooling_290/dv_streams_resampled.csv @@ -0,0 +1,15 @@ +grp,fate,n,streams,share +Coast and north,later recorded as BT,38,2356,0.016129032258064516 +Coast and north,not sampled after 1995,834,2356,0.3539898132427844 +Coast and north,"sampled after 1995, DV only",1484,2356,0.629881154499151 +Columbia,later recorded as BT,121,163,0.7423312883435583 +Columbia,not sampled after 1995,42,163,0.25766871165644173 +Fraser,later recorded as BT,146,547,0.26691042047531993 +Fraser,not sampled after 1995,277,547,0.506398537477148 +Fraser,"sampled after 1995, DV only",124,547,0.226691042047532 +Mackenzie,later recorded as BT,111,329,0.3373860182370821 +Mackenzie,not sampled after 1995,148,329,0.44984802431610943 +Mackenzie,"sampled after 1995, DV only",70,329,0.2127659574468085 +Skeena,later recorded as BT,11,1180,0.009322033898305085 +Skeena,not sampled after 1995,170,1180,0.1440677966101695 +Skeena,"sampled after 1995, DV only",999,1180,0.8466101694915255 diff --git a/data-raw/logs/species_pooling_290/fig_dv_share_by_decade.png b/data-raw/logs/species_pooling_290/fig_dv_share_by_decade.png new file mode 100644 index 00000000..4599feb5 Binary files /dev/null and b/data-raw/logs/species_pooling_290/fig_dv_share_by_decade.png differ diff --git a/data-raw/logs/species_pooling_290/fig_dv_streams_fate.png b/data-raw/logs/species_pooling_290/fig_dv_streams_fate.png new file mode 100644 index 00000000..32974772 Binary files /dev/null and b/data-raw/logs/species_pooling_290/fig_dv_streams_fate.png differ diff --git a/data-raw/logs/species_pooling_290/fig_map_dv_share.png b/data-raw/logs/species_pooling_290/fig_map_dv_share.png new file mode 100644 index 00000000..e6ffa565 Binary files /dev/null and b/data-raw/logs/species_pooling_290/fig_map_dv_share.png differ diff --git a/data-raw/logs/species_pooling_290/fig_map_pooling_scenarios.png b/data-raw/logs/species_pooling_290/fig_map_pooling_scenarios.png new file mode 100644 index 00000000..b7efbb72 Binary files /dev/null and b/data-raw/logs/species_pooling_290/fig_map_pooling_scenarios.png differ diff --git a/data-raw/logs/species_pooling_290/fig_map_skeena_hazelton.png b/data-raw/logs/species_pooling_290/fig_map_skeena_hazelton.png new file mode 100644 index 00000000..f610ca9b Binary files /dev/null and b/data-raw/logs/species_pooling_290/fig_map_skeena_hazelton.png differ diff --git a/data-raw/logs/species_pooling_290/fig_scenarios_rear_gradient.png b/data-raw/logs/species_pooling_290/fig_scenarios_rear_gradient.png new file mode 100644 index 00000000..672d960c Binary files /dev/null and b/data-raw/logs/species_pooling_290/fig_scenarios_rear_gradient.png differ diff --git a/data-raw/logs/species_pooling_290/scenarios.csv b/data-raw/logs/species_pooling_290/scenarios.csv new file mode 100644 index 00000000..7a74e390 --- /dev/null +++ b/data-raw/logs/species_pooling_290/scenarios.csv @@ -0,0 +1,7 @@ +scenario,n_dv_records,rear_n,rear_gradient_p95,rear_gradient_rule,rear_width_n,rear_width_p05,spawn_n,spawn_gradient_p95,spawn_width_n,spawn_width_p05,bridge_loss,rear_gradient_current,rear_gradient_says +S0_whole_skeena,2822,4764,0.13482499999999972,0.1349,3035,1.48,76,0.196425,53,1.16,0.01665360501567398,0.1049,change +S1_hazelton,1970,3988,0.1308949999999999,0.1349,2533,1.47,59,0.19538999999999995,40,1.1235,0.014502923976608188,0.1049,change +S2_noskeena,893,3058,0.120415,0.1249,1844,1.68,18,0.0744549999999999,8,1.4155,0.010125805461798098,0.1049,change +S3_pre1995,543,2829,0.12021999999999998,0.1249,1665,2.072,9,0.10365999999999996,4,8.25,0.011029411764705883,0.1049,change +S4_hazelton_pre1995,1620,3759,0.13101000000000002,0.1349,2354,1.5665000000000002,50,0.198495,36,1.0975,0.015469061876247504,0.1049,change +BT_only,0,2443,0.12533000000000008,0.1249,1469,1.9120000000000001,0,,0,,,0.1049,change diff --git a/data-raw/logs/species_pooling_290/scenarios_dropped.csv b/data-raw/logs/species_pooling_290/scenarios_dropped.csv new file mode 100644 index 00000000..235733d4 --- /dev/null +++ b/data-raw/logs/species_pooling_290/scenarios_dropped.csv @@ -0,0 +1,67 @@ +scenario,watershed_group_code,dv_rows +S1_hazelton,KLUM,299 +S1_hazelton,LKEL,63 +S1_hazelton,LSKE,225 +S1_hazelton,ZYMO,265 +S2_noskeena,BULK,442 +S2_noskeena,KISP,191 +S2_noskeena,KLUM,299 +S2_noskeena,LKEL,63 +S2_noskeena,LSKE,225 +S2_noskeena,MORR,344 +S2_noskeena,MSKE,68 +S2_noskeena,USKE,32 +S2_noskeena,ZYMO,265 +S3_pre1995,ADMS,11 +S3_pre1995,BULK,442 +S3_pre1995,CHWK,15 +S3_pre1995,COTR,3 +S3_pre1995,FINA,1 +S3_pre1995,FINL,1 +S3_pre1995,FIRE,117 +S3_pre1995,FRAN,98 +S3_pre1995,FRCN,24 +S3_pre1995,HARR,20 +S3_pre1995,KISP,191 +S3_pre1995,KLUM,299 +S3_pre1995,LCHL,1 +S3_pre1995,LFRA,11 +S3_pre1995,LKEL,63 +S3_pre1995,LSKE,225 +S3_pre1995,MORK,3 +S3_pre1995,MORR,344 +S3_pre1995,MSKE,68 +S3_pre1995,PARS,1 +S3_pre1995,SETN,8 +S3_pre1995,SLOC,1 +S3_pre1995,TOOD,1 +S3_pre1995,TWAC,1 +S3_pre1995,UNRS,1 +S3_pre1995,UOMI,31 +S3_pre1995,USKE,32 +S3_pre1995,WILL,1 +S3_pre1995,ZYMO,265 +S4_hazelton_pre1995,ADMS,11 +S4_hazelton_pre1995,CHWK,15 +S4_hazelton_pre1995,COTR,3 +S4_hazelton_pre1995,FINA,1 +S4_hazelton_pre1995,FINL,1 +S4_hazelton_pre1995,FIRE,117 +S4_hazelton_pre1995,FRAN,98 +S4_hazelton_pre1995,FRCN,24 +S4_hazelton_pre1995,HARR,20 +S4_hazelton_pre1995,KLUM,299 +S4_hazelton_pre1995,LCHL,1 +S4_hazelton_pre1995,LFRA,11 +S4_hazelton_pre1995,LKEL,63 +S4_hazelton_pre1995,LSKE,225 +S4_hazelton_pre1995,MORK,3 +S4_hazelton_pre1995,PARS,1 +S4_hazelton_pre1995,SETN,8 +S4_hazelton_pre1995,SLOC,1 +S4_hazelton_pre1995,TOOD,1 +S4_hazelton_pre1995,TWAC,1 +S4_hazelton_pre1995,UNRS,1 +S4_hazelton_pre1995,UOMI,31 +S4_hazelton_pre1995,WILL,1 +S4_hazelton_pre1995,ZYMO,265 diff --git a/data-raw/logs/species_pooling_290/stamp.txt b/data-raw/logs/species_pooling_290/stamp.txt new file mode 100644 index 00000000..462790b9 --- /dev/null +++ b/data-raw/logs/species_pooling_290/stamp.txt @@ -0,0 +1,9 @@ +date: 2026-09-27 08:18 PDT +link: 0.52.0 @ 911bed3 +db: docker fwapg localhost:5432 +bcfishobs.observations rows: 373050 +BT + DV records (not Releases): 24337; undated: 692 +evidence: data-raw/query_habitat_thresholds_obs.R on fresh_default (55 WSGs), one run per scenario bundle +scenario numbers from producer runs: S0_whole_skeena, S1_hazelton, S2_noskeena, S3_pre1995, S4_hazelton_pre1995; BT_only from the reimplementation +reimplementation cross-check matched the producer for: S0_whole_skeena, S1_hazelton, S2_noskeena +validator runs: S0_whole_skeena, S1_hazelton, S2_noskeena, S3_pre1995, S4_hazelton_pre1995 diff --git a/data-raw/logs/species_pooling_290/validate_scenarios.csv b/data-raw/logs/species_pooling_290/validate_scenarios.csv new file mode 100644 index 00000000..39bb76c5 --- /dev/null +++ b/data-raw/logs/species_pooling_290/validate_scenarios.csv @@ -0,0 +1,16 @@ +scenario,species_code,stage,n_obs,share_accessible,share_spawning,share_rearing,share_rearing_any,rearing_km,spawning_km +S0_whole_skeena,BT,any,5104,0.991575235109718,0.644004702194357,0.804663009404389,0.824255485893417,78825.1,49453.94 +S0_whole_skeena,BT,rear,1053,0.987654320987654,0.44349477682811,0.659069325735992,0.664767331433998,78825.1,49453.94 +S0_whole_skeena,BT,spawn,82,0.98780487804878,0.463414634146341,0.707317073170732,0.731707317073171,78825.1,49453.94 +S1_hazelton,BT,any,4275,0.993918128654971,0.654736842105263,0.814736842105263,0.835321637426901,78825.1,49453.94 +S1_hazelton,BT,rear,628,0.988853503184713,0.426751592356688,0.656050955414013,0.660828025477707,78825.1,49453.94 +S1_hazelton,BT,spawn,65,0.984615384615385,0.446153846153846,0.707692307692308,0.738461538461539,78825.1,49453.94 +S2_noskeena,BT,any,3259,0.994476833384474,0.699294262043572,0.83798711261123,0.861920834611844,78825.1,49453.94 +S2_noskeena,BT,rear,205,1,0.585365853658537,0.751219512195122,0.75609756097561,78825.1,49453.94 +S2_noskeena,BT,spawn,21,0.952380952380952,0.666666666666667,0.80952380952381,0.904761904761905,78825.1,49453.94 +S3_pre1995,BT,any,2992,0.993983957219251,0.718248663101604,0.849933155080214,0.871991978609626,78825.1,49453.94 +S3_pre1995,BT,rear,2,1,1,1,1,78825.1,49453.94 +S3_pre1995,BT,spawn,11,0.909090909090909,0.727272727272727,0.727272727272727,0.909090909090909,78825.1,49453.94 +S4_hazelton_pre1995,BT,any,4008,0.993512974051896,0.665918163672655,0.822105788423154,0.841067864271457,78825.1,49453.94 +S4_hazelton_pre1995,BT,rear,425,0.983529411764706,0.352941176470588,0.611764705882353,0.616470588235294,78825.1,49453.94 +S4_hazelton_pre1995,BT,spawn,55,0.981818181818182,0.418181818181818,0.672727272727273,0.709090909090909,78825.1,49453.94 diff --git a/data-raw/logs/species_pooling_290/wsg_dv_share.csv b/data-raw/logs/species_pooling_290/wsg_dv_share.csv new file mode 100644 index 00000000..3e9891ec --- /dev/null +++ b/data-raw/logs/species_pooling_290/wsg_dv_share.csv @@ -0,0 +1,389 @@ +watershed_group_code,era,BT,DV,n,dv_share +ADMS,1995 on,44,8,52,0.15384615384615385 +ADMS,before 1995,0,4,4,1 +ALBN,1995 on,0,57,57,1 +ALBN,before 1995,0,41,41,1 +ATLL,before 1995,0,1,1,1 +ATNA,1995 on,0,5,5,1 +ATNA,before 1995,0,9,9,1 +BABL,1995 on,1,166,167,0.9940119760479041 +BABL,before 1995,0,10,10,1 +BABR,1995 on,31,327,358,0.9134078212290503 +BABR,before 1995,0,26,26,1 +BARR,1995 on,5,25,30,0.8333333333333334 +BARR,before 1995,0,5,5,1 +BBAR,1995 on,3,0,3,0 +BBAR,before 1995,13,7,20,0.35 +BEAV,1995 on,2,0,2,0 +BEAV,before 1995,3,1,4,0.25 +BELA,1995 on,0,150,150,1 +BELA,before 1995,0,12,12,1 +BIGC,1995 on,2,0,2,0 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1995,0,38,38,1 +LMUS,before 1995,4,2,6,0.3333333333333333 +LNAR,1995 on,25,288,313,0.9201277955271565 +LNAR,before 1995,0,64,64,1 +LNIC,1995 on,14,2,16,0.125 +LNIC,before 1995,2,6,8,0.75 +LNTH,1995 on,139,6,145,0.041379310344827586 +LNTH,before 1995,15,20,35,0.5714285714285714 +LOMI,1995 on,33,1,34,0.029411764705882353 +LOMI,before 1995,0,4,4,1 +LPCE,1995 on,184,0,184,0 +LPCE,before 1995,4,0,4,0 +LPRO,before 1995,3,1,4,0.25 +LRAN,1995 on,1,6,7,0.8571428571428571 +LRDO,1995 on,0,31,31,1 +LRDO,before 1995,0,14,14,1 +LSAL,before 1995,0,7,7,1 +LSKE,1995 on,9,387,396,0.9772727272727273 +LSKE,before 1995,1,81,82,0.9878048780487805 +LSTR,1995 on,0,8,8,1 +LSTR,before 1995,0,27,27,1 +LTRE,1995 on,3,0,3,0 +MAHD,before 1995,1,3,4,0.75 +MBNK,1995 on,0,1,1,1 +MCGR,1995 on,8,1,9,0.1111111111111111 +MCGR,before 1995,0,46,46,1 +MDEA,1995 on,22,1,23,0.043478260869565216 +MDEA,before 1995,0,2,2,1 +MESI,1995 on,66,0,66,0 +MESI,before 1995,6,9,15,0.6 +MIDR,1995 on,7,0,7,0 +MIDR,before 1995,0,10,10,1 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on,0,1,1,1 +SALR,before 1995,0,7,7,1 +SANJ,1995 on,0,8,8,1 +SANJ,before 1995,0,27,27,1 +SETN,1995 on,433,10,443,0.022573363431151242 +SETN,before 1995,32,51,83,0.6144578313253012 +SEYM,1995 on,0,21,21,1 +SEYM,before 1995,0,3,3,1 +SHER,1995 on,0,6,6,1 +SHER,before 1995,0,47,47,1 +SHUL,1995 on,11,7,18,0.3888888888888889 +SHUL,before 1995,2,38,40,0.95 +SIML,1995 on,1,1,2,0.5 +SIML,before 1995,3,1,4,0.25 +SKGT,1995 on,15,16,31,0.5161290322580645 +SKGT,before 1995,0,3,3,1 +SLOC,1995 on,68,0,68,0 +SLOC,before 1995,14,31,45,0.6888888888888889 +SMAR,1995 on,140,0,140,0 +SMAR,before 1995,48,74,122,0.6065573770491803 +SMOK,1995 on,66,3,69,0.043478260869565216 +SMOK,before 1995,36,31,67,0.4626865671641791 +SPAT,1995 on,5,8,13,0.6153846153846154 +SPAT,before 1995,1,2,3,0.6666666666666666 +SQAM,1995 on,85,409,494,0.8279352226720648 +SQAM,before 1995,0,69,69,1 +STHM,1995 on,2,0,2,0 +STHM,before 1995,1,4,5,0.8 +STIR,1995 on,0,6,6,1 +STIR,before 1995,0,23,23,1 +STUL,1995 on,0,1,1,1 +STUL,before 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1995,19,49,68,0.7205882352941176 +TUYR,1995 on,2,0,2,0 +TUYR,before 1995,1,0,1,0 +TWAC,1995 on,0,1,1,1 +TWAC,before 1995,1,0,1,0 +UARL,1995 on,699,0,699,0 +UARL,before 1995,30,8,38,0.21052631578947367 +UBIR,1995 on,18,70,88,0.7954545454545454 +UBIR,before 1995,0,19,19,1 +UBTN,1995 on,1,0,1,0 +UCHR,1995 on,5,0,5,0 +UCHR,before 1995,2,0,2,0 +UDEN,1995 on,0,13,13,1 +UDEN,before 1995,1,41,42,0.9761904761904762 +UFRA,1995 on,89,0,89,0 +UFRA,before 1995,0,6,6,1 +UHAF,1995 on,181,0,181,0 +UHAF,before 1995,17,0,17,0 +UISR,before 1995,0,2,2,1 +UKEC,1995 on,6,0,6,0 +UKEC,before 1995,2,1,3,0.3333333333333333 +ULRD,1995 on,0,4,4,1 +ULRD,before 1995,3,25,28,0.8928571428571429 +UMUS,1995 on,9,0,9,0 +UMUS,before 1995,1,1,2,0.5 +UNAR,1995 on,1,3,4,0.75 +UNAR,before 1995,0,1,1,1 +UNRS,1995 on,1,0,1,0 +UNRS,before 1995,0,1,1,1 +UNTH,1995 on,131,3,134,0.022388059701492536 +UNTH,before 1995,15,60,75,0.8 +UNUR,1995 on,2,25,27,0.9259259259259259 +UNUR,before 1995,0,51,51,1 +UOMI,1995 on,54,38,92,0.41304347826086957 +UOMI,before 1995,2,5,7,0.7142857142857143 +UPCE,1995 on,1214,1,1215,8.230452674897119e-4 +UPCE,before 1995,18,5,23,0.21739130434782608 +UPRO,1995 on,17,0,17,0 +USHU,1995 on,43,17,60,0.2833333333333333 +USHU,before 1995,6,162,168,0.9642857142857143 +USIK,1995 on,1,0,1,0 +USIK,before 1995,1,0,1,0 +USKE,1995 on,0,5,5,1 +USKE,before 1995,0,25,25,1 +USTK,1995 on,0,2,2,1 +USTK,before 1995,0,4,4,1 +UTRE,1995 on,1,2,3,0.6666666666666666 +UTRE,before 1995,0,3,3,1 +WILL,1995 on,78,2,80,0.025 +WILL,before 1995,7,15,22,0.6818181818181818 +WORC,1995 on,0,138,138,1 +WORC,before 1995,0,33,33,1 +ZYMO,1995 on,20,227,247,0.9190283400809717 +ZYMO,before 1995,0,28,28,1 diff --git a/data-raw/query_habitat_thresholds_obs.R b/data-raw/query_habitat_thresholds_obs.R index b37e1a84..16ee7da9 100644 --- a/data-raw/query_habitat_thresholds_obs.R +++ b/data-raw/query_habitat_thresholds_obs.R @@ -9,7 +9,12 @@ # # Read-only against docker fwapg (:5432). Temp tables only. # -# Rscript data-raw/query_habitat_thresholds_obs.R +# Rscript data-raw/query_habitat_thresholds_obs.R [--pooling=] [--out=] +# +# --pooling names the bundle whose species_pooling.csv decides which +# observation species count as each model species (default: `default`, the +# bundle scored here). --out redirects the outputs, e.g. for a check run +# against a scratch bundle that must not overwrite the committed evidence. # # Writes to data-raw/logs/habitat_thresholds_284/: # obs_ledger.csv counts dropped at each filter step @@ -32,7 +37,13 @@ suppressPackageStartupMessages({ library(ggplot2) }) -dir_out <- file.path("data-raw", "logs", "habitat_thresholds_284") +opt <- function(name, default) { + a <- grep(paste0("^--", name, "="), commandArgs(trailingOnly = TRUE), + value = TRUE) + if (length(a) == 0L) default else sub(paste0("^--", name, "="), "", a[length(a)]) +} +dir_out <- opt("out", file.path("data-raw", "logs", "habitat_thresholds_284")) +pooling_cfg <- opt("pooling", "default") fs::dir_create(dir_out) conn <- lnk_db_conn(dbname = "fwapg", host = "localhost", port = 5432L, @@ -58,36 +69,89 @@ presence <- readr::read_csv(cfg$files$wsg_species_presence$path, transmute(watershed_group_code, bt = bt %in% "t", ch = ch %in% "t", dv = dv %in% "t") dbWriteTable(conn, "t_excl", excl, temporary = TRUE, overwrite = TRUE) -dbWriteTable(conn, "t_presence", presence, temporary = TRUE, overwrite = TRUE) wsg_persisted <- dbGetQuery(conn, sprintf( "SELECT DISTINCT watershed_group_code FROM %s.streams", schema))$watershed_group_code # -- observations, every flag kept so the ledger is exact -------------------- -# DV rows are pooled with BT where the WSG has BT, as the pipeline already -# treats them (observation_species for BT is BT;DV). Inland, DV records are -# bull trout recorded under the old name; on the coast either species occurs, -# and their habitat biology is close enough not to separate here. bcfishobs -# gives BT no life stage or activity at all, so DV records are also the only -# staged char evidence. Pooled BT+DV is the primary BT evidence; BT-only is -# kept beside it as a comparison, so the evidence exists both ways. +# Which observation species count as each model species comes from the +# bundle's pooling tracker (species_pooling.csv via lnk_species_pooling(), +# link#290): per WSG, scoped to region, sub-region or WSG, and only where the +# model species is present. For this bundle that pools DV records into BT in +# the regions the tracker lists. Inland, DV records are bull trout recorded +# under the old name, and bcfishobs gives BT no life stage or activity at all, +# so DV records are also the only staged char evidence. Pooled BT+DV is the +# primary BT evidence; BT-only is kept beside it as a comparison, so the +# evidence exists both ways. `dv_ok` is FALSE for a record whose species is +# neither a model species nor pooled into one in its WSG. +loaded <- suppressWarnings(lnk_load_overrides(lnk_config(pooling_cfg))) +if (is.null(loaded$species_pooling)) { + stop("--pooling=", pooling_cfg, " declares no species_pooling tracker", + call. = FALSE) +} +pool <- lnk_species_pooling(loaded, aoi = presence$watershed_group_code, + species = species) +pool <- pool[pool$scope_level != "self", + c("watershed_group_code", "species_code", "obs_species", + "obs_year_max")] +# One target per observation species per WSG, or the join below would copy +# a record into two species' evidence. +if (anyDuplicated(pool[c("watershed_group_code", "obs_species")])) { + stop("an observation species pools into two model species in one WSG; ", + "this script assigns each record to one species", call. = FALSE) +} +# ...and a model species' own records stay its own: pooling one model species +# into another would relabel them away (the validator would count them twice). +if (any(pool$obs_species %in% species)) { + stop("species_pooling pools a model species (", + paste(unique(pool$obs_species[pool$obs_species %in% species]), + collapse = ", "), ") into another; this script cannot", + call. = FALSE) +} +# The pooling bundle's presence decides where pooling applies; the steps below +# filter on cfg's. If they disagree, pooled records drop silently. +# Keyed by WSG code (never by row position): cfg's WSGs, looked up in each. +presence_flags <- function(p, w) { + p <- as.data.frame(p) + names(p) <- tolower(names(p)) + p <- p[match(w, toupper(p$watershed_group_code)), tolower(species), drop = FALSE] + vapply(p, function(x) as.character(x) %in% "t", logical(length(w))) +} +presence_cfg <- readr::read_csv(cfg$files$wsg_species_presence$path, + show_col_types = FALSE, + col_types = readr::cols(.default = "c")) +w_cfg <- toupper(presence_cfg$watershed_group_code) +if (!identical(presence_flags(loaded$wsg_species_presence, w_cfg), + presence_flags(presence_cfg, w_cfg))) { + stop("--pooling=", pooling_cfg, "'s wsg_species_presence differs from ", + cfg$name, "'s for ", paste(species, collapse = ", "), call. = FALSE) +} +dbWriteTable(conn, "t_pool", pool, temporary = TRUE, overwrite = TRUE) +obs_codes <- sort(unique(c(species, pool$obs_species))) + dbExecute(conn, "DROP TABLE IF EXISTS t_obs") -dbExecute(conn, " +dbExecute(conn, sprintf(" CREATE TEMP TABLE t_obs AS SELECT o.observation_key, o.species_code AS obs_species, - CASE WHEN o.species_code = 'DV' THEN 'BT' ELSE o.species_code END AS species_code, + coalesce(pl.species_code, o.species_code) AS species_code, o.watershed_group_code, o.blue_line_key, o.downstream_route_measure AS m, left(o.match_type, 1) AS match_class, o.activity_code, o.activity, o.life_stage, o.source, o.source_ref, o.observation_date, - o.source LIKE 'Releases Database%' AS is_release, + o.source LIKE 'Releases Database%%' AS is_release, o.observation_key IN (SELECT observation_key FROM t_excl) AS is_excluded, - (o.species_code <> 'DV' OR coalesce(p.bt, false)) AS dv_ok + (o.species_code IN (%1$s) OR pl.species_code IS NOT NULL) AS dv_ok FROM bcfishobs.observations o - LEFT JOIN t_presence p ON p.watershed_group_code = o.watershed_group_code - WHERE o.species_code IN ('CH', 'BT', 'DV')") + LEFT JOIN t_pool pl ON pl.watershed_group_code = o.watershed_group_code + AND pl.obs_species = o.species_code + -- a year-limited row pools only records dated within it + AND (pl.obs_year_max IS NULL + OR extract(year FROM o.observation_date) <= pl.obs_year_max) + WHERE o.species_code IN (%2$s)", + paste(DBI::dbQuoteString(conn, species), collapse = ", "), + paste(DBI::dbQuoteString(conn, obs_codes), collapse = ", "))) # The segment the model tests. Observations are break points (the pipeline # breaks at round(downstream_route_measure)), so a point usually sits on a @@ -201,7 +265,7 @@ ledger <- bind_rows( ledger_step(o0, "0 all CH/BT/DV records"), ledger_step(o1, "1 minus observation_exclusions (data_error | release_exclude)"), ledger_step(o2, "2 minus Releases Database"), - ledger_step(o3, "3 DV kept only where WSG has BT (pooled with BT)"), + ledger_step(o3, "3 pooled species kept only where species_pooling.csv pools them into a present model species"), ledger_step(o4, sprintf("4 in %s WSGs where species present", schema)), ledger_step(o5, "5 joined to a segment"), ledger_step(o6, "6 match type A/B (stream, within 100 m)"), @@ -518,6 +582,12 @@ stamp <- c( dbGetQuery(conn, "SELECT count(*) FROM bcfishobs.observations")[[1]]), sprintf("thresholds: %s", fs::path_rel(cfg$files$parameters_habitat_thresholds$path, fs::path_abs("."))), + sprintf("pooling: %s species_pooling.csv; %s", pooling_cfg, + if (nrow(pool) == 0L) "none" else + paste(unique(paste0(pool$species_code, "<-", pool$obs_species, + ifelse(is.na(pool$obs_year_max), "", + paste0(" (to ", pool$obs_year_max, ")")))), + collapse = ", ")), sprintf("retained observations with 2+ candidate segments (upstream chosen): %d", sum(use$n_cand > 1L, na.rm = TRUE))) writeLines(stamp, file.path(dir_out, "stamp.txt")) diff --git a/data-raw/species_pooling_evidence.R b/data-raw/species_pooling_evidence.R new file mode 100644 index 00000000..a485671b --- /dev/null +++ b/data-raw/species_pooling_evidence.R @@ -0,0 +1,494 @@ +#!