diff --git a/R/lnk_pipeline_break.R b/R/lnk_pipeline_break.R index 267162b..0ae294f 100644 --- a/R/lnk_pipeline_break.R +++ b/R/lnk_pipeline_break.R @@ -164,11 +164,7 @@ lnk_pipeline_break <- function(conn, aoi, cfg, loaded, schema, row <- wsg_sp[wsg_sp$watershed_group_code == aoi, ] if (nrow(row) == 0) return(character(0)) - spp_cols <- c("bt", "ch", "cm", "co", "ct", "dv", - "pk", "rb", "sk", "st", "wct") - present <- vapply(spp_cols, - function(x) identical(row[[x]], "t"), logical(1)) - sp <- toupper(spp_cols[present]) + sp <- .lnk_wsg_species_present(row) # bcfishfobs records cutthroat as CT, CCT, ACT, or CT/RB — all # resolve to the same species in wsg_species_presence. diff --git a/R/lnk_pipeline_species.R b/R/lnk_pipeline_species.R index c640b79..54338de 100644 --- a/R/lnk_pipeline_species.R +++ b/R/lnk_pipeline_species.R @@ -60,11 +60,5 @@ lnk_pipeline_species <- function(cfg, loaded, aoi) { row <- wsg_sp[wsg_sp$watershed_group_code == aoi, ] if (nrow(row) == 0) return(character(0)) - spp_cols <- c("bt", "ch", "cm", "co", "ct", "dv", - "pk", "rb", "sk", "st", "wct") - present <- vapply(spp_cols, - function(x) identical(row[[x]], "t"), logical(1)) - aoi_species <- toupper(spp_cols[present]) - - intersect(configured, aoi_species) + intersect(configured, .lnk_wsg_species_present(row)) } diff --git a/R/utils.R b/R/utils.R index d043b77..4586521 100644 --- a/R/utils.R +++ b/R/utils.R @@ -120,3 +120,21 @@ on.exit(DBI::dbClearResult(res)) DBI::dbColumnInfo(res)$name } + + +#' Species codes flagged present in a wsg_species_presence row. +#' +#' Treats every column except `watershed_group_code` and `notes` as a +#' species presence flag. Returns uppercased codes for cells equal to +#' the literal string `"t"`. +#' +#' Driven by the CSV header rather than a hardcoded vector so adding a +#' new species column (e.g. `ko`) propagates to every callsite without +#' a code edit. See link#106. +#' @noRd +.lnk_wsg_species_present <- function(row) { + spp_cols <- setdiff(names(row), c("watershed_group_code", "notes")) + present <- vapply(spp_cols, + function(x) identical(row[[x]], "t"), logical(1)) + toupper(spp_cols[present]) +} diff --git a/inst/extdata/configs/bcfishpass/overrides/wsg_species_presence.csv b/inst/extdata/configs/bcfishpass/overrides/wsg_species_presence.csv index d4320ec..b109839 100644 --- a/inst/extdata/configs/bcfishpass/overrides/wsg_species_presence.csv +++ b/inst/extdata/configs/bcfishpass/overrides/wsg_species_presence.csv @@ -1,247 +1,247 @@ -watershed_group_code,bt,ch,cm,co,ct,dv,gr,pk,rb,sk,st,wct,notes -ADMS,t,t,,t,t,t,,,t,t,,, -ALBN,,t,t,t,t,t,,,t,t,t,, -ATLL,,,,,,t,t,,t,,,, -ATNA,,t,t,t,t,t,,t,t,t,t,, -BABL,t,t,,t,t,t,,,t,t,t,, -BABR,t,t,,t,t,t,,,t,t,t,, -BARR,t,t,t,,t,t,,,t,t,,, -BBAR,t,t,,t,t,t,,,t,t,,, -BEAV,t,,,,,t,t,,,,,,Mackenzie basin -BELA,,t,t,t,t,t,,t,t,t,t,, -BIGC,t,,,,,,,,t,,,, -BLAR,t,t,,,,t,,,t,,,, -BLUR,t,,,,,t,t,,,,,,Mackenzie basin -BONP,t,t,,t,t,,,t,t,,t,, -BOWR,t,t,,t,,t,,,t,t,,, -BRID,,,,,t,,,,t,,,,Falls 20807 -BRKS,t,t,t,t,t,t,,t,t,t,t,, -BULK,t,t,,t,t,t,,t,t,t,t,, -BULL,t,,,,t,t,t,,t,,,t, -CAMB,,t,t,t,t,t,t,t,t,t,t,, -CANO,t,,,,,t,,,t,,,,Columbia basin -CARP,t,,,,,t,,,t,,,,Mackenzie basin -CARR,t,t,,t,,t,,,t,t,,, -CHES,t,t,,,,t,,,t,t,,, -CHIL,,t,,,,t,,,t,,,, -CHIR,t,,,,,t,,,t,t,t,, -CHUK,,,,,,t,,,,,,,No target species observations -CHWK,t,t,t,t,t,t,,t,t,t,t,, -CLAY,,t,t,t,t,t,,,t,t,t,, -CLRH,t,,,,t,t,,,t,,,t, -CLWR,,t,,t,,t,,,t,,,, -COAL,t,,,,,t,t,,,,,,Mackenzie basin -COLR,t,,,,t,t,,,t,,,t, -COMX,,t,t,t,t,t,,t,t,t,t,, -COTR,t,t,,t,,t,,t,t,,,, -COWN,t,t,t,t,t,t,,t,t,,t,, -CRKD,t,,,,,t,,,t,,,,Mackenzie basin -CRYL,,,,,,,t,,,,,,Mackenzie basin -DEAD,t,t,,t,,,,t,t,t,t,, -DEAL,t,,,,,t,t,,,,,,Mackenzie basin -DEAR,t,,,,,t,t,,,,,,Mackenzie basin -DOGC,t,t,,t,t,t,,,t,t,,, -DRIR,t,t,,,,t,,,t,t,,, -DUNC,t,,,,t,,,,t,,,t, -DUNE,t,,,,,,t,,t,,,,Mackenzie basin -ELKR,t,,,,t,t,t,,t,,,t, -EUCH,,t,,,,t,,,t,,,, -EUCL,t,t,,,,t,,,t,,,, -FINA,t,,,,,t,t,,t,,,,Mackenzie basin -FINL,t,,,,,t,t,,t,,,,Mackenzie basin -FIRE,t,,,,,t,t,,t,,,,Mackenzie basin -FONT,t,,,,,,t,,,,,,Mackenzie basin -FOXR,t,,,,,t,t,,t,,,,Mackenzie basin -FRAN,t,t,,,t,t,,,t,t,,, -FRCN,t,t,t,t,t,t,,t,t,t,t,, -FROG,t,,,,,t,t,,,,,,Mackenzie basin -GATA,t,,,,,,t,,,,,,Mackenzie basin -GLAR,,t,,,,,t,,,,,, -GOLD,,t,t,t,t,t,,,t,t,t,, -GRAI,,t,t,t,t,t,,t,t,t,t,, -GRNL,,,,,,,,,t,,,,No target species observations -GUIC,t,t,,t,t,t,,,t,,t,, -HARR,t,t,t,t,t,t,,t,t,t,t,, -HAYR,,,,,,,,,,,,,Mackenzie basin -HERR,t,t,,,,t,,,t,,,, -HOLB,,,t,t,t,t,,t,t,,t,, -HOMA,t,t,t,t,t,t,,,t,,t,, -HORS,t,t,,t,,t,,,t,t,,, -INGR,t,,,,,t,t,,t,,,,Mackenzie basin -INKR,t,t,,t,t,t,t,,t,t,t,, -ISKR,t,,,,,t,,,t,,,,No target species observations -JENR,,t,,,t,,t,,,,,, -JERV,t,t,t,t,t,t,,t,t,,t,, -KAHN,,,,,,,t,,,,,,Mackenzie basin -KAKC,,,,,,,,,t,,,,Not accessible to target species -KCHL,,,,,,,,,,,,,Mackenzie basin -KEEC,,,,t,,,,,,,,, -KETL,,,,,t,,,,t,,,t, -KHOR,t,,,,t,t,,,t,,,t, -KHTZ,,t,t,t,t,t,,t,t,t,t,, -KINR,t,t,,t,,t,,,t,t,,, -KISK,t,,,,,,t,,t,,,,Mackenzie basin -KISP,t,t,t,t,t,t,,t,t,t,t,, -KITL,,t,t,t,t,t,,t,t,t,t,, -KITR,t,t,t,t,t,t,,t,t,t,t,, -KLAR,t,,,,,t,t,,t,,,,No target species observations -KLIN,t,t,t,t,t,t,,,t,t,t,, -KLUM,t,t,t,t,t,t,,t,t,t,t,, -KNIG,,t,t,t,t,t,,t,t,t,t,, -KOTL,t,,,,t,t,,,t,,,t, -KOTR,t,,,,t,t,,,t,,,t, -KSHR,,t,t,t,t,t,,t,t,,t,, -KTSU,,t,,t,t,,,t,,t,t,,updated based on PSE spawning data -KUMR,,,t,t,t,t,,t,t,t,,, -KUSR,,,,,,t,t,,,,,,No target species observations -LARL,t,,,,t,t,t,,t,,,t, -LBIR,t,t,,t,,t,,,t,,t,, -LBTN,t,,,,,,t,,t,,,,Mackenzie basin -LCHL,t,t,,t,,t,,,t,,,, -LCHR,t,t,,,,t,,,t,,t,, -LDEN,t,t,,t,t,t,,,t,t,t,, -LEUT,,,,,,,,,t,,,,Kenny Dam -LFRA,t,t,t,t,t,t,,t,t,t,t,, -LFRT,,,,,,,t,,t,,,,Mackenzie basin -LHAF,t,,,,,,t,,t,,,,Mackenzie basin -LIAR,t,,,,,t,t,,t,,,,Mackenzie basin -LILL,t,t,t,t,t,t,,,t,t,t,, -LISR,t,t,t,t,t,t,t,,t,t,t,, -LKEC,,,,,,t,t,,,,,,Mackenzie basin -LKEL,t,t,t,t,t,t,,t,t,,t,, -LMUS,t,,,,,t,t,,t,,,,Mackenzie basin -LNAR,t,t,t,t,t,t,,t,t,,t,, -LNIC,t,t,,t,t,t,,t,t,,t,, -LNRS,,,,,t,,,,t,,,, -LNTH,t,t,,t,t,t,,t,t,t,,, -LOMI,t,,,,,t,t,,t,,,,Mackenzie basin -LPCE,t,,,,,,t,,t,,,,Mackenzie basin -LPET,,,,,,,t,,,,,,Mackenzie basin -LPRO,t,,,,,t,t,,t,,,,Mackenzie basin -LRAN,t,,,,,t,t,,,,,,Mackenzie basin -LRDO,,,t,t,t,t,,t,t,t,t,, -LSAL,,t,,,,t,,,t,,,, -LSIK,,,,,,,t,,,,,,Mackenzie basin -LSKE,t,t,t,t,t,t,,t,t,t,t,, -LSTR,,t,,t,t,t,,,t,t,,, -LTRE,t,t,,,t,,,,t,t,,, -MAHD,t,t,,,,t,,,t,,,, -MBNK,,,,t,t,t,,,,,,, -MCGR,t,t,,,,t,,,t,,,, -MDEA,t,,,,,t,t,,t,,,,Mackenzie basin -MESC,,t,,,,,,,t,,,, -MESI,t,,,,,t,t,,t,,,,Mackenzie basin -MFRA,,t,,,,,,,t,,,, -MFRT,,,,,,,t,,,,,,Mackenzie basin -MIDR,t,t,,,,t,,,t,t,,, -MILL,,,,,,,t,,,,,,Mackenzie