/usr/bin/env Rscript +# species_pooling_evidence.R — how DV and BT are recorded through time and +# space, and how sensitive the #284 BT evidence is to where DV -> BT pooling +# applies (link#290). +# +# Read-only against docker fwapg (:5432): session temp tables only. +# +# Rscript data-raw/species_pooling_evidence.R [--validate] +# +# Scenarios (pooling DV records into BT), each a scratch tracker built from +# default's species_pooling.csv: +# S0_whole_skeena Fraser, Mackenzie, Columbia (incl. Kootenay) and the +# whole Skeena (the first seed) +# S1_hazelton the committed tracker: the Skeena only above Hazelton +# (BULK, MORR, KISP, BABL, BABR, SUST, MSKE, USKE) +# S2_noskeena no Skeena +# S3_pre1995 no Skeena, and interior rows limited to records dated +# before 1995 (obs_year_max 1994) +# S4_hazelton_pre1995 S1 with the interior rows limited to before 1995 +# BT_only no pooling (the producer's BT_any comparison set) +# +# Every scenario runs through data-raw/query_habitat_thresholds_obs.R, and its +# numbers come from that run. The rule is also reimplemented over the S0 +# evidence as a cross-check: the script stops unless the two agree for every +# scenario without a year limit. The reimplementation also gives BT_only. With --validate each is also scored +# through data-raw/habitat_validate.R (default:fresh_default, ~5 min each). +# +# Writes to data-raw/logs/species_pooling_290/: +# decade_region.csv BT and DV records by region x decade +# dv_streams_resampled.csv streams with a DV record: last DV year, re-sampled +# after 1995, later recorded as BT +# wsg_dv_share.csv per WSG: BT and DV records before / from 1995 +# scenarios.csv the #284 BT thresholds under each scenario +# scenarios_dropped.csv DV evidence rows each scenario drops, by WSG +# validate_scenarios.csv (--validate) BT capture and km per scenario +# stamp.txt +# fig_*.png + +pkgload::load_all(quiet = TRUE) +suppressPackageStartupMessages({ + library(DBI) + library(dplyr) + library(ggplot2) +}) +sf::sf_use_s2(FALSE) + +do_validate <- "--validate" %in% commandArgs(trailingOnly = TRUE) +dir_out <- file.path("data-raw", "logs", "species_pooling_290") +fs::dir_create(dir_out) +conn <- lnk_db_conn(dbname = "fwapg", host = "localhost", port = 5432L, + user = "postgres", password = "postgres") + +upper_skeena <- c("BULK", "MORR", "KISP", "BABL", "BABR", "SUST", "MSKE", "USKE") +year_cut <- 1995L +regions <- utils::read.csv(.lnk_wsg_regions_path(), stringsAsFactors = FALSE, + na.strings = "") +named_regions <- c("Fraser", "Mackenzie", "Columbia", "Skeena") +grp_of <- function(w) { + r <- regions$region[match(w, regions$watershed_group_code)] + ifelse(r %in% named_regions, r, "Coast and north") +} + +# -- 1. records through time -------------------------------------------------- +obs <- dbGetQuery(conn, " + SELECT observation_key, species_code, watershed_group_code, blue_line_key, + extract(year FROM observation_date)::int AS yr + FROM bcfishobs.observations + WHERE species_code IN ('BT', 'DV') + AND source NOT LIKE 'Releases Database%'") +obs$grp <- grp_of(obs$watershed_group_code) +# a handful of records carry impossible years (2080, 9990): treat as undated +obs$yr[!is.na(obs$yr) & obs$yr > as.integer(format(Sys.Date(), "%Y"))] <- NA +obs$decade <- ifelse(is.na(obs$yr), NA_integer_, pmax(floor(obs$yr / 10) * 10, 1960L)) + +dec <- obs |> + filter(!is.na(decade)) |> + count(grp, decade, species_code) |> + tidyr::pivot_wider(names_from = species_code, values_from = n, values_fill = 0L) |> + mutate(n = BT + DV, dv_share = DV / n) |> + arrange(grp, decade) +readr::write_csv(dec, file.path(dir_out, "decade_region.csv"), na = "") + +res <- obs |> + filter(!is.na(yr)) |> + group_by(grp, blue_line_key) |> + filter(any(species_code == "DV")) |> + summarise(dv_last = max(yr[species_code == "DV"]), + last_any = max(yr), + bt_after_dv = any(species_code == "BT" & yr > dv_last), + .groups = "drop") |> + # A later BT record is the renaming signal, whenever it came, so it wins. + mutate(fate = case_when( + bt_after_dv ~ "later recorded as BT", + last_any <= year_cut ~ "not sampled after 1995", + TRUE ~ "sampled after 1995, DV only")) +res_tab <- res |> + count(grp, fate) |> + group_by(grp) |> + mutate(streams = sum(n), share = n / streams) |> + ungroup() +readr::write_csv(res_tab, file.path(dir_out, "dv_streams_resampled.csv"), na = "") + +wsg_share <- obs |> + filter(!is.na(yr)) |> + mutate(era = ifelse(yr < year_cut, "before 1995", "1995 on")) |> + count(watershed_group_code, era, species_code) |> + tidyr::pivot_wider(names_from = species_code, values_from = n, values_fill = 0L) |> + mutate(n = BT + DV, dv_share = DV / n) +readr::write_csv(wsg_share, file.path(dir_out, "wsg_dv_share.csv"), na = "") + +# -- 2. scenarios through the #284 producer ----------------------------------- +tmp <- withr::local_tempdir() +tracker <- utils::read.csv(lnk_config("default")$files$species_pooling$path, + stringsAsFactors = FALSE, colClasses = "character", + na.strings = character(0)) +scenario_bundle <- function(name, rows) { + d <- file.path(tmp, name) + fs::dir_create(d) + utils::write.csv(rows, file.path(d, "species_pooling.csv"), row.names = FALSE) + writeLines(c(paste("name:", name), + "description: link#290 pooling scenario (scratch)", + "extends: default", "files:", " species_pooling:", + " path: species_pooling.csv"), file.path(d, "config.yaml")) + d +} +hz <- tracker$scope == "Skeena above Hazelton" +sk <- tracker$scope == "Skeena" +interior <- tracker$scope %in% c("Fraser", "Mackenzie", "Columbia", "Kootenay") +if (!any(hz) || !any(sk) || sum(interior) != 4L) { + stop("default's tracker no longer has the rows these scenarios edit", + call. = FALSE) +} +pre1995 <- function(x) { + x$obs_year_max[x$scope %in% c("Fraser", "Mackenzie", "Columbia", "Kootenay")] <- + as.character(year_cut - 1L) + x +} +s0 <- tracker[!hz, ] +s0$pool[s0$scope == "Skeena"] <- "yes" +bundles <- list( + S0_whole_skeena = scenario_bundle("S0_whole_skeena", s0), + S1_hazelton = scenario_bundle("S1_hazelton", tracker), + S2_noskeena = scenario_bundle("S2_noskeena", tracker[!hz, ]), + S3_pre1995 = scenario_bundle("S3_pre1995", pre1995(tracker[!hz, ])), + S4_hazelton_pre1995 = scenario_bundle("S4_hazelton_pre1995", pre1995(tracker))) +scen_label <- c(S0_whole_skeena = "S0 whole Skeena", + S1_hazelton = "S1 above Hazelton (adopted)", + S2_noskeena = "S2 no Skeena", + S3_pre1995 = "S3 no Skeena, interior pre-1995", + S4_hazelton_pre1995 = "S4 above Hazelton, interior pre-1995", + BT_only = "BT records only") + +runs <- lapply(names(bundles), function(s) { + out <- file.path(tmp, paste0("out_", s)) + message("producer: ", s) + st <- system2("Rscript", c("data-raw/query_habitat_thresholds_obs.R", + paste0("--pooling=", bundles[[s]]), + paste0("--out=", out)), + stdout = FALSE, stderr = FALSE) + if (!identical(st, 0L)) stop("producer failed for ", s, call. = FALSE) + out +}) +names(runs) <- names(bundles) + +# -- 3. the rule, reimplemented so S3 can be computed --------------------------- +seg0 <- utils::read.csv(file.path(runs$S0_whole_skeena, "obs_segments.csv"), + stringsAsFactors = FALSE) +yr_of <- obs$yr[match(seg0$observation_key, obs$observation_key)] +seg0$yr <- yr_of +snap49 <- function(x) floor(x * 100) / 100 + 0.0049 +current <- utils::read.csv(lnk_config("default")$files$parameters_habitat_thresholds$path) |> + filter(species_code == "BT") + +metrics <- function(seg) { + bt <- seg[seg$species_code == "BT", ] + bt$loc <- paste(bt$species_code, bt$blue_line_key, round(bt$m)) + pooled <- bt[!duplicated(bt$loc), ] + acc <- pooled[pooled$accessible %in% TRUE, ] + g <- acc$gradient[acc$pred_set %in% c("stream", "river_poly") & !is.na(acc$gradient)] + w <- acc$channel_width[acc$pred_set %in% "stream" & !is.na(acc$channel_width)] + sp <- seg[seg$obs_species == "DV" & seg$is_spawn %in% TRUE & seg$accessible %in% TRUE, ] + sg <- sp$gradient[sp$pred_set %in% c("stream", "river_poly") & !is.na(sp$gradient)] + sw <- sp$channel_width[sp$pred_set %in% "stream" & !is.na(sp$channel_width)] + q <- function(x, p) if (length(x)) unname(stats::quantile(x, p, type = 7)) else NA + tibble( + n_dv_records = sum(bt$obs_species == "DV"), + rear_n = length(g), rear_gradient_p95 = q(g, 0.95), + rear_gradient_rule = snap49(q(g, 0.95)), + rear_width_n = length(w), rear_width_p05 = q(w, 0.05), + spawn_n = length(sg), spawn_gradient_p95 = q(sg, 0.95), + spawn_width_n = length(sw), spawn_width_p05 = q(sw, 0.05)) +} +pre <- function(s) grp_of(s$watershed_group_code) %in% + c("Fraser", "Mackenzie", "Columbia") & !is.na(s$yr) & s$yr < year_cut +keep_dv <- list( + S0_whole_skeena = function(s) rep(TRUE, nrow(s)), + S1_hazelton = function(s) grp_of(s$watershed_group_code) != "Skeena" | + s$watershed_group_code %in% upper_skeena, + S2_noskeena = function(s) grp_of(s$watershed_group_code) != "Skeena", + S3_pre1995 = function(s) pre(s), + S4_hazelton_pre1995 = function(s) pre(s) | s$watershed_group_code %in% upper_skeena, + BT_only = function(s) rep(FALSE, nrow(s))) +# Every scenario's numbers come from its own producer run. The reimplementation +# (over the S0 evidence) is a cross-check for the scenarios without a year +# limit, and supplies BT_only, which has no run of its own. It cannot stand in +# for a year-limited scenario: the producer applies the year to each record +# before it deduplicates locations, while S0's evidence is already +# deduplicated, so a location with DV records on both sides of 1995 would be +# judged by whichever record survived (review, 2026-09-27). +prod_metrics <- function(dir) { + cand <- utils::read.csv(file.path(dir, "candidates.csv")) + cand <- cand[cand$species_code == "BT", ] + g <- function(set, par, col) { + v <- cand[[col]][cand$evidence_set == set & cand$parameter == par] + if (length(v)) v[1] else NA_real_ + } + seg <- utils::read.csv(file.path(dir, "obs_segments.csv")) + tibble( + n_dv_records = sum(seg$species_code == "BT" & seg$obs_species == "DV"), + rear_n = g("BT_any_dv", "rear_gradient_max", "n"), + rear_gradient_p95 = g("BT_any_dv", "rear_gradient_max", "use_quantile"), + rear_gradient_rule = g("BT_any_dv", "rear_gradient_max", "rule_value"), + rear_width_n = g("BT_any_dv", "rear_channel_width_min", "n"), + rear_width_p05 = g("BT_any_dv", "rear_channel_width_min", "use_quantile"), + spawn_n = g("BT_spawn_dv", "spawn_gradient_max", "n"), + spawn_gradient_p95 = g("BT_spawn_dv", "spawn_gradient_max", "use_quantile"), + spawn_width_n = g("BT_spawn_dv", "spawn_channel_width_min", "n"), + spawn_width_p05 = g("BT_spawn_dv", "spawn_channel_width_min", "use_quantile")) +} +reimpl <- function(s) { + k <- seg0$obs_species != "DV" | keep_dv[[s]](seg0) + cbind(scenario = s, metrics(seg0[k, ])) +} +scen <- bind_rows( + lapply(names(runs), function(s) cbind(scenario = s, prod_metrics(runs[[s]]))), + reimpl("BT_only")) + +no_year <- c("S0_whole_skeena", "S1_hazelton", "S2_noskeena") +for (s in no_year) { + cols <- c("n_dv_records", "rear_n", "rear_gradient_p95", "rear_width_n", + "rear_width_p05", "spawn_n", "spawn_gradient_p95", "spawn_width_n", + "spawn_width_p05") + got <- unlist(scen[scen$scenario == s, cols]) + want <- unlist(reimpl(s)[, cols]) + if (!isTRUE(all.equal(unname(got), unname(want), tolerance = 1e-9))) { + stop("reimplementation disagrees with the producer for ", s, ": ", + paste(signif(got, 6), collapse = " "), " vs ", + paste(signif(want, 6), collapse = " "), call. = FALSE) + } +} +bridge <- vapply(names(keep_dv), function(s) { + if (!s %in% names(runs)) return(NA_real_) + b <- utils::read.csv(file.path(runs[[s]], "bridge_bt.csv")) + b <- b[b$set == "BT_any_dv", ] + sum(b$n[b$passes_predicate & !b$rearing & b$accessible]) / sum(b$n) +}, numeric(1)) +scen$bridge_loss <- bridge[scen$scenario] +scen$rear_gradient_current <- current$rear_gradient_max +scen$rear_gradient_says <- ifelse( + abs(scen$rear_gradient_rule - scen$rear_gradient_current) <= 0.005 + 1e-9, + "keep", "change") +readr::write_csv(scen, file.path(dir_out, "scenarios.csv"), na = "") + +dv_by_wsg <- function(dir) { + seg <- utils::read.csv(file.path(dir, "obs_segments.csv")) + count(seg[seg$species_code == "BT" & seg$obs_species == "DV", ], + watershed_group_code, name = "n") +} +dv0 <- dv_by_wsg(runs$S0_whole_skeena) +dropped <- bind_rows(lapply(setdiff(names(runs), "S0_whole_skeena"), function(s) { + d <- full_join(dv0, dv_by_wsg(runs[[s]]), by = "watershed_group_code", + suffix = c("_s0", "_s")) |> + mutate(dv_rows = coalesce(n_s0, 0L) - coalesce(n_s, 0L)) |> + filter(dv_rows != 0L) + if (nrow(d) == 0L) return(NULL) + transmute(d, scenario = s, watershed_group_code, dv_rows) +})) +readr::write_csv(dropped, file.path(dir_out, "scenarios_dropped.csv"), na = "") + +# -- 4. optional: score every scenario through the validator -------------------- +if (do_validate) { + val <- bind_rows(lapply(names(bundles), function(s) { + out <- file.path(tmp, paste0("val_", s)) + message("validator: ", s) + st <- system2("Rscript", c("data-raw/habitat_validate.R", + "--bundles=default:fresh_default", + paste0("--pooling=", bundles[[s]]), + "--species=BT", "--buffers=0", + paste0("--out=", out)), + stdout = FALSE, stderr = FALSE) + if (!identical(st, 0L)) stop("validator failed for ", s, call. = FALSE) + cbind(scenario = s, utils::read.csv(file.path(out, "totals.csv"))) + })) + keep <- intersect(c("scenario", "species_code", "stage", "n_obs", + "share_accessible", "share_spawning", "share_rearing", + "share_rearing_any", "rearing_km", "spawning_km"), + names(val)) + readr::write_csv(val[keep], file.path(dir_out, "validate_scenarios.csv"), na = "") +} + +# -- 5. figures ------------------------------------------------------------------ +grp_levels <- c("Columbia", "Fraser", "Mackenzie", "Skeena", "Coast and north") +grp_cols <- c(Columbia = "#1b9e77", Fraser = "#d95f02", Mackenzie = "#7570b3", + Skeena = "#e7298a", `Coast and north` = "#666666") +theme_set(theme_minimal(base_size = 11) + + theme(panel.grid.minor = element_blank(), legend.position = "bottom")) + +p1 <- ggplot(mutate(dec, grp = factor(grp, grp_levels)), + aes(decade, dv_share, colour = grp)) + + geom_vline(xintercept = year_cut, linetype = "dashed", colour = "grey60") + + annotate("text", x = year_cut, y = 0.03, label = "1995", hjust = -0.15, + size = 3, colour = "grey45") + + geom_line(linewidth = 0.8) + + geom_point(aes(size = n)) + + scale_colour_manual(values = grp_cols, name = NULL) + + scale_size_area(max_size = 6, name = "BT + DV records", + breaks = c(100, 1000, 2500), labels = scales::comma) + + scale_x_continuous(breaks = seq(1960, 2020, 10), + labels = c("≤ 1960s", paste0(seq(1970, 2020, 10), "s"))) + + scale_y_continuous(labels = scales::percent, limits = c(0, 1)) + + labs(x = NULL, y = "DV share of char records") + + guides(colour = guide_legend(nrow = 2), size = guide_legend(nrow = 1)) +ggsave(file.path(dir_out, "fig_dv_share_by_decade.png"), p1, width = 7, + height = 4.5, dpi = 150, bg = "white") + +fate_cols <- c(`later recorded as BT` = "#1b9e77", + `not sampled after 1995` = "#bdbdbd", + `sampled after 1995, DV only` = "#e7298a") +p2 <- ggplot(mutate(res_tab, grp = factor(grp, rev(grp_levels)), + fate = factor(fate, names(fate_cols))), + aes(share, grp, fill = fate)) + + geom_col(width = 0.7) + + geom_text(data = distinct(res_tab, grp, streams) |> + mutate(grp = factor(grp, rev(grp_levels))), + aes(x = 1.01, y = grp, label = scales::comma(streams)), + inherit.aes = FALSE, hjust = 0, size = 3.2, colour = "grey30") + + scale_fill_manual(values = fate_cols, name = NULL) + + scale_x_continuous(labels = scales::percent, limits = c(0, 1.12), + breaks = seq(0, 1, 0.25)) + + labs(x = "Share of streams that carry a DV record (count at right)", y = NULL) +ggsave(file.path(dir_out, "fig_dv_streams_fate.png"), p2, width = 7, + height = 3.8, dpi = 150, bg = "white") + +sc3 <- filter(scen, scenario != "BT_only") |> + mutate(y = rev(seq_len(n())), lab = scen_label[scenario]) +bins <- data.frame(xmin = c(0.12, 0.13, 0.14), xmax = c(0.13, 0.14, 0.15), + rule = c("rule gives 0.1249", "rule gives 0.1349\n(default_tuned)", + "rule gives 0.1449"), + fill = c("#eef3f0", "#e3e0f3", "#eef3f0")) +p3 <- ggplot(sc3, aes(rear_gradient_p95, y)) + + geom_rect(data = bins, aes(xmin = xmin, xmax = xmax, ymin = -Inf, ymax = Inf), + fill = bins$fill, inherit.aes = FALSE) + + geom_text(data = bins, aes(x = xmin + 0.0015, y = max(sc3$y) + 0.7, + label = rule), inherit.aes = FALSE, size = 3, + hjust = 0, colour = "grey35", lineheight = 0.9) + + geom_vline(xintercept = scen$rear_gradient_p95[scen$scenario == "BT_only"], + linetype = "dotted", colour = "#1b9e77") + + annotate("text", x = scen$rear_gradient_p95[scen$scenario == "BT_only"], + y = 0.45, label = "BT records only", size = 3, colour = "#1b9e77", + hjust = -0.05) + + geom_point(aes(size = rear_n), colour = "#7570b3") + + geom_text(aes(label = paste0("n ", scales::comma(rear_n))), nudge_y = 0.32, + size = 3, colour = "grey30") + + scale_size_area(max_size = 6, guide = "none") + + scale_y_continuous(breaks = sc3$y, labels = sc3$lab, + limits = c(0.3, max(sc3$y) + 0.9)) + + scale_x_continuous(limits = c(0.118, 0.15), breaks = c(0.12, 0.13, 0.14), + expand = c(0, 0)) + + labs(x = "BT rearing gradient P95 (accessible, stream + river polygon)", + y = NULL) +ggsave(file.path(dir_out, "fig_scenarios_rear_gradient.png"), p3, width = 7, + height = 3.6, dpi = 150, bg = "white") + +# -- maps ----------------------------------------------------------------------- +wsg <- sf::st_read(conn, query = " + SELECT watershed_group_code, + ST_SimplifyPreserveTopology(geom, 1500) AS geom + FROM whse_basemapping.fwa_watershed_groups_poly", quiet = TRUE) +bc <- sf::st_union(wsg) +hazelton <- sf::st_read(conn, query = " + SELECT ST_LineInterpolatePoint(ST_LineMerge(geom), 0) AS geom + FROM whse_basemapping.fwa_stream_networks_sp + WHERE localcode_ltree = '400.431358'::ltree AND wscode_ltree = '400.431358'::ltree + ORDER BY downstream_route_measure LIMIT 1", quiet = TRUE) +presence <- utils::read.csv(lnk_config("default")$files$wsg_species_presence$path, + stringsAsFactors = FALSE) +bt_present <- toupper(presence$watershed_group_code[presence$bt %in% "t"]) + +share_map <- wsg |> + tidyr::crossing(era = c("before 1995", "1995 on")) |> + left_join(wsg_share, by = c("watershed_group_code", "era")) |> + mutate(dv_share = ifelse(n >= 10, dv_share, NA), + era = factor(era, c("before 1995", "1995 on"))) |> + sf::st_as_sf() +p4 <- ggplot() + + geom_sf(data = share_map, aes(fill = dv_share), colour = "white", linewidth = 0.1) + + geom_sf(data = bc, fill = NA, colour = "grey55", linewidth = 0.15) + + geom_sf(data = hazelton, aes(shape = "Hazelton (Bulkley mouth)"), size = 2.2, + fill = "white", colour = "black") + + scale_shape_manual(values = 21, name = NULL) + + facet_wrap(~era) + + scale_fill_gradient2(low = "#1b9e77", mid = "#f7f7f7", high = "#e7298a", + midpoint = 0.5, labels = scales::percent, + na.value = "grey85", + name = "DV share of char records\n(grey: < 10 records)") + + theme_void(base_size = 11) + + theme(legend.position = "bottom", strip.text = element_text(size = 11), + legend.key.width = grid::unit(1.6, "cm")) +ggsave(file.path(dir_out, "fig_map_dv_share.png"), p4, width = 9, height = 5.4, + dpi = 150, bg = "white") + +pool_state <- function(s) { + interior_wsg <- regions$watershed_group_code[ + regions$region %in% c("Fraser", "Mackenzie", "Columbia")] + full <- switch(s, + S0_whole_skeena = c(interior_wsg, + regions$watershed_group_code[regions$region == "Skeena"]), + S1_hazelton = c(interior_wsg, upper_skeena), + S2_noskeena = interior_wsg, + S4_hazelton_pre1995 = upper_skeena) + dated <- if (s == "S4_hazelton_pre1995") interior_wsg else character(0) + w <- wsg$watershed_group_code + state <- ifelse(!w %in% bt_present, "BT not present", + ifelse(w %in% full, "DV counts as BT", + ifelse(w %in% dated, "DV counts as BT (pre-1995 records)", + "DV kept separate"))) + transform(wsg, scenario = scen_label[[s]], state = state) +} +pmap <- do.call(rbind, lapply(c("S0_whole_skeena", "S1_hazelton", "S2_noskeena", + "S4_hazelton_pre1995"), pool_state)) +pmap$scenario <- factor(pmap$scenario, scen_label[c("S0_whole_skeena", + "S1_hazelton", "S2_noskeena", "S4_hazelton_pre1995")]) +state_cols <- c(`DV counts as BT` = "#7570b3", + `DV counts as BT (pre-1995 records)` = "#b8b3e0", + `DV kept separate` = "#e7298a", `BT not present` = "grey88") +p5 <- ggplot() + + geom_sf(data = pmap, aes(fill = state), colour = "white", linewidth = 0.1) + + geom_sf(data = bc, fill = NA, colour = "grey55", linewidth = 0.15) + + geom_sf(data = hazelton, aes(shape = "Hazelton (Bulkley mouth)"), size = 1.8, + fill = "white", colour = "black") + + scale_shape_manual(values = 21, name = NULL) + + facet_wrap(~scenario, nrow = 2) + + scale_fill_manual(values = state_cols, name = NULL, drop = FALSE) + + theme_void(base_size = 11) + + theme(legend.position = "bottom", strip.text = element_text(size = 11)) + + guides(fill = guide_legend(nrow = 2)) +ggsave(file.path(dir_out, "fig_map_pooling_scenarios.png"), p5, width = 9, + height = 8.4, dpi = 150, bg = "white") + +# Skeena close-up: DV share from 1995 on, with the Hazelton split +sk <- wsg[grp_of(wsg$watershed_group_code) == "Skeena", ] |> + left_join(filter(wsg_share, era == "1995 on"), by = "watershed_group_code") |> + mutate(side = ifelse(watershed_group_code %in% upper_skeena, + "above Hazelton", "below Hazelton")) +lab <- sf::st_coordinates(sf::st_point_on_surface(sf::st_geometry(sk))) +lab <- data.frame(x = lab[, 1], y = lab[, 2], + label = paste0(sk$watershed_group_code, "\n", + ifelse(is.na(sk$n), "", + paste0(scales::percent(sk$dv_share, 1), + " DV (", sk$n, ")")))) +# LKEL is a sliver beside ZYMO: set its label below, clear of ZYMO's +lab$y[sk$watershed_group_code == "LKEL"] <- lab$y[sk$watershed_group_code == "LKEL"] - 22000 +lab$x[sk$watershed_group_code == "LKEL"] <- lab$x[sk$watershed_group_code == "LKEL"] - 15000 +p6 <- ggplot(sk) + + geom_sf(aes(fill = side), colour = "white", linewidth = 0.3) + + geom_sf(data = hazelton, aes(shape = "Hazelton (Bulkley mouth)"), size = 2.6, + fill = "white", colour = "black") + + scale_shape_manual(values = 21, name = NULL) + + geom_text(data = lab, aes(x, y, label = label), size = 2.6, lineheight = 0.9) + + scale_fill_manual(values = c(`above Hazelton` = "#c9c5ea", + `below Hazelton` = "#f6c6de"), name = NULL) + + theme_void(base_size = 11) + + theme(legend.position = "bottom") +ggsave(file.path(dir_out, "fig_map_skeena_hazelton.png"), p6, width = 7, + height = 6.5, dpi = 150, bg = "white") + +# -- stamp ------------------------------------------------------------------------ +writeLines(c( + sprintf("date: %s", format(Sys.time(), "%Y-%m-%d %H:%M %Z")), + sprintf("link: %s @ %s", utils::packageVersion("link"), + system("git rev-parse --short HEAD", intern = TRUE)), + "db: docker fwapg localhost:5432", + sprintf("bcfishobs.observations rows: %s", + dbGetQuery(conn, "SELECT count(*) FROM bcfishobs.observations")[[1]]), + sprintf("BT + DV records (not Releases): %d; undated: %d", nrow(obs), sum(is.na(obs$yr))), + "evidence: data-raw/query_habitat_thresholds_obs.R on fresh_default (55 WSGs), one run per scenario bundle", + sprintf("scenario numbers from producer runs: %s; BT_only from the reimplementation", + paste(names(runs), collapse = ", ")), + sprintf("reimplementation cross-check matched the producer for: %s", + paste(no_year, collapse = ", ")), + sprintf("validator runs: %s", if (do_validate) paste(names(bundles), collapse = ", ") else "not run")), + file.path(dir_out, "stamp.txt")) +DBI::dbDisconnect(conn) +message("wrote ", dir_out) diff --git a/data-raw/wsg_regions.R b/data-raw/wsg_regions.R new file mode 100644 index 00000000..414ad0a8 --- /dev/null +++ b/data-raw/wsg_regions.R @@ -0,0 +1,119 @@ +#!/usr/bin/env Rscript +# wsg_regions.R — build inst/extdata/wsg_regions.csv (link#290). +# +# One row per BC watershed group: the region and sub-region its outlet drains +# to. Geography, not biology, so it ships once at package level; bundles say +# what to do with it (e.g. configs/default/species_pooling.csv). +# +# Inputs: +# - fresh's inst/extdata/wsg_outlet.csv (fresh >= v0.33.0): each group's +# outlet point with its wscode_ltree. The outlet, not the group's +# shallowest code, because a group can touch more than one drainage. +# - data-raw/wsg_regions_defs.csv (hand-curated): `level` region|subregion, +# `name`, `wscode_prefix`, `wsgs`, `note`. A region is matched on the +# outlet code's first segment. A sub-region is either a wscode prefix +# (the longest one, on whole segments, containing the outlet code) or an +# explicit `wsgs` list (semicolon-separated), for a split no prefix can +# draw: MSKE and USKE have their outlets on the Skeena mainstem (400), as +# LSKE does, so "Skeena above Hazelton" is a list. A sub-region row gives +# one or the other, never both, and a group may fall in only one +# sub-region (there is one column). Names marked "draft" in `note` are +# placeholders until someone who knows the coast confirms them. +# +# Rscript data-raw/wsg_regions.R +# +# Fails loud if any group is unassigned, any definition matches nothing, or +# the outlet table is not the 246 groups it should be. + +path_outlet <- system.file("extdata", "wsg_outlet.csv", package = "fresh") +if (!nzchar(path_outlet)) { + stop("fresh's wsg_outlet.csv not found: install fresh >= v0.33.0", + call. = FALSE) +} +repo <- "." +if (!file.exists("DESCRIPTION") || + !any(grepl("^Package: link$", readLines("DESCRIPTION")))) { + stop("run from the link repo root", call. = FALSE) +} + +outlet <- utils::read.csv(path_outlet, colClasses = "character") +defs <- utils::read.csv(file.path(repo, "data-raw", "wsg_regions_defs.csv"), + colClasses = "character") + +stopifnot( + nrow(outlet) == 246L, + !anyDuplicated(outlet$watershed_group_code), + !anyNA(outlet$wscode_ltree), all(nzchar(outlet$wscode_ltree)), + all(defs$level %in% c("region", "subregion")), + !anyDuplicated(defs$wscode_prefix[nzchar(defs$wscode_prefix)]), + # a row is a prefix or a list, never both or neither + xor(nzchar(defs$wscode_prefix), nzchar(defs$wsgs)), + all(!nzchar(defs$wsgs[defs$level == "region"])), + # written unquoted + !any(grepl(",", defs$name, fixed = TRUE)) +) + +# TRUE where `code` equals `prefix` or sits below it, on whole segments. +in_prefix <- function(code, prefix) { + code == prefix | startsWith(code, paste0(prefix, ".")) +} + +reg <- defs[defs$level == "region", ] +if (any(grepl(".", reg$wscode_prefix, fixed = TRUE))) { + stop("a region prefix must be a single wscode segment", call. = FALSE) +} +top <- sub("[.].*$", "", outlet$wscode_ltree) +region <- reg$name[match(top, reg$wscode_prefix)] + +sub_defs <- defs[defs$level == "subregion" & nzchar(defs$wscode_prefix), ] +subregion <- vapply(outlet$wscode_ltree, function(code) { + hit <- sub_defs[in_prefix(code, sub_defs$wscode_prefix), , drop = FALSE] + if (nrow(hit) == 0L) return(NA_character_) + hit$name[which.max(nchar(hit$wscode_prefix))] +}, character(1), USE.NAMES = FALSE) + +list_defs <- defs[defs$level == "subregion" & nzchar(defs$wsgs), ] +listed <- lapply(strsplit(list_defs$wsgs, ";", fixed = TRUE), trimws) +unknown <- setdiff(unlist(listed), outlet$watershed_group_code) +if (length(unknown) > 0L) { + stop("sub-region lists name unknown groups: ", paste(unknown, collapse = ", "), + call. = FALSE) +} +for (i in seq_along(listed)) { + hit <- outlet$watershed_group_code %in% listed[[i]] + clash <- outlet$watershed_group_code[hit & !is.na(subregion)] + if (length(clash) > 0L) { + stop("groups in two sub-regions (", list_defs$name[i], " and another): ", + paste(clash, collapse = ", "), call. = FALSE) + } + subregion[hit] <- list_defs$name[i] +} + +out <- data.frame( + watershed_group_code = outlet$watershed_group_code, + region = region, + subregion = subregion, + wscode_outlet = outlet$wscode_ltree, + stringsAsFactors = FALSE +) +out <- out[order(out$watershed_group_code), ] + +if (anyNA(out$region)) { + stop("groups with no region: ", + paste(out$watershed_group_code[is.na(out$region)], collapse = ", "), + call. = FALSE) +} +pfx <- defs$wscode_prefix[nzchar(defs$wscode_prefix)] +unused <- pfx[!vapply(pfx, function(p) { + any(in_prefix(outlet$wscode_ltree, p)) +}, logical(1))] +if (length(unused) > 0L) { + stop("definitions that match no group: ", paste(unused, collapse = ", "), + call. = FALSE) +} + +utils::write.csv(out, file.path(repo, "inst", "extdata", "wsg_regions.csv"), + row.names = FALSE, na = "", quote = FALSE) +message("wrote ", nrow(out), " groups: ", + paste(sprintf("%s %d", names(table(out$region)), table(out$region)), + collapse = ", ")) diff --git a/data-raw/wsg_regions_defs.csv b/data-raw/wsg_regions_defs.csv new file mode 100644 index 00000000..6b057b4b --- /dev/null +++ b/data-raw/wsg_regions_defs.csv @@ -0,0 +1,21 @@ +level,name,wscode_prefix,wsgs,note +region,Fraser,100,, +region,Mackenzie,200,,Peace and Liard in BC +region,Columbia,300,, +region,Skeena,400,, +region,Nass,500,, +region,Stikine,600,, +region,Taku,700,, +region,Yukon,800,, +region,South Mainland Coast,900,,draft name: Squamish to Seymour Inlet +region,Central Mainland Coast,910,,draft name: Owikeno to Kitimat and the Dean +region,Outer North Coast Islands,915,,draft name: Banks and Porcher Islands; Laredo Inlet; Kitasu Bay +region,East Vancouver Island,920,,draft name +region,West Vancouver Island,930,,draft name +region,Haida Gwaii,940,,Graham Island +region,Haida Gwaii,950,,Moresby Island +region,Unuk,960,,draft name: drains to Alaska +region,Skagit,970,,draft name: drains to Washington +region,Alsek,990,,draft name: Tatshenshini +subregion,Kootenay,300.625474,,Kootenay River mainstem code +subregion,Skeena above Hazelton,,BULK;MORR;KISP;BABL;BABR;SUST;MSKE;USKE,"Upstream of the Bulkley mouth at Hazelton (400.431358); KISP's outlet is below it but the Kispiox enters above. Listed, since MSKE and USKE outlets sit on the Skeena mainstem (400) like LSKE" diff --git a/inst/extdata/configs/default/README.md b/inst/extdata/configs/default/README.md index 4fb26d3f..f193c39d 100644 --- a/inst/extdata/configs/default/README.md +++ b/inst/extdata/configs/default/README.md @@ -24,6 +24,8 @@ Not in this config: | `dimensions.csv` | Source of `rules.yaml` — species × habitat biology encoded for NewGraph defaults. Source of truth is `inst/extdata/parameters_habitat_dimensions.csv` (copied in here on bundle assembly) | | `parameters_fresh.csv` | Per-species fresh overrides (spawn_gradient_min, observation_threshold, etc.) | | `parameters_habitat_thresholds.csv` | Per-species gradient / channel-width / MAD / lake-area thresholds and edge types, read by classify and connect. Starts identical to fresh's copy; provenance in `config.yaml`. | +| `species_pooling.csv` | Which observation species count as evidence for which model species, and where: one dated, sourced row per decision, scoped to a region, sub-region (`inst/extdata/wsg_regions.csv`) or WSG. Either side can be a group from `species_groups.csv`. Read by `lnk_species_pooling()`; columns in `configs/dictionary_species_pooling.csv`. Anything unlisted is not pooled. After an edit, update its `checksum` in `config.yaml` (`lnk_config_verify()` reports the drift until you do). | +| `species_groups.csv` | Named sets of species (`SALMON`, `CHAR`) usable on either side of a pooling row. | | `overrides/` | Shared jurisdiction data — same barrier corrections, PSCIS status overrides, observation exclusions, habitat confirmations as the bcfishpass variant. These are BC-specific facts, not method choices. Redistributed under `LICENSE-bcfishpass` at the repo root. | The bundle is consumed via `lnk_config("default")` + `lnk_load_overrides(cfg)`. Project-experimental configs can declare `extends: default` to inherit this bundle and override specific entries (e.g. point a project's `user_barriers_definite` at a project-local CSV). diff --git a/inst/extdata/configs/default/config.yaml b/inst/extdata/configs/default/config.yaml index e834a3ed..e3f164c5 100644 --- a/inst/extdata/configs/default/config.yaml +++ b/inst/extdata/configs/default/config.yaml @@ -25,6 +25,10 @@ files: path: parameters_fresh.csv parameters_habitat_thresholds: path: parameters_habitat_thresholds.csv + species_pooling: + path: species_pooling.csv + species_groups: + path: species_groups.csv user_habitat_classification: source: bcfp path: overrides/user_habitat_classification.csv @@ -138,6 +142,16 @@ provenance: synced: '2026-09-25' checksum: sha256:7b904a18c29c724737ff24a27750bf05d7bfa281aa4fc1f7ac27c00238db042d shape_checksum: sha256:8de9bc1fcc2c703176a57d8a982bd26da1c49a885af3053f00078003a7e9283f + species_pooling.csv: + source: link (hand-authored; link#290). The DV->BT pooling tracker, one row per decision + synced: '2026-09-27' + checksum: sha256:9c42964e0469a7f098ee2176fcd279d21e98aa048b1b294359e297f14a59830e + shape_checksum: sha256:0c8af50df7fb05abf8bc443bca31d88cc1c8ad6ebffc077ef0bde6b45ed7a550 + species_groups.csv: + source: link (hand-authored; link#290) + synced: '2026-09-26' + checksum: sha256:e6e18111f635427a02c01627c5062db1f9b590aed882c5db3d0881309e56d5fb + shape_checksum: sha256:f26bcf4fdd8096a93bed0c0ddd8f62bb50fe46186d82b121b66a4d5c84ad93e4 overrides/user_habitat_classification.csv: source: https://github.com/smnorris/bcfishpass path: data/user_habitat_classification.csv diff --git a/inst/extdata/configs/default/species_groups.csv b/inst/extdata/configs/default/species_groups.csv new file mode 100644 index 00000000..a5321e29 --- /dev/null +++ b/inst/extdata/configs/default/species_groups.csv @@ -0,0 +1,8 @@ +group_code,species_code +SALMON,CH +SALMON,CM +SALMON,CO +SALMON,PK +SALMON,SK +CHAR,BT +CHAR,DV diff --git a/inst/extdata/configs/default/species_pooling.csv b/inst/extdata/configs/default/species_pooling.csv new file mode 100644 index 00000000..2c889a19 --- /dev/null +++ b/inst/extdata/configs/default/species_pooling.csv @@ -0,0 +1,7 @@ +species_code,species_obs,scope_level,scope,pool,obs_year_max,confidence,rationale,source,verified,issue +BT,DV,region,Fraser,yes,,medium,"Inland DV records are bull trout recorded under the other name; juveniles cannot be told apart in the field and the two hybridize where they co-occur, so habitat evidence is pooled","operator call 2026-09-26; McPhail and Carveth 1993, Field Key to the Freshwater Fishes of British Columbia, pp. 218-219, 223",2026-09-26,#290 +BT,DV,region,Mackenzie,yes,,medium,"Inland DV records are bull trout recorded under the other name; juveniles cannot be told apart in the field and the two hybridize where they co-occur, so habitat evidence is pooled","operator call 2026-09-26; McPhail and Carveth 1993, Field Key to the Freshwater Fishes of British Columbia, pp. 218-219, 223",2026-09-26,#290 +BT,DV,region,Skeena,no,,medium,"Skeena DV is a current name, not a legacy one: 86 % or more of char records in every decade, and 85 % of Skeena DV streams were re-sampled after 1995 and still recorded only DV (research/species_pooling.md). Kept apart below Hazelton; the row below pools the upper Skeena",operator call 2026-09-27; data-raw/logs/species_pooling_290,2026-09-27,#290 +BT,DV,region,Columbia,yes,,medium,"Inland DV records are bull trout recorded under the other name; juveniles cannot be told apart in the field and the two hybridize where they co-occur, so habitat evidence is pooled","operator call 2026-09-26; McPhail and Carveth 1993, Field Key to the Freshwater Fishes of British Columbia, pp. 218-219, 223",2026-09-26,#290 +BT,DV,subregion,Kootenay,yes,,medium,As Columbia; its own row so the Kootenay can diverge from the rest of the Columbia as evidence accrues,operator call 2026-09-26,2026-09-26,#290 +BT,DV,subregion,Skeena above Hazelton,yes,,medium,"Conservative split at Hazelton (operator call): the interior Skeena above the Bulkley mouth is pooled as the interior drainages are; the coastal lower Skeena (LSKE, KLUM, LKEL, ZYMO) is not",operator call 2026-09-27; data-raw/logs/species_pooling_290,2026-09-27,#290 diff --git a/inst/extdata/configs/dictionary_species_groups.csv b/inst/extdata/configs/dictionary_species_groups.csv new file mode 100644 index 00000000..60340ea2 --- /dev/null +++ b/inst/extdata/configs/dictionary_species_groups.csv @@ -0,0 +1,3 @@ +column,type,group,owner,consumed_by,default_when_absent,description,related +group_code,character,key,link,R/lnk_species_pooling.R:188,required,"Name of a set of species, usable on either side of a species_pooling row. Upper-cased; may not equal a species code, and groups may not nest.",species_code +species_code,character,key,link,R/lnk_species_pooling.R:188,required,"One member species, one row each. Must be a species column of wsg_species_presence.",group_code diff --git a/inst/extdata/configs/dictionary_species_pooling.csv b/inst/extdata/configs/dictionary_species_pooling.csv new file mode 100644 index 00000000..3fef9309 --- /dev/null +++ b/inst/extdata/configs/dictionary_species_pooling.csv @@ -0,0 +1,12 @@ +column,type,group,owner,consumed_by,default_when_absent,description,related +species_code,character,rule,link,R/lnk_species_pooling.R:291,required,"The target: a model species code, or a species_groups group_code standing for each of its members. Upper-cased and trimmed.",species_obs +species_obs,character,rule,link,R/lnk_species_pooling.R:292,required,"The evidence: an observation species code, or a group code, whose records count as the target. A species always counts as itself, so a row pairing a species with itself does nothing.",species_code +scope_level,character,rule,link,R/lnk_species_pooling.R:257,required,"region, subregion or wsg. The most specific applicable level wins (wsg over subregion over region).",scope +scope,character,rule,link,R/lnk_species_pooling.R:269,required,"A region or subregion name from inst/extdata/wsg_regions.csv, or a watershed group code. Matched case-insensitively; a name not in the lookup errors.",scope_level +pool,character,rule,link,R/lnk_species_pooling.R:263,required,"yes pools the evidence into the target in this scope; no keeps them apart, and overrides a yes at a broader scope. Anything no row covers is not pooled.",- +obs_year_max,integer,rule,link,R/lnk_species_pooling.R:288,empty (no limit),"Optional. Limits the row to observation records dated in or before this year, for evidence whose meaning changed over time (e.g. a name applied to another species until recording practice caught up). An undated record does not meet a limit. Tied rows must agree on it.",pool +confidence,character,record,link,- (not read; the record of why),-,"low, medium or high: how firmly the evidence supports the decision.",rationale +rationale,character,record,link,- (not read; the record of why),-,Why the decision holds in this scope.,source +source,character,record,link,- (not read; the record of why),-,"Where it comes from: an operator call with its date, a citation, a data set.",rationale +verified,date,record,link,- (not read; the record of why),-,Date the row was last checked (YYYY-MM-DD).,- +issue,character,record,link,- (not read; the record of why),-,The link issue that made or last changed the decision.,- diff --git a/inst/extdata/wsg_regions.csv b/inst/extdata/wsg_regions.csv new file mode 100644 index 00000000..1592115f --- /dev/null +++ b/inst/extdata/wsg_regions.csv @@ -0,0 +1,247 @@ +watershed_group_code,region,subregion,wscode_outlet +ADMS,Fraser,,100.190442.999098.995997.058910 +ALBN,West Vancouver Island,,930.077174 +ATLL,Yukon,,800.936764.858242 +ATNA,Central Mainland Coast,,910.275583.999439 +BABL,Skeena,Skeena above Hazelton,400.536025 +BABR,Skeena,Skeena above Hazelton,400.536025 +BARR,Stikine,,600.273049 +BBAR,Fraser,,100 +BEAV,Mackenzie,,200.692231 +BELA,Central Mainland Coast,,910.275583 +BIGC,Fraser,,100.342455.095384 +BLAR,Fraser,,100.500560 +BLUR,Mackenzie,,200.692231.708347.173706 +BONP,Fraser,,100.190442.506118 +BOWR,Fraser,,100.654493 +BRID,Fraser,,100.190442.998192.349877.237590.984912.950504 +BRKS,West Vancouver Island,,930.862497 +BULK,Skeena,Skeena above Hazelton,400.431358 +BULL,Columbia,Kootenay,300.625474 +CAMB,East Vancouver Island,,920.627155 +CANO,Columbia,,300 +CARP,Mackenzie,,200.948755.936906 +CARR,Fraser,,100.458399.466616 +CHES,Fraser,,100.567134 +CHIL,Fraser,,100.567134.069486 +CHIR,Fraser,,100.342455.328500 +CHUK,Stikine,,600.823383 +CHWK,Fraser,,100.064535 +CLAY,West Vancouver Island,,930.504218 +CLRH,Columbia,,300 +CLWR,Fraser,,100.190442.998192.349877 +COAL,Mackenzie,,200.692231 +COLR,Columbia,,300 +COMX,East Vancouver Island,,920.559826 +COTR,Fraser,,100 +COWN,East Vancouver Island,,920.388982 +CRKD,Mackenzie,,200.948755.936906.932956 +CRYL,Mackenzie,,200.692231.708347.415013 +DEAD,Fraser,,100.190442.712025 +DEAL,Mackenzie,,200.692231.708347 +DEAR,Mackenzie,,200.692231.708347 +DOGC,Fraser,,100 +DRIR,Fraser,,100.567134.179319.815989.532920.992397 +DUNC,Columbia,Kootenay,300.625474.096683 +DUNE,Mackenzie,,200.692231 +ELKR,Columbia,Kootenay,300.625474.584724 +EUCH,Fraser,,100.500560.248839 +EUCL,Fraser,,100.500560 +FINA,Mackenzie,,200.948755 +FINL,Mackenzie,,200.948755.999851 +FIRE,Mackenzie,,200.948755.999851 +FONT,Mackenzie,,200.692231.350733.999823 +FOXR,Mackenzie,,200.948755.999851.345456 +FRAN,Fraser,,100.567134.374775 +FRCN,Fraser,,100 +FROG,Mackenzie,,200.692231.587311 +GATA,Mackenzie,,200.692231.587311.633085 +GLAR,Yukon,,800.901317.610987 +GOLD,West Vancouver Island,,930.508366 +GRAI,Haida Gwaii,,940.349858 +GRNL,Fraser,,100.190442.506118.553154 +GUIC,Fraser,,100.190442.244975.296261 +HARR,Fraser,,100 +HAYR,Mackenzie,,200.893458 +HERR,Fraser,,100.639480.270767 +HOLB,West Vancouver Island,,930.968384 +HOMA,South Mainland Coast,,900.407906 +HORS,Fraser,,100.458399.638146 +INGR,Mackenzie,,200.948755.992594 +INKR,Taku,,700 +ISKR,Stikine,,600.059339 +JENR,Yukon,,800.901317.645839 +JERV,South Mainland Coast,,900.236275 +KAHN,Mackenzie,,200.692231.350733.999823.217968 +KAKC,Stikine,,600.399105 +KCHL,Mackenzie,,200.893458.633613 +KEEC,Outer North Coast Islands,,915.669295.153885 +KETL,Columbia,,300.571168 +KHOR,Columbia,,300 +KHTZ,Central Mainland Coast,,910.524956 +KINR,Nass,,500.441851 +KISK,Mackenzie,,200.948755.789717 +KISP,Skeena,Skeena above Hazelton,400 +KITL,Central Mainland Coast,,910.609623.008239 +KITR,Central Mainland Coast,,910.665062 +KLAR,Stikine,,600.544210 +KLIN,South Mainland Coast,,900.595322 +KLUM,Skeena,,400 +KNIG,South Mainland Coast,,900.598651 +KOTL,Columbia,Kootenay,300.625474 +KOTR,Columbia,Kootenay,300.625474 +KSHR,Central Mainland Coast,,910.998407 +KTSU,Outer North Coast Islands,,915.606604.524213 +KUMR,Central Mainland Coast,,910.733753 +KUSR,Yukon,,800.936764 +LARL,Columbia,,300 +LBIR,Nass,,500.530253 +LBTN,Mackenzie,,200.948755.796981 +LCHL,Fraser,,100.567134 +LCHR,Fraser,,100.342455 +LDEN,Central Mainland Coast,,910.302877 +LEUT,Fraser,,100.567134 +LFRA,Fraser,,100 +LFRT,Mackenzie,,200.692231.350733 +LHAF,Mackenzie,,200.948755.837217 +LIAR,Mackenzie,,200.692231 +LILL,Fraser,,100.077501.955583 +LISR,Stikine,,600.059339 +LKEC,Mackenzie,,200.692231.587311 +LKEL,Skeena,,400.174068 +LMUS,Mackenzie,,200.692231.350733.577347 +LNAR,Nass,,500 +LNIC,Fraser,,100.190442.244975 +LNRS,Fraser,,100.567134 +LNTH,Fraser,,100.190442.998192 +LOMI,Mackenzie,,200.948755.944288 +LPCE,Mackenzie,,200.948755 +LPET,Mackenzie,,200.692231.270936 +LPRO,Mackenzie,,200.692231.350733.577347.047212 +LRAN,Mackenzie,,200.692231.770914.504300 +LRDO,Outer North Coast Islands,,915.620970.426780 +LSAL,Fraser,,100.591289 +LSIK,Mackenzie,,200.692231.350733.999566 +LSKE,Skeena,,400 +LSTR,Stikine,,600 +LTRE,Fraser,,100.567134.179319.815989 +MAHD,Fraser,,100.190442.998192.349877.237590 +MBNK,Outer North Coast Islands,,915.669295.253982 +MCGR,Fraser,,100.639480 +MDEA,Mackenzie,,200.692231.708347 +MESC,Stikine,,600.342012 +MESI,Mackenzie,,200.948755.944297 +MFRA,Fraser,,100 +MFRT,Mackenzie,,200.692231.350733 +MIDR,Fraser,,100.567134.179319.815989.532920 +MILL,Mackenzie,,200.948755.796981.308302 +MMUS,Mackenzie,,200.692231.350733.577347 +MORI,Haida Gwaii,,950.012855 +MORK,Fraser,,100 +MORR,Skeena,Skeena above Hazelton,400.431358.585806 +MPRO,Mackenzie,,200.692231.350733.577347.047212 +MSKE,Skeena,Skeena above Hazelton,400 +MSTR,Stikine,,600 +MURR,Mackenzie,,200.948755.808139.320884 +MURT,Fraser,,100.190442.998192.349877.581724 +MUSK,Fraser,,100.591289.413213 +NAHR,Taku,,700.998191.999667 +NAKR,Taku,,700.999247 +NARC,Fraser,,100 +NASC,Central Mainland Coast,,910.318106 +NASR,Nass,,500 +NATR,Mackenzie,,200.948755.937012 +NAZR,Fraser,,100.500560.326229 +NBNK,Outer North Coast Islands,,915.669295.759486 +NECL,Central Mainland Coast,,910.280177 +NECR,Fraser,,100.567134 +NEVI,East Vancouver Island,,920.954598 +NICL,Fraser,,100.190442.244975 +NIEL,Central Mainland Coast,,910.231256 +NIMP,East Vancouver Island,,920.824808 +OKAN,Columbia,,300.432687 +OSPK,Mackenzie,,200.948755.951156 +OWIK,Central Mainland Coast,,910.118506 +PARA,Mackenzie,,200.948755 +PARK,East Vancouver Island,,920.470275 +PARS,Mackenzie,,200.948755.936902 +PCEA,Mackenzie,,200.948755 +PINE,Mackenzie,,200.948755.808139 +PITR,Stikine,,600.683111 +PORI,Outer North Coast Islands,,915.724877.161993 +QUES,Fraser,,100.458399 +REVL,Columbia,,300 +SAHD,Mackenzie,,200.692231.270936 +SAHT,Mackenzie,,200.692231.350733.487083 +SAJR,Fraser,,100.382626 +SALM,East Vancouver Island,,920.722273 +SALR,Fraser,,100.591289 +SANJ,West Vancouver Island,,930.073434 +SETN,Fraser,,100 +SEYM,South Mainland Coast,,900.690764 +SHEK,Mackenzie,,200.893458.633613.058706 +SHER,Taku,,700.998191.999517 +SHUL,Fraser,,100.190442.999098.995997 +SIML,Columbia,,300.432687.380566 +SKGT,Skagit,,970.106243 +SLOC,Columbia,Kootenay,300.625474.020842 +SMAR,Columbia,Kootenay,300.625474 +SMOK,Mackenzie,,200.948755.667407.370931 +SPAT,Stikine,,600.756349 +SQAM,South Mainland Coast,,900.105574 +STHM,Fraser,,100.190442.999098 +STIR,Stikine,,600 +STUL,Fraser,,100.567134.179319 +STUR,Fraser,,100.567134.179319 +SUST,Skeena,Skeena above Hazelton,400.757844 +SWIR,Yukon,,800.901317.630554 +TABR,Fraser,,100 +TAHR,Stikine,,600.377323 +TAHS,West Vancouver Island,,930.673175 +TAKL,Fraser,,100.567134.179319.815989.532920 +TASR,Fraser,,100.342455.328500.134035 +TATR,Alsek,,990 +TAYR,Nass,,500.617060 +TESR,Yukon,,800.901317 +THOM,Fraser,,100.190442 +TOAD,Mackenzie,,200.692231.445633 +TOBA,South Mainland Coast,,900.391855 +TOOD,Mackenzie,,200.948755.999851 +TSAY,Central Mainland Coast,,910.609623 +TSEA,Mackenzie,,200.692231.270936 +TSIT,East Vancouver Island,,920.782999 +TURN,Mackenzie,,200.692231.587311.296913 +TUTR,Yukon,,800.936764 +TUYR,Stikine,,600.392439 +TWAC,Fraser,,100 +UARL,Columbia,,300 +UBIR,Nass,,500.530253 +UBTN,Mackenzie,,200.948755.796981 +UCHR,Fraser,,100.342455 +UDEN,Central Mainland Coast,,910.302877 +UEUT,Fraser,,100.567134.642019 +UFRA,Fraser,,100 +UFRT,Mackenzie,,200.692231.350733 +UHAF,Mackenzie,,200.948755.837217 +UISR,Stikine,,600.059339 +UJER,Yukon,,800.901317.645839 +UKEC,Mackenzie,,200.692231.587311 +ULRD,Mackenzie,,200.692231 +UMUS,Mackenzie,,200.692231.350733.577347 +UNAR,Nass,,500 +UNRS,Fraser,,100.567134 +UNTH,Fraser,,100.190442.998192 +UNUR,Unuk,,960.195906 +UOMI,Mackenzie,,200.948755.944288 +UPCE,Mackenzie,,200.948755 +UPET,Mackenzie,,200.692231.270936 +UPRO,Mackenzie,,200.692231.350733.577347.047212 +USHU,Fraser,,100.190442.999098.995997.730848 +USIK,Mackenzie,,200.692231.350733.999566 +USKE,Skeena,Skeena above Hazelton,400 +USTK,Stikine,,600 +UTRE,Fraser,,100.567134.179319.815989 +VICT,East Vancouver Island,,920.232404 +WILL,Fraser,,100.594120 +WORC,Central Mainland Coast,,910.881783 +ZYMO,Skeena,,400.221484 diff --git a/man/lnk_habitat_validate.Rd b/man/lnk_habitat_validate.Rd index 7ed839a1..e9d854a2 100644 --- a/man/lnk_habitat_validate.Rd +++ b/man/lnk_habitat_validate.Rd @@ -52,11 +52,21 @@ then \code{loaded$observation_exclusions} must be \code{NULL} (the exclusions ar matched on that key). Species and WSG codes are compared upper-cased and trimmed. Optional: \code{match_type}, \code{source}, \code{is_spawn}, \code{is_rear} (logical, 0/1 or t/true/yes), \code{activity_code}, \code{activity}, -\code{life_stage}.