basin -MMUS,t,,,,,t,t,,t,,,,Mackenzie basin -MORI,,,t,t,t,t,,t,t,t,t,, -MORK,t,t,,,,t,,,t,,,, -MORR,t,t,,t,t,t,,t,t,t,t,, -MPRO,t,,,,,t,t,,t,,,,Mackenzie basin -MSKE,t,t,,t,t,t,t,,t,t,t,, -MSTR,t,,,,,t,t,,t,,t,, -MURR,t,,,,t,t,t,,t,,,,Mackenzie basin -MURT,,,,,,,,,t,,,, -MUSK,,,,,,t,,,t,,,, -NAHR,,t,,,,t,t,,t,,,, -NAKR,,t,,t,,t,t,,t,t,,, -NARC,t,t,,,,t,,t,t,,,, -NASC,,,t,t,t,t,,t,t,t,t,, -NASR,t,t,,t,t,t,,,t,t,t,, -NATR,t,,,,,t,t,,t,,,,Mackenzie basin -NAZR,,t,,,,,,,t,,,, -NBNK,,,,t,t,t,,,,t,,, -NECL,,,t,t,t,t,,t,t,t,t,, -NECR,t,t,,t,,t,,,t,t,,, -NEVI,,,t,t,t,t,,t,t,t,t,, -NICL,,t,,t,,,,,t,,,, -NIEL,,t,t,t,t,t,,t,t,t,t,, -NIMP,,t,t,t,t,t,,t,t,t,t,, -OKAN,t,t,,,t,t,,,t,t,,, -OSPK,t,,,,,t,t,,t,,,,Mackenzie basin -OWIK,,t,t,t,t,t,,t,t,t,t,, -PARA,t,,,,,t,t,,t,,,,Mackenzie basin -PARK,t,t,t,t,t,t,,t,t,,t,, -PARS,t,,,,,t,t,,t,,,,Mackenzie basin -PCEA,t,,,,,t,t,,t,,,,Mackenzie basin -PINE,t,,,,,t,t,,t,,,,Mackenzie basin -PITR,,,,,,t,,,t,,,,No target species observations -PORI,,,t,t,t,t,,t,t,,t,, -QUES,t,t,,t,,t,,t,t,t,,, -REVL,t,,,,t,t,,,t,,,t, -SAHD,,,,,,,t,,,,,,Mackenzie basin -SAHT,,,,,,,,,,,,,Mackenzie basin -SAJR,,,,t,,,,t,t,t,,, -SALM,,t,t,t,t,t,,t,t,,t,, -SALR,,t,,,,t,,,t,,,, -SANJ,,t,t,t,t,t,,t,t,t,t,, -SETN,t,t,t,t,t,t,,t,t,t,t,, -SEYM,,t,t,t,t,t,,t,t,,t,, -SHEK,,,,,,,,,,,,,Mackenzie basin -SHER,,t,,t,t,t,,,t,,t,, -SHUL,t,t,,t,t,t,,t,t,t,,t, -SIML,t,,,,t,t,,,t,,,,No target species observations -SKGT,t,,,,t,t,,,t,,,, -SLOC,t,,,,t,t,,,t,,,t, -SMAR,t,,,,t,t,,,t,,,t, -SMOK,t,,,,t,t,t,,t,,,,Mackenzie basin -SPAT,t,,,,,t,t,,t,,,,No target species observations -SQAM,t,t,t,t,t,t,,t,t,t,t,, -STHM,t,t,,t,t,t,,t,t,t,,, -STIR,,t,,t,t,t,t,,t,t,,, -STUL,,t,,,t,t,,,t,t,,, -STUR,t,t,,,,t,,,t,t,,, -SUST,t,t,t,t,,t,,,t,t,t,, -SWIR,t,t,,,,t,t,,,,,, -TABR,t,t,,,,t,,,t,,,, -TAHR,t,,,,t,t,,,t,t,t,, -TAHS,,t,t,t,t,t,,t,t,t,t,, -TAKL,t,t,,,,t,,,t,t,,, -TASR,t,t,,,,t,,,t,t,,, -TATR,,t,,,,t,t,,t,t,,, -TAYR,t,,,,,t,,,t,,t,, -TESR,,t,,,,,t,,t,,,, -THOM,t,t,,t,t,t,,t,t,t,t,, -TOAD,t,,,,,t,t,,,,,,Mackenzie basin -TOBA,,t,t,t,t,t,,t,t,t,t,, -TOOD,t,,,,,t,t,,t,,,,Mackenzie basin -TSAY,,t,t,t,t,t,,t,t,,t,, -TSEA,,,,,,,t,,,,,,Mackenzie basin -TSIT,,t,t,t,t,t,,t,t,,t,, -TURN,t,,,,,t,t,,t,,,,Mackenzie basin -TUTR,,,,,,,t,,,,,, -TUYR,t,,,,,,t,,,,,,Blockage near mouth of Tuya River -TWAC,t,t,,,,t,,,t,,,, -UARL,t,,,,t,t,,,t,,,t, -UBIR,t,t,,t,,t,,,t,,,, -UBTN,t,,,,,,t,,t,,,,Mackenzie basin -UCHR,t,t,,,,,,,t,,t,, -UDEN,t,t,t,t,,t,,t,t,t,t,,salmon/steelhead added as test for Ulkatcho -UEUT,t,,,,t,t,,,t,,,, -UFRA,t,t,,,,t,,,t,,,, -UFRT,,,,,,,t,,,,,,Mackenzie basin -UHAF,t,,,,,,t,,t,,,,Mackenzie basin -UISR,,,,,,t,,,t,,,,Forrest Kerr Generating Station -UJER,,t,,,,,t,,,,,, -UKEC,t,,,,,t,t,,t,,,,Mackenzie basin -ULRD,t,,,,,t,t,,t,,,,Mackenzie basin -UMUS,t,,,,,t,t,,t,,,,Mackenzie basin -UNAR,t,t,,,t,t,,,t,,t,, -UNRS,t,,,,,t,,,t,,,, -UNTH,t,t,,t,t,t,,,t,,,, -UNUR,t,,,t,t,t,,,t,,,, -UOMI,t,,,,,t,t,,t,,,,Mackenzie basin -UPCE,t,,,,t,t,t,,t,,,,Mackenzie basin -UPET,,,,,,,t,,t,,,,Mackenzie basin -UPRO,t,,,,,,t,,t,,,,Mackenzie basin -USHU,t,t,,t,t,t,,t,t,t,,t, -USIK,t,,,,,,t,,t,,,,Mackenzie basin -USKE,t,t,,t,,t,,,t,t,t,, -USTK,,,,,t,t,t,,t,,t,, -UTRE,t,,,,,t,,,t,t,,, -VICT,,t,t,t,t,t,,,t,,t,, -WILL,t,t,,t,t,t,,,t,,,, -WORC,,t,t,t,t,t,,t,t,,t,, -ZYMO,t,t,,t,t,t,,,t,,t,, +watershed_group_code,bt,ch,cm,co,ct,dv,gr,ko,pk,rb,sk,st,wct,notes +ADMS,t,t,,t,t,t,,,,t,t,,, +ALBN,,t,t,t,t,t,,,,t,t,t,, +ATLL,,,,,,t,t,,,t,,,, +ATNA,,t,t,t,t,t,,,t,t,t,t,, +BABL,t,t,,t,t,t,,,,t,t,t,, +BABR,t,t,,t,t,t,,,,t,t,t,, +BARR,t,t,t,,t,t,,,,t,t,,, +BBAR,t,t,,t,t,t,,,,t,t,,, +BEAV,t,,,,,t,t,,,,,,,Mackenzie basin +BELA,,t,t,t,t,t,,,t,t,t,t,, +BIGC,t,,,,,,,,,t,,,, +BLAR,t,t,,,,t,,,,t,,,, +BLUR,t,,,,,t,t,,,,,,,Mackenzie basin +BONP,t,t,,t,t,,,,t,t,,t,, +BOWR,t,t,,t,,t,,,,t,t,,, +BRID,,,,,t,,,,,t,,,,Falls 20807 +BRKS,t,t,t,t,t,t,,,t,t,t,t,, +BULK,t,t,,t,t,t,,,t,t,t,t,, +BULL,t,,,,t,t,t,,,t,,,t, +CAMB,,t,t,t,t,t,t,,t,t,t,t,, +CANO,t,,,,,t,,,,t,,,,Columbia basin +CARP,t,,,,,t,,t,,t,,,,Mackenzie basin +CARR,t,t,,t,,t,,,,t,t,,, +CHES,t,t,,,,t,,,,t,t,,, +CHIL,,t,,,,t,,,,t,,,, +CHIR,t,,,,,t,,,,t,t,t,, +CHUK,,,,,,t,,,,,,,,No target species observations +CHWK,t,t,t,t,t,t,,,t,t,t,t,, +CLAY,,t,t,t,t,t,,,,t,t,t,, +CLRH,t,,,,t,t,,,,t,,,t, +CLWR,,t,,t,,t,,,,t,,,, +COAL,t,,,,,t,t,,,,,,,Mackenzie basin +COLR,t,,,,t,t,,,,t,,,t, +COMX,,t,t,t,t,t,,,t,t,t,t,, +COTR,t,t,,t,,t,,,t,t,,,, +COWN,t,t,t,t,t,t,,,t,t,,t,, +CRKD,t,,,,,t,,,,t,,,,Mackenzie basin +CRYL,,,,,,,t,,,,,,,Mackenzie basin +DEAD,t,t,,t,,,,,t,t,t,t,, +DEAL,t,,,,,t,t,,,,,,,Mackenzie basin +DEAR,t,,,,,t,t,,,,,,,Mackenzie basin +DOGC,t,t,,t,t,t,,,,t,t,,, +DRIR,t,t,,,,t,,,,t,t,,, +DUNC,t,,,,t,,,,,t,,,t, +DUNE,t,,,,,,t,,,t,,,,Mackenzie basin +ELKR,t,,,,t,t,t,,,t,,,t, +EUCH,,t,,,,t,,,,t,,,, +EUCL,t,t,,,,t,,,,t,,,, +FINA,t,,,,,t,t,,,t,,,,Mackenzie basin +FINL,t,,,,,t,t,,,t,,,,Mackenzie basin +FIRE,t,,,,,t,t,,,t,,,,Mackenzie basin +FONT,t,,,,,,t,,,,,,,Mackenzie basin +FOXR,t,,,,,t,t,,,t,,,,Mackenzie basin +FRAN,t,t,,,t,t,,,,t,t,,, +FRCN,t,t,t,t,t,t,,,t,t,t,t,, +FROG,t,,,,,t,t,,,,,,,Mackenzie basin +GATA,t,,,,,,t,,,,,,,Mackenzie basin +GLAR,,t,,,,,t,,,,,,, +GOLD,,t,t,t,t,t,,,,t,t,t,, +GRAI,,t,t,t,t,t,,,t,t,t,t,, +GRNL,,,,,,,,,,t,,,,No target species observations +GUIC,t,t,,t,t,t,,,,t,,t,, +HARR,t,t,t,t,t,t,,,t,t,t,t,, +HAYR,,,,,,,,,,,,,,Mackenzie basin +HERR,t,t,,,,t,,,,t,,,, +HOLB,,,t,t,t,t,,,t,t,,t,, +HOMA,t,t,t,t,t,t,,,,t,,t,, +HORS,t,t,,t,,t,,,,t,t,,, +INGR,t,,,,,t,t,,,t,,,,Mackenzie basin +INKR,t,t,,t,t,t,t,,,t,t,t,, +ISKR,t,,,,,t,,,,t,,,,No target species observations +JENR,,t,,,t,,t,,,,,,, +JERV,t,t,t,t,t,t,,,t,t,,t,, +KAHN,,,,,,,t,,,,,,,Mackenzie basin +KAKC,,,,,,,,,,t,,,,Not accessible to target species +KCHL,,,,,,,,,,,,,,Mackenzie basin +KEEC,,,,t,,,,,,,,,, +KETL,,,,,t,,,,,t,,,t, +KHOR,t,,,,t,t,,,,t,,,t, +KHTZ,,t,t,t,t,t,,,t,t,t,t,, +KINR,t,t,,t,,t,,,,t,t,,, +KISK,t,,,,,,t,,,t,,,,Mackenzie basin +KISP,t,t,t,t,t,t,,,t,t,t,t,, +KITL,,t,t,t,t,t,,,t,t,t,t,, +KITR,t,t,t,t,t,t,,,t,t,t,t,, +KLAR,t,,,,,t,t,,,t,,,,No target species observations +KLIN,t,t,t,t,t,t,,,,t,t,t,, +KLUM,t,t,t,t,t,t,,,t,t,t,t,, +KNIG,,t,t,t,t,t,,,t,t,t,t,, +KOTL,t,,,,t,t,,t,,t,,,t, +KOTR,t,,,,t,t,,,,t,,,t, +KSHR,,t,t,t,t,t,,,t,t,,t,, +KTSU,,t,,t,t,,,,t,,t,t,,updated based on PSE spawning data +KUMR,,,t,t,t,t,,,t,t,t,,, +KUSR,,,,,,t,t,,,,,,,No target species observations +LARL,t,,,,t,t,t,,,t,,,t, +LBIR,t,t,,t,,t,,,,t,,t,, +LBTN,t,,,,,,t,,,t,,,,Mackenzie basin +LCHL,t,t,,t,,t,,,,t,,,, +LCHR,t,t,,,,t,,,,t,,t,, +LDEN,t,t,,t,t,t,,,,t,t,t,, +LEUT,,,,,,,,,,t,,,,Kenny Dam +LFRA,t,t,t,t,t,t,,,t,t,t,t,, +LFRT,,,,,,,t,,,t,,,,Mackenzie basin +LHAF,t,,,,,,t,,,t,,,,Mackenzie basin +LIAR,t,,,,,t,t,,,t,,,,Mackenzie