} +\code{life_stage}, and \code{observation_date}, which is required when +\code{species_obs} carries a year limit (\code{obs_year_max}).} -\item{species_obs}{Named list mapping a model species to the observation -species codes that count as it. Species not named map to themselves. -Default pools DV records with BT (\code{list(BT = c("BT", "DV"))}).} +\item{species_obs}{Which observation species count as each model species. +Either a named list mapping a model species to observation species +codes, applied in every WSG (default \code{list(BT = c("BT", "DV"))}, which +pools DV records with BT), or a per-WSG data frame with +\code{watershed_group_code}, \code{species_code} and \code{obs_species}, such as +\code{\link[=lnk_species_pooling]{lnk_species_pooling()}} returns, optionally with \code{obs_year_max} (a +pooled record counts only if dated in or before that year; an undated +one does not). In the list form a species not named +maps to itself; in the data frame form a species always counts as +itself, and a WSG and species pair it does not list maps to itself only. +Either way a species is scored only where +\code{loaded$wsg_species_presence} marks it present.} \item{match_types}{Character vector of \code{match_type} classes (first letter) to keep, or \code{NULL} for no match-type filter. Default diff --git a/man/lnk_species_pooling.Rd b/man/lnk_species_pooling.Rd new file mode 100644 index 00000000..70c49abd --- /dev/null +++ b/man/lnk_species_pooling.Rd @@ -0,0 +1,80 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lnk_species_pooling.R +\name{lnk_species_pooling} +\alias{lnk_species_pooling} +\title{Resolve which observation species count as each model species, per WSG} +\usage{ +lnk_species_pooling(loaded, aoi, species, regions = NULL) +} +\arguments{ +\item{loaded}{Named list from \code{\link[=lnk_load_overrides]{lnk_load_overrides()}}. Uses +\code{wsg_species_presence} (required: its species columns are also the set of +known species codes), \code{species_pooling} and \code{species_groups} (both +optional; without a tracker nothing is pooled).} + +\item{aoi}{Character vector of watershed group codes.} + +\item{species}{Character vector of model species codes.} + +\item{regions}{Data frame with \code{watershed_group_code}, \code{region} and +\code{subregion}, or \code{NULL} (default) for the package's +\code{inst/extdata/wsg_regions.csv}.} +} +\value{ +A data frame, one row per WSG x model species x observation +species: \code{watershed_group_code}, \code{species_code}, \code{obs_species}, +\code{scope_level} (\code{self} for the species itself, else the winning row's +level), \code{scope}, \code{rule} (the winning row's number in the tracker, \code{NA} +for \code{self}) and \code{obs_year_max} (the winning row's year limit, \code{NA} for +none; always \code{NA} for \code{self}). Consumers apply the year limit per record, +and an undated record does not meet one. Codes are upper case. +} +\description{ +Reads a bundle's pooling tracker (\code{species_pooling.csv}) and species +groups (\code{species_groups.csv}) and returns, for each watershed group in +\code{aoi} and each model species present there, the observation species +whose records count as evidence for it. The tool knows nothing about any +particular species: pooling Dolly Varden records into bull trout, or all +salmon together, is a row in the tracker. +} +\details{ +A tracker row is \code{species_code} (the model species or a group of them), +\code{species_obs} (the observation species or a group), \code{scope_level} +(\code{region}, \code{subregion} or \code{wsg}), \code{scope} (a name in +\code{inst/extdata/wsg_regions.csv}, or a WSG code) and \code{pool} (\code{yes} / \code{no}). +An optional \code{obs_year_max} limits a pooling row to records dated in or +before that year, for evidence whose meaning changed over time (a name +that was applied to another species until recording practice caught up). +Empty means no limit. Other columns (\code{confidence}, \code{rationale}, \code{source}, +\code{verified}, \code{issue}) are the record of why, and are not read here. + +For each WSG, target and observation species pair, the applicable rows +are resolved in order: +\enumerate{ +\item the most specific scope wins (\code{wsg} over \code{subregion} over \code{region}); +\item at equal scope, the row naming fewer groups wins (a species-to-species +row beats one that names a group); +\item rows still tied must agree on \code{pool} and \code{obs_year_max}, or the call +errors. +} + +Anything no row covers is not pooled. A species always counts as itself, +and a model species yields rows only where \code{wsg_species_presence} marks it +present. +} +\examples{ +cfg <- lnk_config("default") +loaded <- suppressWarnings(lnk_load_overrides(cfg)) + +# Which observation species count as each model species in three groups +# on different drainages? +p <- lnk_species_pooling(loaded, aoi = c("MORR", "ELKR", "COMX"), + species = c("BT", "CO")) +p + +# The pooled rows alone, with the tracker row that decided each one +p[p$scope_level != "self", ] +} +\seealso{ +\code{\link[=lnk_presence]{lnk_presence()}}, \code{\link[=lnk_habitat_validate]{lnk_habitat_validate()}} +} diff --git a/planning/archive/2026-09-issue-290-species-pooling/README.md b/planning/archive/2026-09-issue-290-species-pooling/README.md new file mode 100644 index 00000000..7270e4f3 --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/README.md @@ -0,0 +1,42 @@ +## Outcome + +Moved "which observation species count as which model species" out of code and into data. + +- **The tracker.** `configs/default/species_pooling.csv` holds one dated, sourced row per decision. Each row is scoped to a region, sub-region or WSG, and either side can be a group from `species_groups.csv`. +- **The resolver.** `lnk_species_pooling()` resolves it and knows no species: DV into BT, or all salmon together, is a row. The most specific scope wins, then the row naming fewer groups. Unresolved ties error, and anything unlisted is not pooled. +- **Regions.** `inst/extdata/wsg_regions.csv` is package-level geography. The region is the first segment of each group's *outlet* wscode (LFRA straddles 100 and 900). It is hashed into the `config_hash` of any bundle that declares a tracker. +- **Consumers.** `lnk_habitat_validate()`, `data-raw/habitat_validate.R` and the #284 obs producer take pooling from the tracker. The validator driver resolves it once and applies it to both bundles. +- **Seed.** DV → BT in the Fraser, Mackenzie, Skeena and Columbia/Kootenay (operator call, 2026-09-26). +- **State of knowledge:** [`research/species_pooling.md`](../../../research/species_pooling.md). + +The plan moved twice at the operator's word: regions went package-level rather than into the bundle, and pooling became abstract (species or group on either side) mid-plan. + +**After the PR opened (2026-09-27):** +- The naming-history measurement showed Skeena DV is a current name, not a legacy one. +- At the operator's call, the Skeena is split at Hazelton. Only the upper Skeena pools, through a new list-defined sub-region. +- The tracker gains an optional `obs_year_max` column, so a row can pool only records dated before a year. It is empty in the seed. + +## Measurement + +- **Where the new rule applies.** DV pools into BT in 129 WSGs. It does not in the 29 BT-present WSGs of unlisted regions (Nass, Stikine, Taku, Yukon, the coast), all of which pooled under the old "wherever BT is present" rule. +- **No #284 or #283 number moved.** Predicted before running, and confirmed: + - The #284 obs producer re-runs byte-identical in every CSV and PNG except the province-wide ledger step 3, where DV goes 8,888 → 6,138. The plan review independently derived the same 6,138. + - The #283 validation baseline (55 + 59 WSGs, knowledge @ 508bf44) re-runs byte-identical in all 6 CSVs, before and after the Phase 3 guards. +- **Negative check** (Skeena `pool = no`): ledger DV 2,910 (6,138 − 3,228). 1,929 evidence rows drop, all DV, in exactly the 9 Skeena WSGs; 0 rows are added and the rest are identical. +- **A pre-existing reproducibility defect surfaced.** The #284 producer's `candidates.csv` differs by 1 ulp (1.7e-16 relative) between identical runs, from a double-precision `sum(length_metre)` in its availability SQL. The committed copy was kept; filed as #293. +- **Wrong turns kept:** + - A mutation loop restored from a missing path, so mutations stacked until a control run was added. + - A `sprintf()` over SQL with a literal `LIKE '...%'` crashed the first re-run. + - Round 2 of code review found every dictionary line ref stale after round 1's fixes. Round 3 found that the test written to catch that matched substrings. + - Phase 3's first presence guard compared by row position. + + All four are one mechanism, which review round 3 named: two separately kept lists agree on a key, and disagreement narrows silently instead of failing. Both review loops ended by enumerating the mechanism's reach and guarding each site. +- **Review spend:** 1 plan review and 5 code-check rounds (Phase 2: 3; Phase 3: 2, one below the skill's floor, stated). That is 6 agents, past the ~5 bound. + +## Evidence + +- `data-raw/logs/habitat_thresholds_284/` (refreshed: `obs_ledger.csv`, `stamp.txt`) +- Review files: `review-*.md` here +- Follow-up issue drafts, filed 2026-09-27: `draft_presence_groups_issue.md` → #292, `draft_obs_float_issue.md` → #293 + +Closed by: PR for #290 (branch `290-region-scoped-dv-bt-observation-pooling`) diff --git a/planning/archive/2026-09-issue-290-species-pooling/draft_obs_float_issue.md b/planning/archive/2026-09-issue-290-species-pooling/draft_obs_float_issue.md new file mode 100644 index 00000000..176fb0bd --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/draft_obs_float_issue.md @@ -0,0 +1,9 @@ +Title: query_habitat_thresholds_obs.R: availability km differ run to run in the last bits (float sum order) + +Two runs of `data-raw/query_habitat_thresholds_obs.R` on the same database, commit and bundle differ in `candidates.csv`: `avail_share_below` is `0.11325447588492017` in one run and `0.11325447588492016` in the other, and `ratio_below` differs at the same digit. Measured 2026-09-26 while verifying #290. + +The cause is `sum(s.length_metre) / 1000 AS km` (the availability query, ~line 371). It is a double-precision sum, and Postgres may parallelise the aggregate, so the summation order, and therefore the last bits, vary between runs. link's bar is byte-identical reruns, and this breaks it for a research producer whose outputs are committed as evidence. + +Fix: sum as `numeric` (`sum(s.length_metre::numeric) / 1000`), or round to a fixed number of decimals before writing. Then re-run twice and `cmp` the outputs. The committed CSVs will change in the last digits once, so say so in the commit. + +Relates to #284, #277 diff --git a/planning/archive/2026-09-issue-290-species-pooling/draft_presence_groups_issue.md b/planning/archive/2026-09-issue-290-species-pooling/draft_presence_groups_issue.md new file mode 100644 index 00000000..bf964796 --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/draft_presence_groups_issue.md @@ -0,0 +1,19 @@ +Title: lnk_presence(): move the hard-coded presence groups into the bundle + +**If we do it:** the species groups that promote presence ("any salmon present means all salmon present") are bundle data, logged and hashed like every other model input. **If we never do:** a model input lives in code, outside `config_hash`, and a change to it is invisible to run provenance. + +## Problem + +`lnk_presence()` defaults `groups = list(salmon = c("ch","cm","co","pk","sk"), ct_dv_rb = c("ct","dv","rb"))` (`R/lnk_presence.R:67-70`). The pipeline consumes it (`R/lnk_pipeline_run.R:227`) for bcfishpass-parity presence promotion, so it changes model output. #290 introduced `species_groups.csv` for observation pooling, but deliberately left presence alone: +- the concept differs (presence promotion vs evidence pooling); +- the groups differ (`ct_dv_rb` vs `CHAR` = BT, DV); +- folding them together would change pipeline output. + +## Proposed + +- A bundle file, e.g. `presence_groups.csv` (`group_code, species_code`), or a `role` column in `species_groups.csv`. Whichever it is, declare it under `files:` so it enters `config_hash`. +- `lnk_pipeline_run()` passes it to `lnk_presence(groups = )`. +- `bcfishpass` carries today's two groups verbatim (parity); `default` starts identical. +- Verify byte-identical `streams_access` on ADMS and BULK before and after. + +Relates to #290, #236, #189 diff --git a/planning/archive/2026-09-issue-290-species-pooling/findings.md b/planning/archive/2026-09-issue-290-species-pooling/findings.md new file mode 100644 index 00000000..c40a9da5 --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/findings.md @@ -0,0 +1,69 @@ +# Findings — Region-scoped DV→BT observation pooling (#290) + +## Issue context + +**If we do it:** whether a DV record counts as BT evidence is decided per region, sub-region or WSG, in bundle CSVs that record why, when and from what source. **If we never do:** DV is pooled with BT wherever BT is present. That rule is hard-coded in three places, and it is least defensible in exactly the places where DV and BT differ. + +Split out of #236 (question 1, narrowed to observation evidence). **#284 step 5 is parked until this lands**, because its BT evidence is defined by this rule. + +## Problem + +DV→BT pooling is a biological position, but it lives in code, with one global scope: + +- `R/lnk_habitat_validate.R:202`: `species_obs = list(BT = c("BT", "DV"))`, the default. +- `data-raw/query_habitat_thresholds_obs.R:79-87`: `CASE WHEN species_code = 'DV' THEN 'BT'`, gated only on BT presence in the WSG. +- `inst/extdata/configs/default/parameters_fresh.csv`: `observation_species = BT;DV` for the BT access override. This one is **out of scope here** and stays with #236, which needs multi-rule overrides. It should consume the same table when that lands. + +The rule matters for #284. BT `rear_gradient_max` 0.1249 vs 0.1349 in `default_tuned` is exactly BT-only vs BT+DV pooled, and in BULK and MORR the "BT" evidence is ~90 % DV records (442 DV / 40 BT, 344 DV / 49 BT, raw A/B locations). + +The operator's position (2026-09-26): pool in named regions only, and build up the state of knowledge over time in CSVs. + +## Proposed Solution + +Two bundle files, declared under `files:` so they are logged in `.log_*` and enter `config_hash`. + +**1. `wsg_regions.csv`**, one row per WSG (246): `watershed_group_code, subregion, region`. + +`region` is generated from the first segment of each group's **outlet** `wscode_ltree` (fresh@v0.33.0 `inst/extdata/wsg_outlet.csv`). Reading it at the outlet matters because some groups straddle codes: LFRA touches both 100 and 900. Measured on local fwapg: + +| code | region | e.g. | +|---|---|---| +| 100 | Fraser | LFRA, UNTH, LNTH | +| 200 | Mackenzie | PARS, FINA, LIAR | +| 300 | Columbia | ELKR, KOTL, BULL | +| 400 | Skeena | BULK, MORR | + +The 500–800 and 9xx codes are northern rivers and the coast; names get confirmed when the generator runs. `subregion` is hand-curated, starting with Kootenay under Columbia. The generator is a `data-raw/` script. + +**2. `species_pooling.csv`**, the tracker. Columns: `species_code, species_obs, scope_level, scope, pool, confidence, rationale, source, verified, issue`. + +- `scope_level` is `region`, `subregion` or `wsg`. +- Resolution: **the most specific row wins, and anything unlisted is not pooled.** A WSG row overrides its sub-region, which overrides its region; a WSG with no applicable row keeps DV separate. +- Knowledge accrues as dated, sourced rows. Git history of the file is the record. +- Seed rows: `BT, DV, region, {Fraser, Mackenzie, Skeena, Columbia}, pool = yes` and `BT, DV, subregion, Kootenay, pool = yes`. Source: operator call 2026-09-26 (inland DV are bull trout recorded under the other name). The coast and the north are unlisted. + +`default` declares both files. `bcfishpass` declares neither: it does not pool, since it is the parity reference. + +## Tasks + +- [ ] Generator for `wsg_regions.csv`: region from the outlet code, sub-region from a small curated list; commit the output +- [ ] Seed `species_pooling.csv`; add both to `default`'s `files:` and to the config dictionaries +- [ ] One resolver, e.g. `lnk_species_pooling(cfg, loaded, aoi)` → the per-WSG `species_obs` list. Species-agnostic: it knows nothing about BT or DV +- [ ] `lnk_habitat_validate()` and `data-raw/habitat_validate.R` take `species_obs` from the resolver when the bundle declares the tracker +- [ ] `data-raw/query_habitat_thresholds_obs.R` pools through the resolver instead of the hard-coded `CASE` +- [ ] Re-run #284 step 1 under the regional rule; record how far the BT P95 and the verdicts move in `research/habitat_thresholds.md`, and in `default_tuned` if a value changes +- [ ] Tests: resolution precedence (WSG > sub-region > region > unlisted), unlisted means not pooled, and a bundle without the files keeps today's behaviour + +Out of scope: the access override's `observation_species` (#236), and DV as a modelled species with its own thresholds (#236, fresh). + +Relates to #236, #284, #283, #189 + + + +## Errors Encountered + +| Error | Resolution | +|-------|------------| +| A mutation-test loop restored from a path that did not exist, so later mutations ran stacked on earlier ones | Restore from the absolute repo path on every iteration, and run the unmutated copy first as a control (0 failing) | +| sprintf() over SQL with a literal `LIKE '...%'` fails: "invalid format '%' A'" | Escape as `%%` when wrapping SQL in sprintf | +| Two runs of `query_habitat_thresholds_obs.R` with identical inputs differ in the 17th significant digit of `candidates.csv` availability shares (`0.11325447588492017` vs `…016`) | Pre-existing, not #290. The cause is `sum(s.length_metre)` over double precision (line ~371), whose Postgres parallel-aggregation order varies. An issue is drafted in the final report (sum as `numeric`). The byte-identity check here compares against the run that matched; the committed evidence keeps its CSVs, and only the ledger and stamp are refreshed | diff --git a/planning/archive/2026-09-issue-290-species-pooling/progress.md b/planning/archive/2026-09-issue-290-species-pooling/progress.md new file mode 100644 index 00000000..5a913c44 --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/progress.md @@ -0,0 +1,66 @@ +# Progress — Region-scoped DV→BT observation pooling (#290) + +## Session 2026-09-26 + +- Plan-mode exploration; phases approved by the operator + - `wsg_regions.csv` is package-level; the resolver is `lnk_species_pooling()` + - Mid-plan refinement: pooling is abstract (species or group on either side of a row) +- Created branch `290-region-scoped-dv-bt-observation-pooling` off `origin/main` (`aa02738`, v0.52.0). Local `main` still carries the unpushed `997b876` (MCGR run logs), which is left untouched. +- Scaffolded the PWF baseline +- Next: Phase 1 +- Phase 1: `data-raw/wsg_regions.R` builds `inst/extdata/wsg_regions.csv`. It covers 246 groups in 17 regions (Haida Gwaii spans codes 940 and 950), and Kootenay (7 WSGs: BULL, DUNC, ELKR, KOTL, KOTR, SLOC, SMAR) is the one sub-region. The rebuild is idempotent (`cmp`). + - The guards were proven in a scratch copy: an unmatched prefix, a comma in a name and a missing region row each exit 1 with the named cause. + - Review: self-review and the mutation test. The `/code-check` skill runs on the resolver diff (Phase 2), which carries the logic. + - #290's body was edited: regions are package-level, and pooling is abstract (species or group on either side). +- Phase 2: `lnk_species_pooling()` plus the tracker and groups at the `default` bundle root. They are not in `overrides/`, because the bundle README defines that as shared jurisdiction facts, while pooling is a method choice. Both have dictionaries with tests; `lnk_config_verify` is clean for `default` and for `default_tuned`, which inherits them. + - 37 tests on synthetic codes (AAA/BBB/CCC/GRP). + - Four mutations in a scratch copy each go red: scope precedence inverted (3 failing), the taxon tie-break removed (1), `pool = no` ignored (2), the presence gate removed (1). + - Province-wide, DV pools into BT in 129 WSGs. 29 of the 158 BT-present WSGs are in unlisted regions (Nass, Stikine, Taku, Yukon, the coast), which is where the new rule differs from the old global one. +- Phase 4 check (run from the working tree before commit, into scratch): `query_habitat_thresholds_obs.R` under the regional rule. Every CSV and both PNGs are byte-identical to the committed #284 evidence, except the ledger step-3 row: new label, and DV 8,888 → 6,138. That count was predicted before the run and independently by the plan review. + - Steps 4–7 are identical, because all 55 WSGs are in pooled regions. The stamp gains a `pooling:` line; the n_cand > 1 count is still 45. (The console's "107" is the pre-dedup `o5` message, not a change.) + - A first attempt failed: `sprintf()` over SQL with a literal `LIKE '...%'` (findings table). +- Phase 2 `/code-check`: three rounds, then ended by enumeration. + + | Round | Findings | Fixed | Accepted | Inside previous fix? | + |---|---|---|---|---| + | 1 | 3 fragile: aoi not de-duplicated; unknown species silently dropped; `[1, ]` on an NA regions row | 3 | 0 | — | + | 2 | 2 fragile: every dictionary `consumed_by` ref stale; a vacuous zero-row assertion | 2 | 0 | yes (the R1 fixes shifted the lines) | + | 3 | 2 fragile: the ref test matched substrings; `read.csv("")` reads stdin. Plus 1 site guarded only by accident and 1 duplicated list | 4 | 0 | yes (the R2 test) | + + - Mechanism (named by round 3): two separately maintained lists agree on a key, and disagreement narrows silently instead of failing. + - Its reach, enumerated by round 3, is now guarded site by site: + - unknown keys error; + - the NA-safe `%in%`; + - the token-matching ref test, proven against a planted wrong ref and against real drift (6 of 7 stale refs caught); + - non-empty guards on subset assertions; + - one `.lnk_presence_species_cols()` for three copies of the exclusion list; + - `.lnk_wsg_regions_path()` stops on a missing file. + - Also added: `.lnk_config_hash()` hashes `wsg_regions.csv` for tracker bundles (the plan review's G7), and its mocked test goes red when the block is removed. +- Phase 3: `lnk_habitat_validate()` accepts a per-WSG `species_obs` data frame, checked as a data frame first (plan review B3). + - Rules: its own presence ∩ the table; an unlisted pair maps to itself; rows are deduplicated. + - The driver gains `--pooling=`, defaulting to the first bundle that declares a tracker. It resolves once, over the union of both bundles' WSGs, and stamps the choice. + - The obs query joins the resolved table instead of the hard-coded `CASE`, and gains `--pooling=` and `--out=`. + - Tests: + - 3 new, including end-to-end: the df form's `summary` is identical to the list form, and an empty df drops DV record `o2`; + - bypassing the df branch in a copy turns all 3 red. +- Phase 4 negative check: a scratch bundle with Skeena `pool = no`. + - Ledger step-3 DV is 2,910, as predicted (6,138 − 3,228). + - 1,929 evidence rows drop, all DV and all Skeena, in exactly the 9 Skeena WSGs (BULK, KISP, KLUM, LKEL, LSKE, MORR, MSKE, USKE, ZYMO). + - 0 rows are added, and the remaining rows are identical. +- Phase 3 `/code-check`: two rounds, then ended by enumeration. This is one round short of the skill's three-round floor, deliberately: review spend was at 6 agents, and the only round-2 finding was a single site, now keyed and proven. + + | Round | Findings | Fixed | Accepted | Inside previous fix? | + |---|---|---|---|---| + | 1 | 3 fragile: CH<-BT relabelled silently; pooling-bundle vs scored-bundle presence disagreement drops silently; the zero-row stamp prints `"<-"` | 3 | 0 | — | + | 2 | 1 fragile: the query's presence check compared by row position (a renamed WSG slipped through) | 1 | 0 | yes | + + - Enumeration of the mechanism's reach in this diff, each site guarded: + - the pool ↔ observations join (uniqueness and model-species guards); + - the query presence check, keyed by WSG; + - the driver presence check, keyed by WSG; + - the validator df ↔ its own presence (intersection and self fallback); + - the resolved WSG set, the union of both bundles'; + - stamps, "none" when empty. + - Proven with scratch bundles, each stopping with the named cause: CH<-BT, a blanked MORR presence, a MORR→MORQ rename, and the driver on a mismatched presence. `default` still runs clean. + - `candidates.csv` differs from the committed copy by at most 1.7e-16 relative (1 ulp) between identical runs. This is pre-existing: a float `sum()` in the availability SQL (findings table; issue drafted). +- Phase 4 final, from committed `ba9de76`: the validator baseline (default vs bcfishpass, 55 + 59 WSGs, knowledge @ 508bf44) reproduces all 6 CSVs byte-identically, and the presence guard passes on the real pair. The #284 evidence is refreshed: ledger step 3 and the stamp (clean, `pooling:` line). `candidates.csv` was restored to its committed bytes because it differed only by 1-ulp float noise. Full suite: 2135 pass; 3 fail, all tunnel-down in untouched files. diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-hazelton-round1.md b/planning/archive/2026-09-issue-290-species-pooling/review-hazelton-round1.md new file mode 100644 index 00000000..16f5516c --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-hazelton-round1.md @@ -0,0 +1,54 @@ +# Review — commit 773672e (Hazelton split + obs_year_max), round 1 + +## Findings + +- **[severity: bug]** data-raw/species_pooling_evidence.R:165-231 (with `keep_dv$S3_pre1995` / + `S4_hazelton_pre1995` at :193-201) — the reimplementation cannot reproduce the producer for the + year-limited scenarios, so the new "must match for every scenario" check will likely `stop()` + for S3 and S4. It is the "two lists agree on a key" mechanism with the order of operations + reversed: + - The producer applies the year limit **per record, before** deduplication + (`t_obs` LEFT JOIN year condition, then `o7` groups by `obs_species x loc`, keeps the lowest + `observation_key`, and ORs `is_spawn`/`is_rear` across the group; + query_habitat_thresholds_obs.R:143-150, 256-262). + - The reimplementation applies the year to S0's **already-deduplicated** rows: `seg0$yr` is the + year of the one surviving record per location (the lowest key), and its `is_spawn`/`is_rear` + are the OR over **all** records there, post-1995 ones included. + - So a location with DV records on both sides of 1995 is (a) kept by the producer via its + pre-1995 record but dropped by the reimplementation whenever the surviving S0 record is + post-1995 or undated, which changes `rear_n` and the rear quantiles; and (b) counted as + spawning by the reimplementation when only a post-1995 record carried the spawn flag, which + changes `spawn_n` and the spawn quantiles. + - Measured read-only against docker fwapg (bcfishobs DV, not Releases, match A/B, Fraser / + Mackenzie / Columbia WSGs persisted in `fresh_default`, loc = blue_line_key x round(m), + lowest key by `COLLATE "C"` like `dplyr::arrange`): 10 locations straddle 1995; at **5** the + surviving record is post-1995/undated and there is no BT record at the same location to hold + it in `BT_any_dv`, and at **2** the spawn flag comes only from a post-1995 record. Exclusions, + presence, attachment and accessibility filters come after this, so some may drop out, but the + check has 7 independent chances to fire. + - Effect: the running regeneration stops at "reimplementation disagrees with the producer for + S3_pre1995" (loud, not silent), and if a mismatch happened to cancel, `scenarios.csv`'s S3/S4 + rows would still be the reimplementation's numbers, not the producer's. Since every scenario + now runs through the producer, the S3/S4 metrics can be read from its own `candidates.csv`, + or the reimplementation restricted to the scenarios with no year limit (S0-S2, BT_only). + - Not the year boundary: `yr < 1995` vs `extract(year) <= 1994` agree on integers, and the + future-year-to-NA rule (:72) and SQL both exclude 2080/9990 from a 1994 limit. + +## Checked, not findings + +- `R/lnk_species_pooling.R`: tie check on `paste(pool, obs_year_max)` treats NA consistently; + `.lnk_sp_year()` handles readr's all-empty logical column, doubles, quoted strings and blanks; + self rows never collide with pooled rows (`grid$target != grid$obs`); scope names are validated + case-insensitively against `wsg_regions.csv`, so a tracker/lookup name mismatch errors. +- A custom tracker **without** `obs_year_max` (a tibble from `lnk_load_overrides()`) makes + `p$obs_year_max %||% ...` (:288) emit "Unknown or uninitialised column: `obs_year_max`". Result + is correct (NULL, then no limit); it is only a warning, noted in case anything runs with + `options(warn = 2)`. +- `R/lnk_habitat_validate.R`: spec `unique()` then `anyDuplicated(obs_species)` correctly refuses + two limits for one obs species and collapses the self row; the year join sits in the JOIN (an + undated record fails `NULL <= y`, as intended); the missing-`observation_date` guard runs before + the query; the validator dedups after the SQL filter, so it has no analogue of the finding above. + Both test files pass (51 and 120, 0 warnings). +- `data-raw/wsg_regions.R`: `colClasses = "character"` keeps `""` as `""`, so the `xor()` guard is + sound; list-vs-prefix and list-vs-list overlaps error; unknown and empty list entries error. +- `config.yaml` checksum for `species_pooling.csv` matches the file (sha256 9c42964e...). diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-p3-round1.md b/planning/archive/2026-09-issue-290-species-pooling/review-p3-round1.md new file mode 100644 index 00000000..0c942cc6 --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-p3-round1.md @@ -0,0 +1,77 @@ +# Review — Phase 3 staged diff, round 1 (#290) + +Scope: R/lnk_habitat_validate.R, tests/testthat/test-lnk_habitat_validate.R, +data-raw/habitat_validate.R, data-raw/query_habitat_thresholds_obs.R (context: +R/lnk_species_pooling.R). Validator test file run under NOT_CRAN=true against +local docker fwapg: FAIL 0 | PASS 113. No blocker found. Three findings, all +low severity: two are the "two lists agree on a key" mechanism, latent today, +and one is a stamp that can misreport. + +## Findings + +- **[fragile]** data-raw/query_habitat_thresholds_obs.R:94-101. The + one-target guard runs *after* the self rows are dropped, so it only checks + pooled rows against each other. Say a tracker row pools one model species + into the other in some WSG (for example `CH <- BT`, or a group row that + expands to it). The `(W, BT)` pair then appears once and the guard passes. + But `coalesce(pl.species_code, o.species_code)` relabels every BT record in + W as CH, so it silently stops being BT evidence. The validator counts such a + record for both species, so the two consumers would disagree without + saying so. The comment says the guard makes sure each record is assigned to + one species, but it does not stop a record leaving its own species. This is + latent: default's tracker pools only DV into BT, and the script's species + are fixed at CH and BT. The fix is to also refuse any + `pool$obs_species %in% species`. + +- **[fragile]** data-raw/habitat_validate.R:216-235 and + data-raw/query_habitat_thresholds_obs.R:87-93. The pooling table comes from + the **pooling bundle's** `wsg_species_presence`. `lnk_species_pooling()` + emits no row for a WSG where that bundle marks the model species absent. + The consumer then filters on a **different** presence table: the scored + bundle's in the validator, and `cfg` ("default") at step 4 in the query + script. Suppose the scored bundle marks BT present in a WSG where the + pooling bundle marks it absent. `.lnk_hv_spec()` then maps BT to itself + only there, so DV is dropped with no error. In the driver, the + same-observations assertion (line ~368) catches this only on *shared* WSGs. + A WSG scored by one bundle only narrows silently. In the query script, with + `--pooling=`, those DV rows fall out at step 3 instead of step 4. It + is latent today, because I measured the default and bcfishpass presence + tables as identical (246 rows; bt, ch and dv differ in 0 WSGs). A cheap + guard would assert that the pooling bundle's presence equals each scored + bundle's (or `cfg`'s) for `species` over the aoi. + +- **[fragile]** data-raw/habitat_validate.R:237-240 and + data-raw/query_habitat_thresholds_obs.R:555-557. The stamp's rule list is + built as `paste(unique(paste0(x$species_code, "<-", x$obs_species)), + collapse = ", ")`. On zero pooled rows it returns `"<-"`, not `""`: the + `paste()` zero-length trap, which I measured (it prints `[1] "<-"`). A + tracker that pools nothing in the run's WSGs, such as a scratch bundle with + every row `pool = no`, then stamps `0 WSG x species pairs pooled (<-)` in + the driver and `pooling: X species_pooling.csv; <-` in the query script. + The query script's stamp has no count beside it, so `<-` is all a reader + sees. This is minor, but the stamp is the provenance record. Guard it with + `if (nrow(pooled) == 0L) "none" else ...`. + +## Checked and clean + +- A data frame passes `is.list()` in the `stopifnot`. The data-frame branch + in `.lnk_hv_species_obs()` runs first and returns before the list checks. + The list-form checks moved there with the same logic, and zero-row data + frames normalise without error. +- `c(list(...), args_pool)` keeps the data frame as a single `species_obs` + argument, and an empty `args_pool` leaves the default in place. +- The mixed positional `%1$s` / `%2$s` placeholders and the `%%` escape in the + query `sprintf` are correct, and no other `%` sits in that SQL string. The + IN-lists are quoted with `dbQuoteString`. An empty `species` would give + `IN ()`, which is a loud SQL error rather than a silent one. +- `t_pool` is written with RPostgres's default `row.names = FALSE`. A + zero-row `pool` creates typed text columns, and the LEFT JOIN still works. +- `lnk_config(...)$files$species_pooling` resolves to default's file for + `default_tuned`, which inherits it, so the sha256 in the stamp is taken over + the right file. +- `--pooling=bcfishpass` (which has no tracker) and `--pooling=` (empty) both + fail loud. +- Dropping the `'DV' -> 'BT'` `CASE` changes nothing downstream. Unpooled DV + records now carry `species_code = 'DV'`, but they are removed at step 3 + (`dv_ok` FALSE) before any `species_code` test. `BT_spawn_dv` and + `BT_rear_dv` select by `obs_species`. diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-p3-round2.md b/planning/archive/2026-09-issue-290-species-pooling/review-p3-round2.md new file mode 100644 index 00000000..bea1c67f --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-p3-round2.md @@ -0,0 +1,54 @@ +# Review — #290 phase 3, round 2 (staged diff) + +Scope: the round-1 fixes plus the rest of the staged diff (R/lnk_habitat_validate.R, +data-raw/habitat_validate.R, data-raw/query_habitat_thresholds_obs.R, tests). +Test file `test-lnk_habitat_validate.R` run against docker fwapg with NOT_CRAN=true: +113 pass / 0 fail / 0 skip. + +## Findings + +- **[fragile]** data-raw/query_habitat_thresholds_obs.R:112-127 (`presence_cols()`): + the round-1 presence-equality assert **drops the key it sorts on**. + `p[] <- lapply(p, ...)` turns `watershed_group_code` into a logical too, so the code + removes the column, and the tables are compared **by row position** after sorting. So + two presence tables with the same row count and the same CH/BT flag pattern in sort + order compare `identical()` even when their WSG codes differ. That is the named + mechanism, one axis over from the fix: the flags are checked but the key is not. + `lnk_species_pooling(loaded, aoi = presence$watershed_group_code, ...)` then finds no + pooling-presence row for the cfg WSG. It returns nothing for that WSG, so its DV + records get `dv_ok = FALSE` and are dropped at ledger step 3. Nothing fails. + + Repro (scratch copy, nothing in the repo edited): + `scratchpad/probe_cols.R`. Take the default bundle's loaded presence and change + `MORR` to `MORQ`, which sorts into the same slot. Then: + - `presence_cols` still reports `identical: TRUE`. + - The pooling table has 0 MORR rows, against 3 from the clean table. + - The same happens for `MORS`. + + Fix: compare the key too. Convert only the species columns and keep + `toupper(trimws(watershed_group_code))` as a column. Or key the comparison with + `match()` over cfg's WSGs, the way the driver's `presence_flags(p, w)` already does. + The driver's version is keyed, so it does not have this hole. + +## Checked and clean + +- Driver `presence_flags()`: keyed on `w` via `match()`. A WSG missing from one table + gives NA -> FALSE, and that differs from a "t" in the other table, so it stops. A WSG + missing from both is FALSE on both sides. This matches `lnk_species_pooling()` and + `.lnk_hv_spec()`, which both return nothing for it. A species column missing from one + table fails loudly ("undefined columns"). An all-empty column read by read.csv + (logical NA) reads as FALSE, as it does in `.lnk_wsg_species_present()`. + default and bcfishpass differ only in `gr` (LARL), so `--bundles=default:…,bcfishpass:…` + with CH,BT passes, as probed. +- Query one-target guard and model-into-model guard: both run on the non-self rows. + A group row such as `CH <- CHAR` trips the duplicate guard or the model-species guard. + The `LEFT JOIN t_pool` cannot fan out once `(wsg, obs_species)` is unique. `sprintf` has + the `%%` escaped on the only LIKE, and the positional `%1$s`/`%2$s` are correct. +- Zero pooled rows: both stamps say "none". A zero-row `t_pool` writes and joins fine. +- `.lnk_hv_species_obs()`: the data-frame branch is tested before the list checks. A + zero-row frame, a tibble or factor columns normalise correctly, and NA or empty codes + are rejected before the `nzchar` test. +- `default_tuned` (extends) resolves `species_pooling` to the parent's file. `digest` is + in DESCRIPTION. +- The `$` partial-match risk on `files$species_pooling` / `loaded$species_pooling`: no + bundle has a key with that prefix. diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-plan.md b/planning/archive/2026-09-issue-290-species-pooling/review-plan.md new file mode 100644 index 00000000..8903ed9f --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-plan.md @@ -0,0 +1,32 @@ +# Plan review (#290), Plan agent, 2026-09-26 + +The agent is read-only, so its reply was transcribed here. Triage is in the right-hand column. + +| id | finding | triage | +|---|---|---| +| B1 | `obs_ledger.csv` step 3 is province-wide; the DV row goes 8888 → 6138 (Skeena 3228, Fraser 1294, Mackenzie 1044, Columbia 572; 2750 coastal/northern drop) | Adopted as the acceptance: every CSV identical except that ledger row = 6138 (independently predicted here before the review arrived) | +| B2 | `stamp.txt` embeds the date and SHA; PNGs not guaranteed stable | Adopted: stamp excluded, PNGs compared visually | +| B3 | a data.frame passes `is.list()`, so `species_obs` silently maps species to themselves | Fix: branch on `is.data.frame()` first and check the columns | +| G1 | the validator's data-frame semantics: own presence ∩ df; missing (wsg, sp) → self; dedupe | Adopted | +| G2 | resolve over the union of both bundles' WSGs | Already done in the driver | +| G3 | stamp which pooling was applied | Adopted (stamp line); no `summary.csv` column, to keep the byte-identity check | +| G4 | `--pooling` defaulting to the first bundle is a trap | Adopted: default is the first bundle that declares a tracker; stamped | +| G5 | the query script cannot aim at a scratch bundle | Adopted: `--pooling=` | +| G6 | one target per observation | Already asserted in the query script | +| G7 | `wsg_regions.csv` is outside `config_hash` | Adopted: hash it by a fixed name when the bundle declares `species_pooling` | +| G8 | dictionary tests must loop over declaring bundles only | Already done | +| G9 | provenance wording; a checksum bump on every tracker edit | Files live at the bundle root, not `overrides/`; the README row notes the bump | +| G10 | three meanings of "no tracker" | Chosen: the resolver without a tracker = no pooling; the driver falls back to the validator's list default only when no bundle declares one. #290's body gets updated | +| G11 | FISS absence taxa still globally pooled | Out of scope (#284 step 5 plan); covered WSGs are all in pooled regions | +| G12 | the #284 logs README states the method | Adopted | +| O1 | tick Phase 1 | Done in `c76274f` | +| O2 | DB matches the committed stamps; no persist during verification | Noted | +| A1 | DV×BT contact records sit mostly in pooled regions; LFRA, CHWK as `wsg` candidates | Recorded in research | +| A2 | LFRA outlet 100 while its Boundary Bay streams are 900; one sub-region column | Documented | +| A3 | known species = presence columns; bcfishobs `SA`, `C`, `BT/DV` are not poolable | Documented | +| A5 | target-group vs obs-group tie at equal rank; identical duplicates accepted | Documented | +| S1 | `lnk_presence()`'s hard-coded groups are a different concept | Out of scope; a follow-up issue is drafted in the final report | +| S2 | the validator's list default is still a global literal | Noted for later deprecation | +| AC1 | the baseline is 55 + 59 WSGs, not 5 | Adopted: full re-run with knowledge @ 508bf44 if available | +| AC2 | the negative check reaches 9 Skeena WSGs; ledger → 2910 | Adopted | +| AC3 | duplicated Validation line | Fixed | diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-round1.md b/planning/archive/2026-09-issue-290-species-pooling/review-round1.md new file mode 100644 index 00000000..87c9304a --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-round1.md @@ -0,0 +1,24 @@ +# Code-check review, round 1: `lnk_species_pooling()` (#290, commit 2 staged diff) + +Reviewer: subagent, 2026-09-26. The tree was not modified; probes ran in R through `pkgload::load_all()` with scripts in the session scratchpad. + +## Findings + +- **[fragile]** R/lnk_species_pooling.R:71 and the `lapply(aoi, ...)` at :90. `aoi` is normalised but never de-duplicated, so a repeated or case-variant WSG gives a repeated block of rows. Measured: `aoi = c("MORR", "MORR", "morr"), species = "BT"` returned 6 rows, BT<-BT three times and BT<-DV three times, where 2 were expected. The output is meant to be joined against observations by the validator and drivers in the next commit. A duplicated pooling row fans that join out and double-counts evidence without raising anything. `species` does not have this problem because `intersect()` de-duplicates it. Fix: either `aoi <- unique(norm(aoi))` or stop on `anyDuplicated(norm(aoi))`. + +- **[fragile]** R/lnk_species_pooling.R:94 (`present <- intersect(species, ...)`). A model species that is not a known species code, such as a typo like `"BTT"` or a code missing from the presence columns, is silently dropped. Measured: `species = "BTT"` returns a 0-row frame, which looks exactly like "absent from this WSG". `known_species` is already computed at :83, and the tracker side already fails loud on unknown codes (`expand()`, :231). Fix: `stop()` on `setdiff(species, known_species)`, which makes the two sides consistent. + +- **[fragile]** R/lnk_species_pooling.R:96 (`regions[regions$watershed_group_code == w, ][1, ]`) and :92 (`presence[... == w, ]` then `prow[1, ]`). Logical indexing with an NA key produces an all-NA row in position order. With a `regions` frame that has an NA `watershed_group_code` row ahead of the real one, `[1, ]` picks the NA row, `reg$region` becomes NA, and region rules silently stop applying. Measured: `regions = data.frame(watershed_group_code = c(NA, "W1"), region = c("South", "North"))` with a `North` pooling row gave W1 only its self row. The shipped `wsg_regions.csv` has no NA or duplicate codes (verified), so this bites only on a caller-supplied `regions` or a future edit to the lookup. The code also never checks that `regions` has the `region` / `subregion` columns or a unique code column. Fix: `which()` instead of the logical index, plus a uniqueness/NA check on `regions$watershed_group_code`. + +## Checked and fine + +- read.csv coercion: `pool = TRUE` is caught ("pool must be yes or no"). A scope of `NA` read as NA is caught ("empty scope"). All-empty subregion columns and `na.strings = ""` on the lookup behave. Empty or whitespace cells are caught per column. +- Zero-row tracker and groups, a one-row tracker (`mapply` path), and no pooled rows surviving: all give correctly typed empty or self-only frames. +- Group expansion that gives the same pair from two rows: it resolves deterministically to the lowest rule number, and a tie that disagrees on pool errors. Overlapping groups, and group codes that clash with species codes or with nested groups, are rejected. +- Output order and rownames are deterministic. The keys are upper-case ASCII codes, so locale collation does not change the order. +- Provenance: `lnk_config_verify()` is clean for `default` and for `default_tuned`, which inherits via `extends:`. The config, config_verify, stamp, load, log, load_overrides, dictionaries and species_pooling test files all pass, and `data-raw/audit_configs.R` exits 0. Adding a `files:` entry changes `default`'s config_hash. That is expected for a changed bundle and breaks no pinned test. +- Dictionary `consumed_by` line refs (205/211/217/238/239) point at the lines that read those columns. + +## Note, not a defect + +`default_extrabreaks` and `default_rearbreaks` are standalone (`extends: ~`) copies of `default` and do not declare the tracker, so under those bundles nothing is pooled. That matches the documented no-tracker fallback. It does mean a validator run on them will score BT without DV evidence while `default` / `default_tuned` pool it. Worth deciding on purpose before the consumers land. diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-round2.md b/planning/archive/2026-09-issue-290-species-pooling/review-round2.md new file mode 100644 index 00000000..b4fffeec --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-round2.md @@ -0,0 +1,72 @@ +# Code-check round 2 — staged diff for #290 (lnk_species_pooling + config hash) + +Reviewer scope: staged diff only (unstaged data-raw/ and research/ edits excluded). + +## Findings + +- **[fragile]** `inst/extdata/configs/dictionary_species_pooling.csv:2-6` and + `inst/extdata/configs/dictionary_species_groups.csv:2-3` — every `consumed_by` + file:line ref is stale. The round-1 fixes pushed the code down and the dictionaries were + not updated. Measured against the staged `R/lnk_species_pooling.R` (the staged copy and + the working tree match): + + | column | dictionary says | line it names | actual line | + |---|---|---|---| + | species_pooling.species_code | 258 | `stop("species_pooling names '"...` | 264 (`t_code <- up(p$species_code[i])`) | + | species_pooling.species_obs | 259 | the stop message | 265 (`o_code <- up(p$species_obs[i])`) | + | species_pooling.scope_level | 225 | `bad <- which(is.na(v) ...` | 231 (`level <- tolower(trimws(p$scope_level))`) | + | species_pooling.pool | 231 | the scope_level line | 237 (`pool <- tolower(trimws(p$pool))`) | + | species_pooling.scope | 237 | the pool line | 243 (`key <- up(p$scope)`) | + | species_groups.group_code / species_code | 171 | a lone `}` | 182 / 183 | + + Round 1 accepted the file:line convention itself, but these refs are wrong. That matters + because CLAUDE.md presents `consumed_by` as machine-verified (24/24), and three of the + refs point at a different column's parse line, which misleads anyone tracing a column. + No test or audit checks these refs, so nothing will catch the drift. + +- **[fragile]** `tests/testthat/test-lnk_species_pooling.R` (last block, "the shipped + default bundle resolves over every region") — both assertions on `pooled` pass when it + has zero rows: `expect_false(anyNA(character(0)))` and `expect_true(all(logical(0)))`. + So if `lnk_load_overrides()` stopped surfacing `species_pooling` (a key rename, a failed + read), the default bundle would pool nothing and this test would stay green. Today the + shipped bundle gives 129 pooled rows (Fraser 52, Mackenzie 49, Skeena 12, Columbia 9, + Kootenay 7), so the test does exercise something. Only the guard is vacuous. + +## Checked and clean + +- **Config hash is host-independent.** The regions file is named by the fixed string + `link:wsg_regions.csv` and digested by content. `system.file()` resolves to `inst/` under + load_all and to the installed copy under R CMD check, with identical bytes. + `wsg_regions.csv` is git-tracked and not in `.Rbuildignore`. The hash moves only for + bundles that declare `species_pooling`: `default` and `default_tuned` (which inherits + it). `bcfishpass`, `default_extrabreaks` and `default_rearbreaks` are unchanged. The + `default` hash moves anyway because two new files are declared, so a changed hash + against pre-#290 log rows is expected, not a regression. +- **The mocked test is valid.** `local_mocked_bindings()` with no `.package` targets the + link namespace, and `.lnk_config_hash()` looks `.lnk_wsg_regions_path` up there, so the + mock is seen. The test fails if the mock did not take, because the edit goes to the + tempfile only. The repo already uses the same pattern (test-lnk_access.R, + test-lnk_pipeline_load.R), and it does not use `.package`, so the testthat >= 3.0.0 pin + is fine for it. +- **The round-1 fixes hold.** + - `aoi` and `species` are de-duplicated after normalising. + - An unknown species errors. It is checked against the presence *columns*, independent of + which WSGs have presence rows. + - Row selection uses `which()`, and more than one presence row errors. + - An NA `region` in a caller frame produces NA rows in `hit`, but + `hit$target %in% present` drops them, so no all-NA row reaches the output. + - A WSG absent from presence yields no rows. That matches `lnk_pipeline_species()`, + which returns `character(0)` for an absent AOI. +- **Zero-length and recycling traps.** + - `self` is built only when `present` is non-empty. + - The pooled frame uses `rep(w, nrow(won))`. + - `data.frame(grid, ...)` is built only when `nrow(grid) > 0`. + - The empty-output schema matches the populated one. +- **Provenance and loading.** + - `lnk_config_verify("default")` reports no drift or missing file for the two new + provenance entries. + - The `source: link (hand-authored...)` form matches `dimensions.csv` and + `parameters_fresh.csv`, and `sync_bcfishpass_csvs.R` filters on the exact smnorris URL, + so it ignores these entries. + - The loaded tracker comes back all-character, with `pool` as "yes"/"no". +- **Tests.** The pooling, log and dictionaries test files pass under `NOT_CRAN=true`. diff --git a/planning/archive/2026-09-issue-290-species-pooling/review-round3.md b/planning/archive/2026-09-issue-290-species-pooling/review-round3.md new file mode 100644 index 00000000..570dcab0 --- /dev/null +++ b/planning/archive/2026-09-issue-290-species-pooling/review-round3.md @@ -0,0 +1,74 @@ +# Review round 3 — #290 staged diff (lnk_species_pooling + hash + dictionaries) + +Scope: staged diff only. Ran the three affected test files (all green), `lnk_config_verify("default")` +(new checksums match), and probes/mutations on a copy under the scratchpad. No repo file was edited +other than this one. + +## The mechanism + +All five earlier findings share one assumption: **two independently maintained lists agree on a +key, and a disagreement between them narrows the result silently instead of failing.** The key +was a WSG code (aoi vs presence rows vs the regions frame), a species code (the `species` argument +vs presence columns), or a line number (dictionary `consumed_by` vs the code). Each time, the +disagreement went through a filter-shaped operation — `intersect()`, `==` inside `[`, `[1, ]`, a +filtered subset — whose "no match" output (zero rows, an NA row, a duplicate row, a stale line) +looks the same as a legitimate "nothing applies". The fixes all turn one disagreement into an +error or an assertion. R2's line-ref drift is the same thing with a slower fuse: the two lists +matched when they were written, and nothing re-checked them once the code moved. + +## Findings + +- **[severity: fragile]** tests/testthat/test-dictionaries.R:236 (the new + "consumed_by refs land on their column" test): `grepl(d$column[i], line, fixed = TRUE)` is a + **substring** match. Short column names are substrings of other identifiers on nearby lines: + `scope` is inside `scope_level`, `pool` is inside `species_pooling`, and `group_code` and + `species_code` both appear in roxygen and error-message text. So a stale ref that lands on the + wrong column's line still passes. Proven on a copy: I pointed the `scope` ref at line 231 + (`level <- tolower(trimws(p$scope_level))`) and the test **passed**. A separate mutation on + `species_code` did fail, so the guard is partial rather than dead. + Stale shifts within ±15 lines that it still accepts: + - `scope`: 4 shifts, 2 of them onto `scope_level` lines. + - `pool`: 5 shifts, 3 of them onto `species_pooling ...` error strings. + - `group_code`: 3 shifts, one onto a roxygen comment. + - `species_code` (groups): 2 shifts. + - `scope_level`: 1 shift. + + This is the same mechanism again: the guard for "two lists agree" compares them loosely enough + that a disagreement still reads as agreement. A token match fixes it, e.g. + `grepl(sprintf("(\\$|\")%s(\\b|\")", col), line)`, or `(? subregion > region); + 2. then taxon specificity (a row naming both sides as species beats a row naming a group); + 3. any tie left with a different `pool` errors. +- **The resolver contains no species or group literal.** Tests use synthetic codes (`AAA`, `BBB`, group `GRP`) so none of them can pass by accident on BT/DV. +- **Group codes are validated:** a group code may not collide with a species code, and groups do not nest. + +## Decisions (gate) + +- **`wsg_regions.csv` is package-level** (`inst/extdata/`), one copy, because it is geography. Bundles declare only `species_pooling.csv`, the biological tracker. +- **The resolver is exported as `lnk_species_pooling()`**, because #236's access override will consume it too. +- **Resolution rule:** the most specific row wins (wsg > subregion > region). Anything unlisted is not pooled. A species always counts as itself, and the model species must still be present in the WSG (`wsg_species_presence`), as today. +- **Fallback:** a bundle without the tracker keeps today's behaviour (the validator's list default). Only `default` declares it, and `default_tuned` inherits it. `bcfishpass`, `default_extrabreaks` and `default_rearbreaks` are unchanged. +- **Seed:** `BT, DV, region` for Fraser, Mackenzie, Skeena and Columbia, plus `subregion` Kootenay, all `pool = yes`, source "operator call 2026-09-26". Kootenay is inside Columbia already; its row is there so the tracker can diverge later. + +## Phase 1: Region lookup +- [x] `data-raw/wsg_regions_defs.csv`, hand-curated: `level, name, wscode_prefix`, holding 18 region rows and the Kootenay sub-region row. The coastal and cross-border names are drafted from their member WSGs and marked as drafts in the generator header. +- [x] `data-raw/wsg_regions.R`, which reads fresh's `wsg_outlet.csv` and the defs, then assigns region by top code and sub-region by the longest matching prefix. It writes `inst/extdata/wsg_regions.csv` (`watershed_group_code, region, subregion, wscode_outlet`). + - It asserts 246 rows, every WSG with a region, and every def matched at least once. +- [x] Edit #290's body: regions are package-level (decided at this gate). + +## Phase 2: Tracker and resolver +- [x] `inst/extdata/configs/default/species_pooling.csv` (bundle root, not `overrides/`: the README defines that as shared jurisdiction facts) with the seed rows. + - Columns: `species_code, species_obs, scope_level, scope, pool, confidence, rationale, source, verified, issue`. + - Declared under `default`'s `files:`, with a provenance entry and checksum. +- [x] `inst/extdata/configs/default/overrides/species_groups.csv` (SALMON, CHAR), declared under `files:` with provenance, plus its dictionary +- [x] Tests for groups: expansion on either side, the taxon-specificity tie-break, a colliding group code errors, a nested group errors +- [x] `inst/extdata/configs/dictionary_species_pooling.csv`, a column dictionary, covered by `tests/testthat/test-dictionaries.R`. +- [x] Tests first, in `tests/testthat/test-lnk_species_pooling.R`: + - precedence (wsg > subregion > region); + - a more specific `pool = no` overrides a region's `yes`; + - unlisted means not pooled; + - the species counts as itself; + - the presence gate; + - an unknown scope, a bad `scope_level` or conflicting rows at one level error. +- [x] `R/lnk_species_pooling.R`: `lnk_species_pooling(loaded, aoi, species)` returns `watershed_group_code, species_code, obs_species, scope_level, scope`. It is species-agnostic, and its `@examples` run against the shipped files. +- [x] `lnk_config_verify(lnk_config("default"))` is clean; `default_tuned` inherits the file + +## Phase 3: Consumers +- [x] `lnk_habitat_validate()`: `species_obs` also accepts the resolver's data frame, applied per WSG; the list form and its default are unchanged. Add tests for both forms. +- [x] `data-raw/habitat_validate.R`: add `--pooling=`, defaulting to the first bundle. The driver resolves once and passes the same table to both bundles, which keeps the same-observations assertion true. A bundle without the tracker falls back to the list default. +- [x] `data-raw/query_habitat_thresholds_obs.R`: replace the hard-coded `CASE` and `dv_ok` with a join to the resolved table, pushed as a temp table. The BT-only comparison set is kept. +- [x] Update the method lines in `research/habitat_validation.md` and `research/habitat_thresholds.md` ("DV counts as BT in the regions `species_pooling.csv` lists"). + +## Phase 4: Verification +- [x] Re-run `query_habitat_thresholds_obs.R`. `data-raw/logs/habitat_thresholds_284/` must come out byte-identical to what is committed, since all 55 WSGs are in pooled regions. Any diff gets root-caused, not accepted. +- [x] Re-run `habitat_validate.R` on the #283 5-WSG check. `summary.csv` rows must be identical to the committed baseline. +- [x] Negative check with a scratch bundle that sets Skeena to `pool = no`: BULK and MORR DV records drop out of BT, and nothing else moves. This proves the resolver is wired and not bypassed. +- [x] Record the per-region pooled-WSG counts in `research/` (the tracker's state of knowledge) and link it from #290 + +## Validation + +- [x] `devtools::test()`: 2135 pass, 3 fail. The 3 are all the `:63333` bcfishpass tunnel being down (`test-lnk_db_conn.R:10`, `test-lnk_wsg_resolve.R:143`, `:154`), in files and functions this branch does not touch. +- [x] `devtools::document()` and `pkgdown::check_pkgdown()` clean +- [x] `lintr`: **not clean**, recorded as-is. + - New code adds hanging-indent `indentation_linter` style lints, the same pattern as the repo's existing backlog (67 in `test-lnk_log.R` on main). + - Plus 3 `object_usage_linter` false positives: `.lnk_presence_species_cols` and `.lnk_wsg_regions_path` are absent from the stale installed package. +- [x] `/code-check`: + - Phase 2: three rounds, ended by enumeration. + - Phase 3: two rounds, ended by enumeration, one below the skill's floor (stated in progress.md). + - Phase 1 (generator) and Phase 4 (docs and evidence): self-review and mutation tests only. +- [x] PWF checkboxes match landed work +- [ ] `/planning-archive`, then `/gh-pr-push` ("Fixes #290"); edit #284's body so step 5 is unparked + +Out of scope: the access override's `observation_species` (#236), which will consume `lnk_species_pooling()`; the FISS absence taxa in the driver (#284 step 5 plan); logging the tracker into `.log_*` (the pipeline does not consume it yet). + +## Reused +- fresh `inst/extdata/wsg_outlet.csv` (outlet codes); `lnk_config()`, `lnk_load_overrides()`, `lnk_config_verify()` +- `.lnk_hv_spec()` and `.lnk_wsg_species_present()` (`R/lnk_habitat_validate.R`), for the per-WSG shape and the presence gate +- `tests/testthat/test-dictionaries.R` (the dictionary coverage pattern) diff --git a/research/README.md b/research/README.md index ae38c544..128a7567 100644 --- a/research/README.md +++ b/research/README.md @@ -30,6 +30,7 @@ renamed. |---|---| | [`habitat_thresholds.md`](habitat_thresholds.md) | CH and BT gradient and channel-width thresholds: observation evidence, literature, and the `default_tuned` candidates | | [`habitat_validation.md`](habitat_validation.md) | Scoring a run against fish observations (`lnk_habitat_validate()`): capture, cost, miss reasons, absences; `default` vs `bcfishpass` baseline | +| [`species_pooling.md`](species_pooling.md) | Which observation species count as evidence for which model species, by region: the state of knowledge behind `species_pooling.csv` | ## Runs, scope and infrastructure diff --git a/research/habitat_thresholds.md b/research/habitat_thresholds.md index 1ad32d68..2279c984 100644 --- a/research/habitat_thresholds.md +++ b/research/habitat_thresholds.md @@ -1,6 +1,6 @@ # Habitat thresholds — CH and BT gradient and channel width -**Verified:** 2026-09-26 · **Issues:** #284 (this), #283 (the validator, [`habitat_validation.md`](habitat_validation.md)), #282 (`default_tuned`) · **Produced by:** `data-raw/query_habitat_thresholds_obs.R`, `data-raw/query_habitat_thresholds_fiss.R` → `data-raw/logs/habitat_thresholds_284/`; literature review archived with #284's PWF (`literature.md`) · **Status:** candidates set in `default_tuned`, **unscored** +**Verified:** 2026-09-27 · **Issues:** #284 (this), #290 (the pooling tracker), #283 (the validator, [`habitat_validation.md`](habitat_validation.md)), #282 (`default_tuned`) · **Produced by:** `data-raw/query_habitat_thresholds_obs.R`, `data-raw/query_habitat_thresholds_fiss.R` → `data-raw/logs/habitat_thresholds_284/`; literature review archived with #284's PWF (`literature.md`) · **Status:** candidates set in `default_tuned`, **unscored** ## Verdict @@ -36,18 +36,19 @@ of this section, with what they moved. `observation_exclusions` (`data_error | release_exclude`) and `Releases Database` records removed. The rest are restricted to the 55 WSGs persisted in `fresh_default` where `wsg_species_presence` marks the species, match types A/B, one per species × - `blue_line_key` × metre. That leaves CH 1,745 locations and BT 2,560, plus 2,822 DV - pooled with BT (5,104 BT+DV locations once shared locations are counted once). The quantiles, + `blue_line_key` × metre. That leaves CH 1,745 locations and BT 2,560, plus 1,970 DV + pooled with BT where `species_pooling.csv` pools them (4,275 BT+DV locations once shared + locations are counted once; see Change 4). The quantiles, selection ratios and floor test use the ones on accessible segments; for gradient that means accessible *and* on a stream edge or river polygon (CH 226 spawning-staged and 497 - rearing-staged; BT+DV 4,764, BT alone 2,443). The bridge share and the `user_habitat_classification` + rearing-staged; BT+DV 3,988, BT alone 2,443). The bridge share and the `user_habitat_classification` overlap use all of them. `obs_ledger.csv` has every step. - **The segment the model tests.** The pipeline breaks streams at every retained observation, so 99 % of points sit within 1 m of a break. The segment *starting* at the point (the upstream one) is used. A 100 m FWA window gradient from geometry Z checks it independently of link's breaks. The two agree for CH spawning (P95 0.044 vs 0.042) but not everywhere. **CH rearing is 0.060 vs 0.062, and the window value would - snap to 0.0649 and flip that verdict to "change".** Pooled BT+DV is 0.135 vs 0.149; the + snap to 0.0649 and flip that verdict to "change".** Pooled BT+DV is 0.131 vs 0.145; the window value would snap to 0.1449, one step above the candidate. The segment gradient is used because it is what the model tests; the window values are why the scoring questions below keep the higher values in play. @@ -87,10 +88,22 @@ of this section, with what they moved. enough not to separate for this. So BT+DV is the primary BT evidence, and DV is no longer capped at low confidence. BT records alone are kept beside it in `candidates.csv` (`evidence_role = "comparison: BT records only"`) and `bridge_bt.csv` - (`set = BT_any`), so the evidence exists both ways. Pooling moved one value: BT rearing gradient 0.1249 → 0.1349. It also + (`set = BT_any`), so the evidence exists both ways. Pooling moved one value: BT rearing gradient 0.1249 → 0.1349. Since #290 the pooling is data, not code (`species_pooling.csv`): the region rule alone moved no number here, and the Hazelton split that followed is Change 4. It also lifted the low-confidence cap on DV staged records, which is why the BT spawning gradient and width rows below became literature vetoes instead of weak evidence. +- **Change 4 (link#290): DV is pooled with BT only where `species_pooling.csv` says so, and + the Skeena is split at Hazelton.** The naming history shows interior DV is a legacy name + but Skeena DV is a current one ([`species_pooling.md`](species_pooling.md)). So DV counts + as BT in the Fraser, Mackenzie and Columbia, and in the Skeena only above Hazelton + (BULK, MORR, KISP, BABL, BABR, SUST, MSKE, USKE). 852 DV records in LSKE, KLUM, LKEL and + ZYMO drop out. + - **BT rearing gradient:** P95 0.1348 → 0.1309, n 4,764 → 3,988. The rule still gives + **0.1349**, but it now clears the 0.13 line that would drop it to 0.1249 by only + 0.0009. + - **BT spawning width:** P5 1.16 → 1.12 m, rule 1.2 → 1.1 m. It is vetoed either way. + - No verdict moved. + ## Chinook (CH) **Spawning gradient — keep 0.0449.** The P95 of 226 spawning observations is 0.044, @@ -158,14 +171,14 @@ polygon where gradient is tested. | Evidence | n | P95 | Rule | |---|---|---|---| -| BT+DV pooled (primary) | 4,764 | 0.135 | 0.1349 | +| BT+DV pooled (primary) | 3,988 | 0.131 | 0.1349 | | BT records only (comparison) | 2,443 | 0.125 | 0.1249 | -| DV rearing-staged | 991 | 0.158 | — | +| DV rearing-staged | 587 | 0.154 | — | -- Pooled selection is ~0.7 from 5 to 12 %, dropping to 0.42 at 12–15 % and 0.26 at +- Pooled selection is ~0.7 from 5 to 12 %, dropping to 0.41 at 12–15 % and 0.24 at 15–20 %. -- DV rearing records are selected (ratio ≥ 1) from 1 % to 12 % (1.37 at 10.5–12 %), and - drop to 0.70 at 12–15 %. +- DV rearing records are selected (ratio ≥ 1) from 6 % to 12 % (1.43 at 10.5–12 %), and + drop to 0.72 at 12–15 %. - The literature agrees: Isaak et al. (2015) trim natal habitat at 15 % (< 1 % of occurrences above it), with a maximum habitat slope of 14.7 %; Porter et al. (2008) found BT CPUE highest in the steeper Thompson streams. @@ -184,8 +197,8 @@ The literature vetoes it: redd sites are < 1 % (McPhail & Murray, via Ford et al and spawning reaches are "relatively low gradient" (McPhail & Baxter 1996). No source gives a numeric reach-scale maximum. -**Spawning width — keep 2 m (medium).** DV spawning P5 is 1.2 m (n 53), and the rule -says 1.2. The literature vetoes it: the source for 2 m in spawners, Hagen et al. (2015, +**Spawning width — keep 2 m (medium).** DV spawning P5 is 1.12 m (n 40), and the rule +says 1.1. The literature vetoes it: the source for 2 m in spawners, Hagen et al. (2015, §4.1.2, Parsnip and Pack), gives it as **wetted** width, the limit of use by migratory spawners. Wetted runs narrower than the channel width the model tests, so 2 m of channel width is, if anything, generous. Resident BT do spawn in smaller streams (McPhail & @@ -193,7 +206,7 @@ Baxter 1996), but no source gives a number for them, so this stays open for scor **Rearing width — keep 1.5 m (medium).** -- Pooled P5 is 1.48 m (BT alone 1.91 m), and pooled selection is ≥ 1 from 3 m. +- Pooled P5 is 1.47 m (BT alone 1.91 m), and pooled selection is ≥ 1 from 3 m. - FISS presence sites have a P5 of 1.9 m, with none below 1.5. - Juvenile occurrence is "very unlikely" below 2 m wetted width (Dunham & Rieman 1999, as cited in Dunham & Chandler 2001, pp. 3 and 26). @@ -202,8 +215,8 @@ The pooled P5 sits on the current value; nothing argues for a lower one. **`spawn_gradient_min` — keep 0.** DV spawning selection is 2.2 in the flattest bin. -**`cluster_bridge_gradient` — keep 0.05.** Only 1.7 % of pooled BT+DV observations (85 -of 5,104; BT alone 1.2 %, 31 of 2,560) sit on accessible segments that pass the rearing +**`cluster_bridge_gradient` — keep 0.05.** Only 1.5 % of pooled BT+DV observations (62 +of 4,275; BT alone 1.2 %, 31 of 2,560) sit on accessible segments that pass the rearing predicate yet end up `rearing = FALSE` (`bridge_bt.csv`). What the bridge does, from fresh's `.frs_cluster_both()`: a rearing cluster is kept if diff --git a/research/habitat_validation.md b/research/habitat_validation.md index e81ab5d5..d10d8466 100644 --- a/research/habitat_validation.md +++ b/research/habitat_validation.md @@ -1,6 +1,6 @@ # Habitat validation against fish observations -**Verified:** 2026-09-26 · **Issues:** #283 (this), #284 (step 5 scores with it), #203 (full-key joins), fresh#218 · **Produced by:** `lnk_habitat_validate()` via `data-raw/habitat_validate.R` → `data-raw/logs/habitat_validate_283/` (link @ `0c19e0a`) · **Status:** baseline only; `default_tuned` not yet scored +**Verified:** 2026-09-27 · **Issues:** #283 (this), #284 (step 5 scores with it), #290 (pooling as data), #203 (full-key joins), fresh#218 · **Produced by:** `lnk_habitat_validate()` via `data-raw/habitat_validate.R` → `data-raw/logs/habitat_validate_283/` (link @ `0c19e0a`) · **Status:** baseline only; `default_tuned` not yet scored ## What it measures @@ -24,8 +24,12 @@ that both retained the same observations. - **Observations:** `bcfishobs.observations` with `observation_exclusions` (`data_error | release_exclude`) and every `Releases Database` record removed. Species - must be present in the WSG per `wsg_species_presence`. DV records count as BT where BT - is present (the #284 pooling). Match types are A/B only (stream, within 100 m). One + must be present in the WSG per `wsg_species_presence`. Which observation species count + as each model species comes from the pooling bundle's `species_pooling.csv` via + `lnk_species_pooling()` ([`species_pooling.md`](species_pooling.md), #290): for + `default`, DV counts as BT in the Fraser, Mackenzie, Skeena and Columbia, where BT is + present. The driver resolves it once, from the first bundle that declares a tracker (or + `--pooling=`), and applies it to both bundles; `stamp.txt` records which. Match types are A/B only (stream, within 100 m). One location per species × `blue_line_key` × metre, which is staged if any record there is. - **Other sources:** `observations` takes any table or data frame that has `species_code`, `watershed_group_code`, `blue_line_key` and @@ -85,16 +89,16 @@ that both retained the same observations. | CH | spawn | 245 | default | 98.4 | 88.2 | 91.4 | 50.0 (n 8) | | | | CH | rear | 510 | bcfishpass | 76.5 | 84.1 | 84.1 | | | | | CH | rear | 510 | default | 77.5 | 84.7 | 84.7 | | | | -| BT | any | 4,600 | bcfishpass | 64.5 | 81.7 | 81.7 | 64.5 | 46,512 | 76,872 | -| BT | any | 4,600 | default | 65.4 | 81.1 | 82.8 | 65.4 | 47,099 | 75,280 | -| BT | rear | 1,047 | bcfishpass | 41.8 | 63.6 | 63.6 | | | | -| BT | rear | 1,047 | default | 44.3 | 65.9 | 66.5 | | | | -| BT | spawn | 81 | bcfishpass | 45.7 | 70.4 | 70.4 | | | | -| BT | spawn | 81 | default | 45.7 | 70.4 | 72.8 | | | | +| BT | any | 3,771 | bcfishpass | 66.3 | 83.6 | 83.6 | 66.3 | 46,512 | 76,872 | +| BT | any | 3,771 | default | 66.9 | 82.3 | 84.1 | 66.9 | 47,099 | 75,280 | +| BT | rear | 622 | bcfishpass | 40.7 | 64.5 | 64.5 | | | | +| BT | rear | 622 | default | 42.6 | 65.6 | 66.1 | | | | +| BT | spawn | 64 | bcfishpass | 43.8 | 71.9 | 71.9 | | | | +| BT | spawn | 64 | default | 43.8 | 70.3 | 73.4 | | | | BT has no `user_habitat_classification` rows, so its outside-UHC share is its share. -- **BT:** `default` captures slightly more rear-staged locations (66.5 vs 63.6 % on any +- **BT:** `default` captures slightly more rear-staged locations (66.1 vs 64.5 % on any rearing) with 1,592 km *less* rearing. That is the edge-type rule (bcfishpass's BT `rear: []` tests any edge), not the thresholds, which are the same in both bundles. - **CH:** `default` models 6,032 km (28 %) more rearing for 1.1 points more stream @@ -108,18 +112,29 @@ BT has no `user_habitat_classification` rows, so its outside-UHC share is its sh modelled spawning, 678–686 on rearing. Most FISS sampling is juvenile electrofishing, which says little about BT spawning. Not decision-grade. -**Misses** (`misses.csv`, `default` over its 55 WSGs, any stage): BT 344 `fails_gradient`, 160 -`width_null`, 126 `fails_width`, 100 `fails_gradient_and_width`, 89 `post_predicate` -(clustering or gating), 42 `not_accessible`. CH 51 `fails_gradient`, 47 `width_null`, +**Misses** (`misses.csv`, `default` over its 55 WSGs, any stage): BT 268 `fails_gradient`, 130 +`width_null`, 103 `fails_width`, 83 `fails_gradient_and_width`, 63 `post_predicate` +(clustering or gating), 26 `not_accessible`. CH 51 `fails_gradient`, 47 `width_null`, 27 `not_accessible`. For BT the gradient maximum is the binding threshold, which is -what #284 moved. NULL width is the second: 160 locations, which is consistent with +what #284 moved. NULL width is the second: 130 locations, which is consistent with #284's finding that 49 % of accessible BT stream length has no width. `misses_binned.csv` carries the gradient × width bins for each. ## Reconciliation with #284 -At buffer 0 on its own 55 WSGs, `fresh_default` retains **5,104** BT+DV and **1,745** CH -locations, exactly #284's pooled counts. The filters are the same code path. +At buffer 0 on its own 55 WSGs, `fresh_default` retains **4,275** BT+DV and **1,745** CH +locations, exactly #284's pooled counts under the Hazelton split. The filters are the same +code path. + +**Under the #290 tracker.** The driver takes DV→BT pooling from `default`'s +`species_pooling.csv`, resolved once and applied to both bundles. +- **The region rule alone** reproduced the pre-#290 CSVs byte for byte, because every WSG + in both schemas is in a pooled region. +- **The Hazelton split then moved BT.** 852 DV records in LSKE, KLUM, LKEL and ZYMO no + longer count, so the shared BT set falls from 4,600 to 3,771 locations, and the + rear-staged set from 1,047 to 622. The BT rows above are the re-run (knowledge @ + 508bf44, same database); the CH rows are unchanged, byte for byte. +- [`species_pooling.md`](species_pooling.md) has the scenarios. ## Using it for #284 step 5 diff --git a/research/species_pooling.md b/research/species_pooling.md new file mode 100644 index 00000000..28dee5b8 --- /dev/null +++ b/research/species_pooling.md @@ -0,0 +1,204 @@ +# Species pooling: which observations count as which species + +**Verified:** 2026-09-27 · **Issues:** #290 (this), #236 (access override, which should read the same table), #284 (the BT evidence it defines) · **Produced by:** `lnk_species_pooling()` over `configs/default/species_pooling.csv` and `inst/extdata/wsg_regions.csv` (`data-raw/wsg_regions.R`); counts below from local fwapg, bcfishobs 373,050 rows; the naming history and scenario sensitivity from `data-raw/species_pooling_evidence.R` → `data-raw/logs/species_pooling_290/` · **Status:** DV → BT pooled in the Fraser, Mackenzie, Columbia/Kootenay and the Skeena above Hazelton; `obs_year_max` available, unused + +## What it is + +An observation record is evidence for a model species. Which records count is a biological +position, and it varies by place and time: a Dolly Varden record from the interior Fraser +before the 1990s is usually a bull trout recorded under the old name, while one on the +coast, or anywhere in the Skeena today, is at least as likely a Dolly Varden. So the rule is data, one dated and sourced row per decision, and the state of +knowledge accrues as rows. + +- **`species_pooling.csv`** (bundle root; `default` declares it, `default_tuned` inherits + it): `species_code` (the target) and `species_obs` (the evidence), each a species or a + group from `species_groups.csv`; `scope_level` (`region`, `subregion`, `wsg`) and + `scope`; `pool` (`yes` / `no`); an optional `obs_year_max` (the row pools only records + dated in or before that year; an undated record does not qualify); and the record of why (`confidence`, `rationale`, + `source`, `verified`, `issue`). Columns: `configs/dictionary_species_pooling.csv`. +- **`species_groups.csv`**: named sets (`SALMON` = CH, CM, CO, PK, SK; `CHAR` = BT, DV). + A group may not share a code with a species, and groups do not nest. Only + `lnk_species_pooling()` reads it. `lnk_presence()`'s presence groups are a separate, + pipeline-facing concept and still live in code. +- **`inst/extdata/wsg_regions.csv`** (package-level, since it is geography): each WSG's + region and sub-region. It is also hashed into the `config_hash` of any bundle declaring + a tracker, because a region reassignment changes what pools. + +**Resolution**, per WSG, target and evidence species: the most specific scope wins (wsg > +subregion > region); at equal scope the row naming fewer groups wins; rows still tied +must agree on `pool` and `obs_year_max`, or the call errors. Two identical rows are accepted. A row whose +target is a group and a row whose evidence is a group tie at the same rank, so they must +agree. Anything unlisted is **not pooled**, a species always counts as itself, and the +target must be present in the WSG (`wsg_species_presence`). + +The known species are the `wsg_species_presence` columns. bcfishobs codes that are not +columns there (`SA` salmon general, `C`, the mixed `BT/DV`) cannot be pooled, and a group +named like one of them would not be caught by the collision check. + +## Regions + +The region is the first segment of each group's **outlet** `wscode_ltree` (fresh +`inst/extdata/wsg_outlet.csv`, fresh ≥ v0.33.0; built with 0.34.0 installed), not of +its shallowest code, because a group can touch two drainages. LFRA's outlet is `100`, so +it is Fraser, although its Boundary Bay streams are coded `900`. The thresholds query's +segment-level `region` column calls those `900`: a small, known inconsistency. A +sub-region is the longest whole-segment wscode prefix listed in +`data-raw/wsg_regions_defs.csv`. There is one sub-region column, so nested sub-regions +are not expressible. Coastal and cross-border region names are drafts, marked in that +file. + +## State of knowledge, 2026-09-27 + +| Region | WSGs | BT present | DV present | DV → BT pooled | +|---|---|---|---|---| +| Fraser | 68 | 52 | 54 | 52 | +| Mackenzie | 65 | 49 | 39 | 49 | +| Columbia (incl. Kootenay, 7) | 17 | 16 | 15 | 16 | +| Skeena (above Hazelton, 8) | 12 | 12 | 12 | **8** | +| Stikine | 16 | 8 | 13 | — | +| Central Mainland Coast | 15 | 3 | 15 | — | +| East Vancouver Island | 9 | 2 | 9 | — | +| Yukon | 8 | 1 | 3 | — | +| Nass | 7 | 7 | 7 | — | +| South Mainland Coast | 7 | 4 | 7 | — | +| West Vancouver Island | 7 | 1 | 7 | — | +| Outer North Coast Islands | 6 | 0 | 4 | — | +| Taku | 4 | 1 | 4 | — | +| Haida Gwaii | 2 | 0 | 2 | — | +| Alsek, Skagit, Unuk | 1 each | 0, 1, 1 | 1 each | — | + +DV pools into BT in **125 WSGs**. It is not pooled in **33 BT-present WSGs**: +- the 4 Skeena groups below Hazelton (KLUM, LKEL, LSKE, ZYMO); +- the 29 in unlisted regions: BARR, BRKS, COWN, HOMA, INKR, ISKR, JERV, KINR, KITR, KLAR, + KLIN, LBIR, LDEN, LISR, LNAR, MSTR, NASR, PARK, SKGT, SPAT, SQAM, SWIR, TAHR, TAYR, TUYR, + UBIR, UDEN, UNAR and UNUR. + +Before #290 every one of those pooled, because the rule was "wherever BT is present". +- **The region rule** moved no #284 or #283 number, since all their WSGs are in pooled + regions. +- **The Hazelton split** (2026-09-27) did. It dropped 852 DV records in the four lower + Skeena groups. + +**The seed is an operator call** (2026-09-26): inland, DV records are bull trout recorded +under the other name. The Skeena rows were revised on 2026-09-27, also by operator call, +after the naming history below. The Skeena region row is `no`; the sub-region `Skeena +above Hazelton` (listed membership in `data-raw/wsg_regions_defs.csv`) is `yes`. McPhail and Carveth (1993) support treating inland char records as +unreliable to species: juveniles "can not be reliably identified except biochemically", +and the two hybridize where they co-occur (#236 has the passage). Confidence is `medium` +on every row. + +**Where the next rows are likely to go.** Mixed records in bcfishobs (`BT/DV`, `DV/BT`, +`DVxBT`) mark the contact zones: +- Skeena 48 (KLUM 26, SUST 15, MORR 4); +- Mackenzie 25 (FIRE 19, UOMI 5); +- Fraser 20 (LFRA 18); +- the Skagit (SKGT 6), and 3 each in KITR, HOMA and LBIR, which are unlisted regions. + +The lower Fraser tributaries (LFRA, CHWK) are coastal-influenced, and are the first +candidates for a `wsg` row, either way. The unlisted coastal and northern BT-present WSGs +(Nass and Stikine above all) are where a `pool = yes` row would need evidence rather than +an assumption. + +## How DV and BT are recorded through time + +The DV share of all BT and DV records (`decade_region.csv`; releases removed; 24,337 records, 692 undated), with the record count in brackets: + +| | ≤ 1960s | 1970s | 1980s | 1990s | 2000s | 2010s | +|---|---|---|---|---|---|---| +| Columbia | 89 % (36) | 87 % (474) | 67 % (177) | **1 %** (1,384) | 0 % (743) | 0 % (1,631) | +| Fraser | 93 % (46) | 86 % (310) | 89 % (478) | 37 % (1,089) | 14 % (605) | 5 % (1,081) | +| Mackenzie | 94 % (16) | 74 % (453) | 57 % (348) | 23 % (1,016) | 9 % (1,456) | 7 % (1,562) | +| **Skeena** | 100 % (24) | 100 % (346) | 100 % (141) | **91 %** (1,742) | **86 %** (450) | **98 %** (447) | +| Coast and north | 100 % (56) | 100 % (554) | 100 % (764) | 96 % (2,247) | 89 % (1,030) | 83 % (2,461) | + +**In the interior the name changed.** +- Char were mostly recorded as DV until the 1980s, and the name flips to BT through the 1990s, consistent with bull trout being recognised as a separate species and recording practice catching up. +- The streams that carry a DV record show what happened after (`dv_streams_resampled.csv`; a later BT record counts first, whenever it came): + + | Region | Streams with a DV record | Later recorded as BT | Not sampled after 1995 | Sampled after 1995, DV only | + |---|---|---|---|---| + | Columbia | 163 | 74 % | 26 % | 0 % | + | Fraser | 547 | 27 % | 51 % | 23 % | + | Mackenzie | 329 | 34 % | 45 % | 21 % | + | Skeena | 1,180 | **1 %** | 14 % | **85 %** | + | Coast and north | 2,356 | 2 % | 35 % | 63 % | + +- In the Fraser and Mackenzie about half the DV streams were fished in the inventory era and never again, so their only char evidence is an old "DV" that is almost certainly a bull trout. Where they were re-sampled, it often came back BT (74 % in the Columbia, where no DV stream was re-sampled without a BT record). Pooling is well founded there. + +## The Skeena is a different case + +- Skeena DV is **not** a legacy name. It is still 86 % or more of char records in every decade, the 2010s included. +- 85 % of Skeena DV streams were sampled again after 1995 and still recorded only DV. Only 1 % were ever later recorded as BT. +- Whatever these fish are (true Dolly Varden, a local recording convention, or both), the naming-change argument that justifies interior pooling does not cover them. Pooling the Skeena is a judgement, and it carries the most weight: 1,929 of the 2,822 DV records the first seed pooled into the #284 evidence are Skeena records, mostly from the 1990s on. The adopted split keeps the 1,077 above Hazelton and drops the 852 below. + +## Sensitivity: what pooling does to the #284 BT evidence + +Each scenario is a scratch tracker run through the #284 producer (`scenarios.csv`, +`data-raw/species_pooling_evidence.R`): +- **S0:** the first seed, with the whole Skeena pooled. +- **S1: the adopted tracker.** The Skeena pools only above Hazelton, where the Bulkley + joins it (BULK, MORR, KISP, BABL, BABR, SUST, MSKE, USKE), and LSKE, KLUM, LKEL and ZYMO + are kept apart. +- **S2:** no Skeena pooling. +- **S3:** no Skeena, and interior rows limited to records before 1995 (`obs_year_max` + 1994). +- **S4:** S1 with the interior rows limited to records before 1995. + +A reimplementation of the rule over the S0 evidence reproduces the producer exactly for +S0–S2, and supplies the BT-only row. + +It cannot stand in for S3 or S4. The producer applies the year to each record before it +deduplicates locations, so an earlier draft of this table, which took S3 from the +reimplementation, was slightly off: 537 DV records against the true 543, and a P95 of +0.1203 against 0.1202. Review caught it. + +| | DV records pooled | Rearing n | Rearing gradient P95 | Rule gives | Rearing width P5 | Spawning n (DV staged) | Bridge loss | +|---|---|---|---|---|---|---|---| +| S0 whole Skeena | 2,822 | 4,764 | 0.1348 | **0.1349** | 1.48 m | 76 | 1.7 % | +| **S1 above Hazelton (adopted)** | 1,970 | 3,988 | 0.1309 | **0.1349** | 1.47 m | 59 | 1.5 % | +| S2 no Skeena | 893 | 3,058 | 0.1204 | **0.1249** | 1.68 m | 18 | 1.0 % | +| S3 no Skeena, interior pre-1995 | 543 | 2,829 | 0.1202 | **0.1249** | 2.07 m | 9 | 1.1 % | +| S4 above Hazelton, interior pre-1995 | 1,620 | 3,759 | 0.1310 | **0.1349** | 1.57 m | 50 | 1.5 % | +| BT records only | 0 | 2,443 | 0.1253 | **0.1249** | 1.91 m | 0 | 1.2 % (from #284's `bridge_bt.csv`) | + +- **`default_tuned`'s BT `rear_gradient_max` of 0.1349 now hangs on a thread.** + - The rule floors the P95 to the hundredth. Under the adopted split (S1) the P95 is + 0.1309, only **0.0009** above the 0.13 line where the result drops to 0.1249; S4 is + 0.0010 above it. A handful of records would flip either. + - Without the upper Skeena (S2, S3), the rule gives 0.1249, the BT-only value. + - #284 step 5 should score both values. +- **Rearing width** stays within the rule's 0.5 m keep band in every scenario except S3. + S3's 2.07 m is past it, so on that evidence the rule would tighten rearing width to + about 2.1 m. It has not been checked against the literature. +- **The staged spawning evidence** is mostly DV. Without the upper Skeena it nearly + vanishes (18 records in S2, 9 in S3). + +**Validator scores** (`validate_scenarios.csv`, `default` on `fresh_default`, BT, buffer 0). +The model is the same in every row; only the evidence changes. + +| | Any stage: n | Capture on any rearing | Rear-staged: n | Capture on any rearing | +|---|---|---|---|---| +| S0 | 5,104 | 82.4 % | 1,053 | 66.5 % | +| **S1 (adopted)** | 4,275 | 83.5 % | 628 | 66.1 % | +| S2 | 3,259 | 86.2 % | 205 | 75.6 % | +| S3 | 2,992 | 87.2 % | 2 | — | +| S4 | 4,008 | 84.1 % | 425 | 61.6 % | + +Skeena DV records sit on modelled BT rearing less often than the rest. That fits them +being partly true Dolly Varden, in smaller and steeper water than the interior bull trout +the thresholds describe. + +Most of the "rear-staged" BT evidence is DV, because bcfishobs gives BT no life stage: +- 848 of S0's 1,053 staged records are Skeena DV; +- limiting the interior to pre-1995 records leaves 2 staged records without the Skeena + (S3), too few to read. + +## What this leaves open + +- **The year column exists but is empty.** Filling the interior rows with + `obs_year_max = 1994` is S4. It keeps 0.1349, cuts the pooled evidence by 350 DV + records, and rests on the mechanism the naming history shows. +- **The Hazelton split is a judgement.** Every Skeena group above and below it is + mostly DV (72 to 100 % from 1995 on). +- **The 0.1349 vs 0.1249 question** is #284 step 5's to settle by scoring. Its margin + under the adopted tracker is 0.0009. diff --git a/tests/testthat/test-dictionaries.R b/tests/testthat/test-dictionaries.R index 97d3df1c..7e2e8b34 100644 --- a/tests/testthat/test-dictionaries.R +++ b/tests/testthat/test-dictionaries.R @@ -183,3 +183,62 @@ test_that("every bundle declares its own parameters_habitat_thresholds", { info = sprintf("bundle %s declares no parameters_habitat_thresholds", b)) } }) + +# -- dictionary_species_pooling / dictionary_species_groups (#290) ----------- + +# Only bundles that declare the file carry it; a bundle without a tracker pools +# nothing, which is the documented fallback, so absence is not a failure here. +declaring <- function(stem) { + Filter(function(b) !is.null(lnk_config(b)$files[[stem]]), bundle_names()) +} + +for (stem in c("species_pooling", "species_groups")) { + test_that(sprintf("dictionary_%s has the expected shape", stem), { + d <- dict_read(stem) + expect_true(all(c("column", "type", "group", "owner", "consumed_by", + "default_when_absent", "description", + "related") %in% names(d))) + expect_false(any(duplicated(d$column))) + expect_true(all(filled(d$column))) + expect_true(all(filled(d$description))) + expect_true(all(d$owner == "link")) + }) + + test_that(sprintf("dictionary_%s matches every declaring bundle's CSV", stem), { + d <- dict_read(stem) + bundles <- declaring(stem) + expect_gt(length(bundles), 0) + for (b in bundles) { + expect_setequal(bundle_cols(b, stem), d$column) + } + }) +} + +test_that("species_pooling / species_groups consumed_by refs land on their column", { + # Hand-maintained file:line refs drift whenever the code above them moves + # (#290 review round 2 found every one stale). Each link-side ref must point + # at a line that names its column. Source-tree only: an installed package + # has no R/ directory. + src <- testthat::test_path("..", "..", "R") + skip_if_not(dir.exists(src), "R/ source not available") + n_refs <- 0L + for (stem in c("species_pooling", "species_groups")) { + d <- dict_read(stem) + for (i in seq_len(nrow(d))) { + refs <- regmatches(d$consumed_by[i], + gregexpr("R/[A-Za-z0-9_.]+\\.R:[0-9]+", d$consumed_by[i]))[[1]] + for (ref in refs) { + n_refs <- n_refs + 1L + f <- file.path(src, basename(sub(":[0-9]+$", "", ref))) + n <- as.integer(sub("^.*:", "", ref)) + line <- readLines(f, warn = FALSE)[n] + # whole token: `scope` must not match `scope_level`, nor `pool` + # match `species_pooling` + tok <- paste0("(? %s", stem, d$column[i], line)) + } + } + } + expect_gt(n_refs, 0) +}) diff --git a/tests/testthat/test-lnk_habitat_validate.R b/tests/testthat/test-lnk_habitat_validate.R index 44e4731a..358b2d75 100644 --- a/tests/testthat/test-lnk_habitat_validate.R +++ b/tests/testthat/test-lnk_habitat_validate.R @@ -93,12 +93,43 @@ test_that(".lnk_hv_spec admits observation species only where the model species "BBBB CH CH")) }) +test_that(".lnk_hv_spec applies a per-WSG species_obs data frame (#290)", { + presence <- data.frame( + watershed_group_code = c("AAAA", "BBBB", "CCCC"), + bt = c("t", "t", ""), ch = c("t", "t", "t"), notes = "", + stringsAsFactors = FALSE) + so <- link:::.lnk_hv_species_obs(data.frame( + watershed_group_code = c("AAAA", "AAAA", "CCCC", "aaaa"), + species_code = c("BT", "BT", "BT", "bt"), + obs_species = c("BT", "DV", "DV", "dv "))) + s <- link:::.lnk_hv_spec(presence, aoi = c("AAAA", "BBBB", "CCCC"), + species = c("BT", "CH"), species_obs = so) + got <- paste(s$watershed_group_code, s$species_code, s$obs_species) + # AAAA pools (deduplicated); BBBB is unlisted, so BT is itself only; + # CCCC lists a pooling row but BT is absent there, so it yields nothing + expect_setequal(got, c("AAAA BT BT", "AAAA BT DV", "AAAA CH CH", + "BBBB BT BT", "BBBB CH CH", "CCCC CH CH")) +}) + +test_that(".lnk_hv_species_obs rejects a malformed species_obs", { + expect_error(link:::.lnk_hv_species_obs( + data.frame(watershed_group_code = "AAAA", species_code = "BT")), + "obs_species") + expect_error(link:::.lnk_hv_species_obs( + data.frame(watershed_group_code = "AAAA", species_code = "BT", + obs_species = NA)), "NA") + expect_error(link:::.lnk_hv_species_obs(list(c("BT", "DV"))), "named list") + expect_identical(link:::.lnk_hv_species_obs(list(bt = c("bt", "dv"))), + list(BT = c("BT", "DV"))) +}) + test_that(".lnk_hv_spec returns a typed empty frame when nothing is present", { presence <- data.frame(watershed_group_code = "AAAA", bt = "", stringsAsFactors = FALSE) s <- link:::.lnk_hv_spec(presence, "AAAA", "BT", list()) expect_identical(nrow(s), 0L) - expect_named(s, c("watershed_group_code", "species_code", "obs_species")) + expect_named(s, c("watershed_group_code", "species_code", "obs_species", + "obs_year_max")) }) test_that(".lnk_hv_dedup merges records at one location and ORs their stages", { @@ -306,6 +337,58 @@ test_that("species_obs values are case-insensitive", { expect_identical(v$summary$n_obs[v$summary$stage == "any"], 4L) }) +test_that("a species_obs data frame scores the same as the equivalent list", { + conn <- validate_conn() + s <- local_validate_fixture(conn) + v_list <- run_validate(conn, s, aoi = "AAAA", + species_obs = list(BT = c("BT", "DV"))) + v_df <- run_validate(conn, s, aoi = "AAAA", species_obs = data.frame( + watershed_group_code = "AAAA", species_code = "BT", obs_species = "DV")) + expect_identical(v_df$summary, v_list$summary) + v_none <- run_validate(conn, s, aoi = "AAAA", species_obs = data.frame( + watershed_group_code = character(0), species_code = character(0), + obs_species = character(0))) + # o2 is the fixture's one admissible DV record (it shares a location with + # BT record o7, so location counts cannot tell the two apart) + expect_true("o2" %in% v_df$observations$observation_key) + expect_false("o2" %in% v_none$observations$observation_key) +}) + +test_that("obs_year_max admits only pooled records dated within it (#290)", { + conn <- validate_conn() + s <- local_validate_fixture(conn) + so <- data.frame(watershed_group_code = "AAAA", species_code = "BT", + obs_species = "DV", obs_year_max = 1994L) + # the fixture has no observation_date, which a year limit needs + expect_error(run_validate(conn, s, aoi = "AAAA", species_obs = so), + "observation_date") + DBI::dbExecute(conn, sprintf( + "ALTER TABLE %s.observations ADD COLUMN observation_date date", s)) + DBI::dbExecute(conn, sprintf( + "UPDATE %s.observations SET observation_date = '1990-06-01'", s)) + v_old <- run_validate(conn, s, aoi = "AAAA", species_obs = so) + expect_true("o2" %in% v_old$observations$observation_key) + DBI::dbExecute(conn, sprintf( + "UPDATE %s.observations SET observation_date = '2005-06-01' + WHERE observation_key = 'o2'", s)) + v_new <- run_validate(conn, s, aoi = "AAAA", species_obs = so) + expect_false("o2" %in% v_new$observations$observation_key) + # an undated DV record does not meet the limit either + DBI::dbExecute(conn, sprintf( + "UPDATE %s.observations SET observation_date = NULL + WHERE observation_key = 'o2'", s)) + v_na <- run_validate(conn, s, aoi = "AAAA", species_obs = so) + expect_false("o2" %in% v_na$observations$observation_key) + # BT's own records carry no limit. o2 (DV) shares a location with BT record + # o7, so with o2 admitted the location is keyed o2 (BT;DV), and without it + # the same location is keyed o7 (BT only). + o <- function(v, k) v$observations[v$observations$observation_key == k, ] + expect_identical(o(v_old, "o2")$obs_species, "BT;DV") + expect_identical(o(v_new, "o7")$obs_species, "BT") + expect_setequal(c(setdiff(v_old$observations$observation_key, "o2"), "o7"), + v_new$observations$observation_key) +}) + test_that("observations can be a data frame from any source", { conn <- validate_conn() s <- local_validate_fixture(conn) diff --git a/tests/testthat/test-lnk_log.R b/tests/testthat/test-lnk_log.R index 82f2853a..325d4851 100644 --- a/tests/testthat/test-lnk_log.R +++ b/tests/testthat/test-lnk_log.R @@ -94,6 +94,25 @@ test_that(".lnk_config_hash changes when config.yaml pipeline$schema changes", { expect_false(identical(before, after)) }) +test_that(".lnk_config_hash moves with the region lookup only for a tracker bundle", { + # #290: a pooling tracker is scoped by the package's wsg_regions.csv, which + # sits outside the bundle, so a region edit must move the hash. + regions <- withr::local_tempfile(fileext = ".csv") + file.copy(system.file("extdata", "wsg_regions.csv", package = "link"), + regions) + local_mocked_bindings(.lnk_wsg_regions_path = function() regions) + with_tracker <- lnk_config("default") + without <- lnk_config("bcfishpass") + expect_false(is.null(with_tracker$files$species_pooling)) + expect_true(is.null(without$files$species_pooling)) + h1 <- .lnk_config_hash(with_tracker) + b1 <- .lnk_config_hash(without) + + cat("ZZZZ,Nowhere,,999\n", file = regions, append = TRUE) + expect_false(identical(h1, .lnk_config_hash(with_tracker))) + expect_identical(b1, .lnk_config_hash(without)) +}) + test_that(".lnk_config_hash tolerates a missing declared file", { dir <- local_bundle_copy("default") cfg <- lnk_config(dir) diff --git a/tests/testthat/test-lnk_species_pooling.R b/tests/testthat/test-lnk_species_pooling.R new file mode 100644 index 00000000..62ad202c --- /dev/null +++ b/tests/testthat/test-lnk_species_pooling.R @@ -0,0 +1,245 @@ +# lnk_species_pooling() (#290). Synthetic species (AAA, BBB, CCC), group +# (GRP) and geography, so no assertion can pass on the shipped BT/DV rows by +# accident: the resolver must know nothing about any real species. + +regions_fx <- data.frame( + watershed_group_code = c("W1", "W2", "W3", "W4"), + region = c("North", "North", "South", "South"), + subregion = c("Hill", NA, NA, NA), + stringsAsFactors = FALSE +) + +presence_fx <- data.frame( + watershed_group_code = c("W1", "W2", "W3", "W4"), + aaa = c("t", "t", "t", ""), + bbb = c("t", "t", "t", "t"), + ccc = c("t", "t", "t", "t"), + notes = "", + stringsAsFactors = FALSE +) + +pool_row <- function(species_code, species_obs, scope_level, scope, + pool = "yes") { + data.frame(species_code = species_code, species_obs = species_obs, + scope_level = scope_level, scope = scope, pool = pool, + stringsAsFactors = FALSE) +} + +loaded_fx <- function(pooling, groups = NULL) { + list(species_pooling = pooling, species_groups = groups, + wsg_species_presence = presence_fx) +} + +obs_for <- function(res, w, sp) { + sort(res$obs_species[res$watershed_group_code == w & res$species_code == sp]) +} + +test_that("a region row pools in every WSG of the region and nowhere else", { + res <- lnk_species_pooling( + loaded_fx(pool_row("AAA", "BBB", "region", "North")), + aoi = c("W1", "W2", "W3"), species = "AAA", regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), c("AAA", "BBB")) + expect_identical(obs_for(res, "W2", "AAA"), c("AAA", "BBB")) + expect_identical(obs_for(res, "W3", "AAA"), "AAA") +}) + +test_that("unlisted means not pooled, and a species always counts as itself", { + res <- lnk_species_pooling( + loaded_fx(pool_row("AAA", "BBB", "region", "North")), + aoi = "W3", species = c("AAA", "CCC"), regions = regions_fx) + expect_identical(obs_for(res, "W3", "AAA"), "AAA") + expect_identical(obs_for(res, "W3", "CCC"), "CCC") + expect_identical(unique(res$scope_level), "self") +}) + +test_that("the more specific scope wins: wsg over subregion over region", { + p <- rbind(pool_row("AAA", "BBB", "region", "North", "yes"), + pool_row("AAA", "BBB", "subregion", "Hill", "no"), + pool_row("AAA", "BBB", "wsg", "W1", "yes")) + res <- lnk_species_pooling(loaded_fx(p), aoi = c("W1", "W2"), + species = "AAA", regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), c("AAA", "BBB")) + expect_identical(res$scope_level[res$watershed_group_code == "W1" & + res$obs_species == "BBB"], "wsg") + expect_identical(obs_for(res, "W2", "AAA"), c("AAA", "BBB")) + + # without the wsg row, the subregion's "no" beats the region's "yes" + res2 <- lnk_species_pooling(loaded_fx(p[1:2, ]), aoi = "W1", + species = "AAA", regions = regions_fx) + expect_identical(obs_for(res2, "W1", "AAA"), "AAA") +}) + +test_that("a group expands on either side of a rule", { + g <- data.frame(group_code = c("GRP", "GRP"), species_code = c("AAA", "BBB"), + stringsAsFactors = FALSE) + # target is the group: every member admits CCC + res <- lnk_species_pooling( + loaded_fx(pool_row("GRP", "CCC", "region", "North"), g), + aoi = "W1", species = c("AAA", "BBB", "CCC"), regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), c("AAA", "CCC")) + expect_identical(obs_for(res, "W1", "BBB"), c("BBB", "CCC")) + expect_identical(obs_for(res, "W1", "CCC"), "CCC") + + # both sides the group: members pool with each other + res2 <- lnk_species_pooling( + loaded_fx(pool_row("GRP", "GRP", "region", "North"), g), + aoi = "W1", species = c("AAA", "BBB"), regions = regions_fx) + expect_identical(obs_for(res2, "W1", "AAA"), c("AAA", "BBB")) + expect_identical(obs_for(res2, "W1", "BBB"), c("AAA", "BBB")) +}) + +test_that("at equal scope, a species row beats a group row", { + g <- data.frame(group_code = c("GRP", "GRP"), species_code = c("AAA", "BBB"), + stringsAsFactors = FALSE) + p <- rbind(pool_row("GRP", "GRP", "region", "North", "yes"), + pool_row("AAA", "BBB", "region", "North", "no")) + res <- lnk_species_pooling(loaded_fx(p, g), aoi = "W1", + species = c("AAA", "BBB"), regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), "AAA") + expect_identical(obs_for(res, "W1", "BBB"), c("AAA", "BBB")) +}) + +test_that("a scope beats taxon specificity: a wsg group row beats a region species row", { + g <- data.frame(group_code = c("GRP", "GRP"), species_code = c("AAA", "BBB"), + stringsAsFactors = FALSE) + p <- rbind(pool_row("AAA", "BBB", "region", "North", "no"), + pool_row("GRP", "GRP", "wsg", "W1", "yes")) + res <- lnk_species_pooling(loaded_fx(p, g), aoi = "W1", species = "AAA", + regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), c("AAA", "BBB")) +}) + +test_that("a tie left with a different pool errors, naming both rows", { + p <- rbind(pool_row("AAA", "BBB", "region", "North", "yes"), + pool_row("AAA", "BBB", "region", "North", "no")) + expect_error( + lnk_species_pooling(loaded_fx(p), aoi = "W1", species = "AAA", + regions = regions_fx), + "conflict.*rows 1, 2") + # agreeing duplicates are not a conflict + p$pool <- "yes" + expect_no_error(lnk_species_pooling(loaded_fx(p), aoi = "W1", + species = "AAA", regions = regions_fx)) +}) + +test_that("the model species must be present in the WSG", { + res <- lnk_species_pooling( + loaded_fx(pool_row("AAA", "BBB", "region", "South")), + aoi = c("W3", "W4"), species = "AAA", regions = regions_fx) + expect_identical(obs_for(res, "W3", "AAA"), c("AAA", "BBB")) + expect_identical(obs_for(res, "W4", "AAA"), character(0)) +}) + +test_that("no tracker means no pooling, not an error", { + res <- lnk_species_pooling(loaded_fx(NULL), aoi = "W1", + species = c("AAA", "BBB"), regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), "AAA") + expect_identical(obs_for(res, "W1", "BBB"), "BBB") +}) + +test_that("bad rows fail loud", { + bad <- function(p, g = NULL, re) { + expect_error(lnk_species_pooling(loaded_fx(p, g), aoi = "W1", + species = "AAA", regions = regions_fx), + re) + } + bad(pool_row("AAA", "BBB", "basin", "North"), re = "scope_level") + bad(pool_row("AAA", "BBB", "region", "Nowhere"), re = "Nowhere") + bad(pool_row("AAA", "BBB", "wsg", "W9"), re = "W9") + bad(pool_row("AAA", "BBB", "region", "North", "maybe"), re = "pool") + bad(pool_row("AAA", "ZZZ", "region", "North"), re = "ZZZ") + bad(pool_row("AAA", NA, "region", "North"), re = "species_obs") + # a group code that is also a species code + bad(pool_row("AAA", "BBB", "region", "North"), + g = data.frame(group_code = "CCC", species_code = "AAA"), re = "CCC") + # a group inside a group + bad(pool_row("AAA", "BBB", "region", "North"), + g = data.frame(group_code = c("GRP", "GR2"), species_code = c("AAA", "GRP")), + re = "nest") + expect_error(lnk_species_pooling(loaded_fx(NULL), aoi = "W9", + species = "AAA", regions = regions_fx), + "W9") +}) + +test_that("a repeated or differently cased WSG yields its rows once", { + res <- lnk_species_pooling( + loaded_fx(pool_row("AAA", "BBB", "region", "North")), + aoi = c("W1", "W1", "w1"), species = c("AAA", "aaa"), regions = regions_fx) + expect_identical(nrow(res), 2L) +}) + +test_that("an unknown model species errors rather than reading as absent", { + expect_error(lnk_species_pooling(loaded_fx(NULL), aoi = "W1", + species = "AAX", regions = regions_fx), + "AAX") +}) + +test_that("a malformed region lookup fails loud", { + r <- rbind(regions_fx, regions_fx[1, ]) + expect_error(lnk_species_pooling(loaded_fx(NULL), aoi = "W1", + species = "AAA", regions = r), "unique") + r <- regions_fx + r$watershed_group_code[2] <- NA + expect_error(lnk_species_pooling(loaded_fx(NULL), aoi = "W1", + species = "AAA", regions = r), "NA") + expect_error(lnk_species_pooling(loaded_fx(NULL), aoi = "W1", + species = "AAA", + regions = regions_fx[c("watershed_group_code", + "region")]), + "subregion") +}) + +test_that("codes and scopes are matched case- and whitespace-insensitively", { + res <- lnk_species_pooling( + loaded_fx(pool_row(" aaa", "bbb ", "Region", " north")), + aoi = "w1", species = "aaa", regions = regions_fx) + expect_identical(obs_for(res, "W1", "AAA"), c("AAA", "BBB")) +}) + +test_that("obs_year_max is carried from the winning row, NA when empty", { + p <- rbind(pool_row("AAA", "BBB", "region", "North"), + pool_row("AAA", "BBB", "wsg", "W1")) + p$obs_year_max <- c("1994", "") + res <- lnk_species_pooling(loaded_fx(p), aoi = c("W1", "W2"), + species = "AAA", regions = regions_fx) + y <- function(w) res$obs_year_max[res$watershed_group_code == w & + res$obs_species == "BBB"] + # W1: the wsg row wins and has no limit; W2: the region row's 1994 + expect_identical(y("W1"), NA_integer_) + expect_identical(y("W2"), 1994L) + expect_true(all(is.na(res$obs_year_max[res$scope_level == "self"]))) + expect_type(res$obs_year_max, "integer") +}) + +test_that("tied rows that disagree on obs_year_max error; bad years are refused", { + p <- rbind(pool_row("AAA", "BBB", "region", "North"), + pool_row("AAA", "BBB", "region", "North")) + p$obs_year_max <- c("1994", "2000") + expect_error(lnk_species_pooling(loaded_fx(p), aoi = "W1", species = "AAA", + regions = regions_fx), "obs_year_max") + for (bad in c("199x", "1994.5", "3000")) { + q <- pool_row("AAA", "BBB", "region", "North") + q$obs_year_max <- bad + expect_error(lnk_species_pooling(loaded_fx(q), aoi = "W1", species = "AAA", + regions = regions_fx), "obs_year_max") + } +}) + +test_that("the shipped default bundle resolves over every region", { + cfg <- lnk_config("default") + loaded <- suppressWarnings(lnk_load_overrides(cfg)) + regions <- utils::read.csv(system.file("extdata", "wsg_regions.csv", + package = "link"), + stringsAsFactors = FALSE) + res <- lnk_species_pooling(loaded, aoi = regions$watershed_group_code, + species = unique(toupper( + loaded$parameters_fresh$species_code))) + expect_true(all(c("watershed_group_code", "species_code", "obs_species", + "scope_level", "scope", "rule", "obs_year_max") %in% + names(res))) + # every row that pools is traced to a tracker row + pooled <- res[res$scope_level != "self", ] + expect_gt(nrow(pooled), 0) + expect_false(anyNA(pooled$rule)) + expect_true(all(pooled$species_code != pooled$obs_species)) +})