basin +LILL,t,t,t,t,t,t,,,,t,t,t,, +LISR,t,t,t,t,t,t,t,,,t,t,t,, +LKEC,,,,,,t,t,,,,,,,Mackenzie basin +LKEL,t,t,t,t,t,t,,,t,t,,t,, +LMUS,t,,,,,t,t,,,t,,,,Mackenzie basin +LNAR,t,t,t,t,t,t,,,t,t,,t,, +LNIC,t,t,,t,t,t,,,t,t,,t,, +LNRS,,,,,t,,,,,t,,,, +LNTH,t,t,,t,t,t,,,t,t,t,,, +LOMI,t,,,,,t,t,,,t,,,,Mackenzie basin +LPCE,t,,,,,,t,,,t,,,,Mackenzie basin +LPET,,,,,,,t,,,,,,,Mackenzie basin +LPRO,t,,,,,t,t,,,t,,,,Mackenzie basin +LRAN,t,,,,,t,t,,,,,,,Mackenzie basin +LRDO,,,t,t,t,t,,,t,t,t,t,, +LSAL,,t,,,,t,,,,t,,,, +LSIK,,,,,,,t,,,,,,,Mackenzie basin +LSKE,t,t,t,t,t,t,,,t,t,t,t,, +LSTR,,t,,t,t,t,,,,t,t,,, +LTRE,t,t,,,t,,,,,t,t,,, +MAHD,t,t,,,,t,,,,t,,,, +MBNK,,,,t,t,t,,,,,,,, +MCGR,t,t,,,,t,,,,t,,,, +MDEA,t,,,,,t,t,,,t,,,,Mackenzie basin +MESC,,t,,,,,,,,t,,,, +MESI,t,,,,,t,t,,,t,,,,Mackenzie basin +MFRA,,t,,,,,,,,t,,,, +MFRT,,,,,,,t,,,,,,,Mackenzie basin +MIDR,t,t,,,,t,,,,t,t,,, +MILL,,,,,,,t,,,,,,,Mackenzie basin +MMUS,t,,,,,t,t,,,t,,,,Mackenzie basin +MORI,,,t,t,t,t,,,t,t,t,t,, +MORK,t,t,,,,t,,,,t,,,, +MORR,t,t,,t,t,t,,,t,t,t,t,, +MPRO,t,,,,,t,t,,,t,,,,Mackenzie basin +MSKE,t,t,,t,t,t,t,,,t,t,t,, +MSTR,t,,,,,t,t,,,t,,t,, +MURR,t,,,,t,t,t,,,t,,,,Mackenzie basin +MURT,,,,,,,,,,t,,,, +MUSK,,,,,,t,,,,t,,,, +NAHR,,t,,,,t,t,,,t,,,, +NAKR,,t,,t,,t,t,,,t,t,,, +NARC,t,t,,,,t,,,t,t,,,, +NASC,,,t,t,t,t,,,t,t,t,t,, +NASR,t,t,,t,t,t,,,,t,t,t,, +NATR,t,,,,,t,t,t,,t,,,,Mackenzie basin +NAZR,,t,,,,,,,,t,,,, +NBNK,,,,t,t,t,,,,,t,,, +NECL,,,t,t,t,t,,,t,t,t,t,, +NECR,t,t,,t,,t,,,,t,t,,, +NEVI,,,t,t,t,t,,,t,t,t,t,, +NICL,,t,,t,,,,,,t,,,, +NIEL,,t,t,t,t,t,,,t,t,t,t,, +NIMP,,t,t,t,t,t,,,t,t,t,t,, +OKAN,t,t,,,t,t,,,,t,t,,, +OSPK,t,,,,,t,t,,,t,,,,Mackenzie basin +OWIK,,t,t,t,t,t,,,t,t,t,t,, +PARA,t,,,,,t,t,,,t,,,,Mackenzie basin +PARK,t,t,t,t,t,t,,,t,t,,t,, +PARS,t,,,,,t,t,t,,t,,,,Mackenzie basin +PCEA,t,,,,,t,t,,,t,,,,Mackenzie basin +PINE,t,,,,,t,t,,,t,,,,Mackenzie basin +PITR,,,,,,t,,,,t,,,,No target species observations +PORI,,,t,t,t,t,,,t,t,,t,, +QUES,t,t,,t,,t,,,t,t,t,,, +REVL,t,,,,t,t,,,,t,,,t, +SAHD,,,,,,,t,,,,,,,Mackenzie basin +SAHT,,,,,,,,,,,,,,Mackenzie basin +SAJR,,,,t,,,,,t,t,t,,, +SALM,,t,t,t,t,t,,,t,t,,t,, +SALR,,t,,,,t,,,,t,,,, +SANJ,,t,t,t,t,t,,,t,t,t,t,, +SETN,t,t,t,t,t,t,,,t,t,t,t,, +SEYM,,t,t,t,t,t,,,t,t,,t,, +SHEK,,,,,,,,,,,,,,Mackenzie basin +SHER,,t,,t,t,t,,,,t,,t,, +SHUL,t,t,,t,t,t,,,t,t,t,,t, +SIML,t,,,,t,t,,,,t,,,,No target species observations +SKGT,t,,,,t,t,,,,t,,,, +SLOC,t,,,,t,t,,,,t,,,t, +SMAR,t,,,,t,t,,,,t,,,t, +SMOK,t,,,,t,t,t,,,t,,,,Mackenzie basin +SPAT,t,,,,,t,t,,,t,,,,No target species observations +SQAM,t,t,t,t,t,t,,,t,t,t,t,, +STHM,t,t,,t,t,t,,,t,t,t,,, +STIR,,t,,t,t,t,t,,,t,t,,, +STUL,,t,,,t,t,,,,t,t,,, +STUR,t,t,,,,t,,,,t,t,,, +SUST,t,t,t,t,,t,,,,t,t,t,, +SWIR,t,t,,,,t,t,,,,,,, +TABR,t,t,,,,t,,,,t,,,, +TAHR,t,,,,t,t,,,,t,t,t,, +TAHS,,t,t,t,t,t,,,t,t,t,t,, +TAKL,t,t,,,,t,,,,t,t,,, +TASR,t,t,,,,t,,,,t,t,,, +TATR,,t,,,,t,t,,,t,t,,, +TAYR,t,,,,,t,,,,t,,t,, +TESR,,t,,,,,t,,,t,,,, +THOM,t,t,,t,t,t,,,t,t,t,t,, +TOAD,t,,,,,t,t,,,,,,,Mackenzie basin +TOBA,,t,t,t,t,t,,,t,t,t,t,, +TOOD,t,,,,,t,t,,,t,,,,Mackenzie basin +TSAY,,t,t,t,t,t,,,t,t,,t,, +TSEA,,,,,,,t,,,,,,,Mackenzie basin +TSIT,,t,t,t,t,t,,,t,t,,t,, +TURN,t,,,,,t,t,,,t,,,,Mackenzie basin +TUTR,,,,,,,t,,,,,,, +TUYR,t,,,,,,t,,,,,,,Blockage near mouth of Tuya River +TWAC,t,t,,,,t,,,,t,,,, +UARL,t,,,,t,t,,,,t,,,t, +UBIR,t,t,,t,,t,,,,t,,,, +UBTN,t,,,,,,t,,,t,,,,Mackenzie basin +UCHR,t,t,,,,,,,,t,,t,, +UDEN,t,t,t,t,,t,,,t,t,t,t,,salmon/steelhead added as test for Ulkatcho +UEUT,t,,,,t,t,,,,t,,,, +UFRA,t,t,,,,t,,,,t,,,, +UFRT,,,,,,,t,,,,,,,Mackenzie basin +UHAF,t,,,,,,t,,,t,,,,Mackenzie basin +UISR,,,,,,t,,,,t,,,,Forrest Kerr Generating Station +UJER,,t,,,,,t,,,,,,, +UKEC,t,,,,,t,t,,,t,,,,Mackenzie basin +ULRD,t,,,,,t,t,,,t,,,,Mackenzie basin +UMUS,t,,,,,t,t,,,t,,,,Mackenzie basin +UNAR,t,t,,,t,t,,,,t,,t,, +UNRS,t,,,,,t,,,,t,,,, +UNTH,t,t,,t,t,t,,,,t,,,, +UNUR,t,,,t,t,t,,,,t,,,, +UOMI,t,,,,,t,t,,,t,,,,Mackenzie basin +UPCE,t,,,,t,t,t,,,t,,,,Mackenzie basin +UPET,,,,,,,t,,,t,,,,Mackenzie basin +UPRO,t,,,,,,t,,,t,,,,Mackenzie basin +USHU,t,t,,t,t,t,,,t,t,t,,t, +USIK,t,,,,,,t,,,t,,,,Mackenzie basin +USKE,t,t,,t,,t,,,,t,t,t,, +USTK,,,,,t,t,t,,,t,,t,, +UTRE,t,,,,,t,,,,t,t,,, +VICT,,t,t,t,t,t,,,,t,,t,, +WILL,t,t,,t,t,t,,,,t,,,, +WORC,,t,t,t,t,t,,,t,t,,t,, +ZYMO,t,t,,t,t,t,,,,t,,t,, diff --git a/inst/extdata/configs/default/overrides/wsg_species_presence.csv b/inst/extdata/configs/default/overrides/wsg_species_presence.csv index d4320ec..b109839 100644 --- a/inst/extdata/configs/default/overrides/wsg_species_presence.csv +++ b/inst/extdata/configs/default/overrides/wsg_species_presence.csv @@ -1,247 +1,247 @@ -watershed_group_code,bt,ch,cm,co,ct,dv,gr,pk,rb,sk,st,wct,notes -ADMS,t,t,,t,t,t,,,t,t,,, -ALBN,,t,t,t,t,t,,,t,t,t,, -ATLL,,,,,,t,t,,t,,,, -ATNA,,t,t,t,t,t,,t,t,t,t,, -BABL,t,t,,t,t,t,,,t,t,t,, -BABR,t,t,,t,t,t,,,t,t,t,, -BARR,t,t,t,,t,t,,,t,t,,, -BBAR,t,t,,t,t,t,,,t,t,,, -BEAV,t,,,,,t,t,,,,,,Mackenzie basin -BELA,,t,t,t,t,t,,t,t,t,t,, -BIGC,t,,,,,,,,t,,,, -BLAR,t,t,,,,t,,,t,,,, -BLUR,t,,,,,t,t,,,,,,Mackenzie basin -BONP,t,t,,t,t,,,t,t,,t,, -BOWR,t,t,,t,,t,,,t,t,,, -BRID,,,,,t,,,,t,,,,Falls 20807 -BRKS,t,t,t,t,t,t,,t,t,t,t,, -BULK,t,t,,t,t,t,,t,t,t,t,, -BULL,t,,,,t,t,t,,t,,,t, -CAMB,,t,t,t,t,t,t,t,t,t,t,, -CANO,t,,,,,t,,,t,,,,Columbia basin -CARP,t,,,,,t,,,t,,,,Mackenzie basin -CARR,t,t,,t,,t,,,t,t,,, -CHES,t,t,,,,t,,,t,t,,, -CHIL,,t,,,,t,,,t,,,, -CHIR,t,,,,,t,,,t,t,t,, -CHUK,,,,,,t,,,,,,,No target species observations -CHWK,t,t,t,t,t,t,,t,t,t,t,, -CLAY,,t,t,t,t,t,,,t,t,t,, -CLRH,t,,,,t,t,,,t,,,t, -CLWR,,t,,t,,t,,,t,,,, -COAL,t,,,,,t,t,,,,,,Mackenzie basin -COLR,t,,,,t,t,,,t,,,t, -COMX,,t,t,t,t,t,,t,t,t,t,, -COTR,t,t,,t,,t,,t,t,,,, -COWN,t,t,t,t,t,t,,t,t,,t,, -CRKD,t,,,,,t,,,t,,,,Mackenzie basin -CRYL,,,,,,,t,,,,,,Mackenzie basin -DEAD,t,t,,t,,,,t,t,t,t,, -DEAL,t,,,,,t,t,,,,,,Mackenzie basin -DEAR,t,,,,,t,t,,,,,,Mackenzie basin -DOGC,t,t,,t,t,t,,,t,t,,, -DRIR,t,t,,,,t,,,t,t,,, -DUNC,t,,,,t,,,,t,,,t, -DUNE,t,,,,,,t,,t,,,,Mackenzie basin -ELKR,t,,,,t,t,t,,t,,,t, -EUCH,,t,,,,t,,,t,,,, -EUCL,t,t,,,,t,,,t,,,, -FINA,t,,,,,t,t,,t,,,,Mackenzie basin -FINL,t,,,,,t,t,,t,,,,Mackenzie basin -FIRE,t,,,,,t,t,,t,,,,Mackenzie basin -FONT,t,,,,,,t,,,,,,Mackenzie basin -FOXR,t,,,,,t,t,,t,,,,Mackenzie basin -FRAN,t,t,,,t,t,,,t,t,,, -FRCN,t,t,t,t,t,t,,t,t,t,t,, -FROG,t,,,,,t,t,,,,,,Mackenzie basin -GATA,t,,,,,,t,,,,,,Mackenzie basin -GLAR,,t,,,,,t,,,,,, -GOLD,,t,t,t,t,t,,,t,t,t,, -GRAI,,t,t,t,t,t,,t,t,t,t,, -GRNL,,,,,,,,,t,,,,No target species observations -GUIC,t,t,,t,t,t,,,t,,t,, -HARR,t,t,t,t,t,t,,t,t,t,t,, -HAYR,,,,,,,,,,,,,Mackenzie basin -HERR,t,t,,,,t,,,t,,,, -HOLB,,,t,t,t,t,,t,t,,t,, -HOMA,t,t,t,t,t,t,,,t,,t,, -HORS,t,t,,t,,t,,,t,t,,, -INGR,t,,,,,t,t,,t,,,,Mackenzie basin -INKR,t,t,,t,t,t,t,,t,t,t,, -ISKR,t,,,,,t,,,t,,,,No target species observations -JENR,,t,,,t,,t,,,,,, -JERV,t,t,t,t,t,t,,t,t,,t,, -KAHN,,,,,,,t,,,,,,Mackenzie basin -KAKC,,,,,,,,,t,,,,Not accessible to target species -KCHL,,,,,,,,,,,,,Mackenzie basin -KEEC,,,,t,,,,,,,,, -KETL,,,,,t,,,,t,,,t, -KHOR,t,,,,t,t,,,t,,,t, -KHTZ,,t,t,t,t,t,,t,t,t,t,, -KINR,t,t,,t,,t,,,t,t,,, -KISK,t,,,,,,t,,t,,,,Mackenzie basin -KISP,t,t,t,t,t,t,,t,t,t,t,, -KITL,,t,t,t,t,t,,t,t,t,t,, -KITR,t,t,t,t,t,t,,t,t,t,t,, -KLAR,t,,,,,t,t,,t,,,,No target species observations -KLIN,t,t,t,t,t,t,,,t,t,t,, -KLUM,t,t,t,t,t,t,,t,t,t,t,, -KNIG,,t,t,t,t,t,,t,t,t,t,, -KOTL,t,,,,t,t,,,t,,,t, -KOTR,t,,,,t,t,,,t,,,t, -KSHR,,t,t,t,t,t,,t,t,,t,, -KTSU,,t,,t,t,,,t,,t,t,,updated based on PSE spawning data -KUMR,,,t,t,t,t,,t,t,t,,, -KUSR,,,,,,t,t,,,,,,No target species observations -LARL,t,,,,t,t,t,,t,,,t, -LBIR,t,t,,t,,t,,,t,,t,, -LBTN,t,,,,,,t,,t,,,,Mackenzie basin -LCHL,t,t,,t,,t,,,t,,,, -LCHR,t,t,,,,t,,,t,,t,, -LDEN,t,t,,t,t,t,,,t,t,t,, -LEUT,,,,,,,,,t,,,,Kenny Dam -LFRA,t,t,t,t,t,t,,t,t,t,t,, -LFRT,,,,,,,t,,t,,,,Mackenzie basin -LHAF,t,,,,,,t,,t,,,,Mackenzie basin -LIAR,t,,,,,t,t,,t,,,,Mackenzie basin -LILL,t,t,t,t,t,t,,,t,t,t,, -LISR,t,t,t,t,t,t,t,,t,t,t,, -LKEC,,,,,,t,t,,,,,,Mackenzie basin -LKEL,t,t,t,t,t,t,,t,t,,t,, -LMUS,t,,,,,t,t,,t,,,,Mackenzie basin -LNAR,t,t,t,t,t,t,,t,t,,t,, -LNIC,t,t,,t,t,t,,t,t,,t,, -LNRS,,,,,t,,,,t,,,, -LNTH,t,t,,t,t,t,,t,t,t,,, -LOMI,t,,,,,t,t,,t,,,,Mackenzie basin -LPCE,t,,,,,,t,,t,,,,Mackenzie basin -LPET,,,,,,,t,,,,,,Mackenzie basin -LPRO,t,,,,,t,t,,t,,,,Mackenzie basin -LRAN,t,,,,,t,t,,,,,,Mackenzie basin -LRDO,,,t,t,t,t,,t,t,t,t,, -LSAL,,t,,,,t,,,t,,,, -LSIK,,,,,,,t,,,,,,Mackenzie basin -LSKE,t,t,t,t,t,t,,t,t,t,t,, -LSTR,,t,,t,t,t,,,t,t,,, -LTRE,t,t,,,t,,,,t,t,,, -MAHD,t,t,,,,t,,,t,,,, -MBNK,,,,t,t,t,,,,,,, -MCGR,t,t,,,,t,,,t,,,, -MDEA,t,,,,,t,t,,t,,,,Mackenzie basin -MESC,,t,,,,,,,t,,,, -MESI,t,,,,,t,t,,t,,,,Mackenzie basin -MFRA,,t,,,,,,,t,,,, -MFRT,,,,,,,t,,,,,,Mackenzie basin -MIDR,t,t,,,,t,,,t,t,,, -MILL,,,,,,,t,,,,,,Mackenzie basin -MMUS,t,,,,,t,t,,t,,,,Mackenzie basin -MORI,,,t,t,t,t,,t,t,t,t,, -MORK,t,t,,,,t,,,t,,,, -MORR,t,t,,t,t,t,,t,t,t,t,, -MPRO,t,,,,,t,t,,t,,,,Mackenzie basin -MSKE,t,t,,t,t,t,t,,t,t,t,, -MSTR,t,,,,,t,t,,t,,t,, -MURR,t,,,,t,t,t,,t,,,,Mackenzie basin -MURT,,,,,,,,,t,,,, -MUSK,,,,,,t,,,t,,,, -NAHR,,t,,,,t,t,,t,,,, -NAKR,,t,,t,,t,t,,t,t,,, -NARC,t,t,,,,t,,t,t,,,, -NASC,,,t,t,t,t,,t,t,t,t,, -NASR,t,t,,t,t,t,,,t,t,t,, -NATR,t,,,,,t,t,,t,,,,Mackenzie basin -NAZR,,t,,,,,,,t,,,, -NBNK,,,,t,t,t,,,,t,,, -NECL,,,t,t,t,t,,t,t,t,t,, -NECR,t,t,,t,,t,,,t,t,,, -NEVI,,,t,t,t,t,,t,t,t,t,, -NICL,,t,,t,,,,,t,,,, -NIEL,,t,t,t,t,t,,t,t,t,t,, -NIMP,,t,t,t,t,t,,t,t,t,t,, -OKAN,t,t,,,t,t,,,t,t,,, -OSPK,t,,,,,t,t,,t,,,,Mackenzie basin -OWIK,,t,t,t,t,t,,t,t,t,t,, -PARA,t,,,,,t,t,,t,,,,Mackenzie basin -PARK,t,t,t,t,t,t,,t,t,,t,, -PARS,t,,,,,t,t,,t,,,,Mackenzie basin -PCEA,t,,,,,t,t,,t,,,,Mackenzie basin -PINE,t,,,,,t,t,,t,,,,Mackenzie basin -PITR,,,,,,t,,,t,,,,No target species observations -PORI,,,t,t,t,t,,t,t,,t,, -QUES,t,t,,t,,t,,t,t,t,,, -REVL,t,,,,t,t,,,t,,,t, -SAHD,,,,,,,t,,,,,,Mackenzie basin -SAHT,,,,,,,,,,,,,Mackenzie basin -SAJR,,,,t,,,,t,t,t,,, -SALM,,t,t,t,t,t,,t,t,,t,, -SALR,,t,,,,t,,,t,,,, -SANJ,,t,t,t,t,t,,t,t,t,t,, -SETN,t,t,t,t,t,t,,t,t,t,t,, -SEYM,,t,t,t,t,t,,t,t,,t,, -SHEK,,,,,,,,,,,,,Mackenzie basin -SHER,,t,,t,t,t,,,t,,t,, -SHUL,t,t,,t,t,t,,t,t,t,,t, -SIML,t,,,,t,t,,,t,,,,No target species observations -SKGT,t,,,,t,t,,,t,,,, -SLOC,t,,,,t,t,,,t,,,t, -SMAR,t,,,,t,t,,,t,,,t, -SMOK,t,,,,t,t,t,,t,,,,Mackenzie basin -SPAT,t,,,,,t,t,,t,,,,No target species observations -SQAM,t,t,t,t,t,t,,t,t,t,t,, -STHM,t,t,,t,t,t,,t,t,t,,, -STIR,,t,,t,t,t,t,,t,t,,, -STUL,,t,,,t,t,,,t,t,,, -STUR,t,t,,,,t,,,t,t,,, -SUST,t,t,t,t,,t,,,t,t,t,, -SWIR,t,t,,,,t,t,,,,,, -TABR,t,t,,,,t,,,t,,,, -TAHR,t,,,,t,t,,,t,t,t,, -TAHS,,t,t,t,t,t,,t,t,t,t,, -TAKL,t,t,,,,t,,,t,t,,, -TASR,t,t,,,,t,,,t,t,,, -TATR,,t,,,,t,t,,t,t,,, -TAYR,t,,,,,t,,,t,,t,, -TESR,,t,,,,,t,,t,,,, -THOM,t,t,,t,t,t,,t,t,t,t,, -TOAD,t,,,,,t,t,,,,,,Mackenzie basin -TOBA,,t,t,t,t,t,,t,t,t,t,, -TOOD,t,,,,,t,t,,t,,,,Mackenzie basin -TSAY,,t,t,t,t,t,,t,t,,t,, -TSEA,,,,,,,t,,,,,,Mackenzie basin -TSIT,,t,t,t,t,t,,t,t,,t,, -TURN,t,,,,,t,t,,t,,,,Mackenzie basin -TUTR,,,,,,,t,,,,,, -TUYR,t,,,,,,t,,,,,,Blockage near mouth of Tuya River -TWAC,t,t,,,,t,,,t,,,, -UARL,t,,,,t,t,,,t,,,t, -UBIR,t,t,,t,,t,,,t,,,, -UBTN,t,,,,,,t,,t,,,,Mackenzie basin -UCHR,t,t,,,,,,,t,,t,, -UDEN,t,t,t,t,,t,,t,t,t,t,,salmon/steelhead added as test for Ulkatcho -UEUT,t,,,,t,t,,,t,,,, -UFRA,t,t,,,,t,,,t,,,, -UFRT,,,,,,,t,,,,,,Mackenzie basin -UHAF,t,,,,,,t,,t,,,,Mackenzie basin -UISR,,,,,,t,,,t,,,,Forrest Kerr Generating Station -UJER,,t,,,,,t,,,,,, -UKEC,t,,,,,t,t,,t,,,,Mackenzie basin -ULRD,t,,,,,t,t,,t,,,,Mackenzie basin -UMUS,t,,,,,t,t,,t,,,,Mackenzie basin -UNAR,t,t,,,t,t,,,t,,t,, -UNRS,t,,,,,t,,,t,,,, -UNTH,t,t,,t,t,t,,,t,,,, -UNUR,t,,,t,t,t,,,t,,,, -UOMI,t,,,,,t,t,,t,,,,Mackenzie basin -UPCE,t,,,,t,t,t,,t,,,,Mackenzie basin -UPET,,,,,,,t,,t,,,,Mackenzie basin -UPRO,t,,,,,,t,,t,,,,Mackenzie basin -USHU,t,t,,t,t,t,,t,t,t,,t, -USIK,t,,,,,,t,,t,,,,Mackenzie basin -USKE,t,t,,t,,t,,,t,t,t,, -USTK,,,,,t,t,t,,t,,t,, -UTRE,t,,,,,t,,,t,t,,, -VICT,,t,t,t,t,t,,,t,,t,, -WILL,t,t,,t,t,t,,,t,,,, -WORC,,t,t,t,t,t,,t,t,,t,, -ZYMO,t,t,,t,t,t,,,t,,t,, +watershed_group_code,bt,ch,cm,co,ct,dv,gr,ko,pk,rb,sk,st,wct,notes +ADMS,t,t,,t,t,t,,,,t,t,,, +ALBN,,t,t,t,t,t,,,,t,t,t,, +ATLL,,,,,,t,t,,,t,,,, +ATNA,,t,t,t,t,t,,,t,t,t,t,, +BABL,t,t,,t,t,t,,,,t,t,t,, +BABR,t,t,,t,t,t,,,,t,t,t,, +BARR,t,t,t,,t,t,,,,t,t,,, +BBAR,t,t,,t,t,t,,,,t,t,,, +BEAV,t,,,,,t,t,,,,,,,Mackenzie basin +BELA,,t,t,t,t,t,,,t,t,t,t,, +BIGC,t,,,,,,,,,t,,,, +BLAR,t,t,,,,t,,,,t,,,, +BLUR,t,,,,,t,t,,,,,,,Mackenzie basin +BONP,t,t,,t,t,,,,t,t,,t,, +BOWR,t,t,,t,,t,,,,t,t,,, +BRID,,,,,t,,,,,t,,,,Falls 20807 +BRKS,t,t,t,t,t,t,,,t,t,t,t,, +BULK,t,t,,t,t,t,,,t,t,t,t,, +BULL,t,,,,t,t,t,,,t,,,t, +CAMB,,t,t,t,t,t,t,,t,t,t,t,, +CANO,t,,,,,t,,,,t,,,,Columbia basin +CARP,t,,,,,t,,t,,t,,,,Mackenzie basin +CARR,t,t,,t,,t,,,,t,t,,, +CHES,t,t,,,,t,,,,t,t,,, +CHIL,,t,,,,t,,,,t,,,, +CHIR,t,,,,,t,,,,t,t,t,, +CHUK,,,,,,t,,,,,,,,No target species observations +CHWK,t,t,t,t,t,t,,,t,t,t,t,, +CLAY,,t,t,t,t,t,,,,t,t,t,, +CLRH,t,,,,t,t,,,,t,,,t, +CLWR,,t,,t,,t,,,,t,,,, +COAL,t,,,,,t,t,,,,,,,Mackenzie basin +COLR,t,,,,t,t,,,,t,,,t, +COMX,,t,t,t,t,t,,,t,t,t,t,, +COTR,t,t,,t,,t,,,t,t,,,, +COWN,t,t,t,t,t,t,,,t,t,,t,, +CRKD,t,,,,,t,,,,t,,,,Mackenzie basin +CRYL,,,,,,,t,,,,,,,Mackenzie basin +DEAD,t,t,,t,,,,,t,t,t,t,, +DEAL,t,,,,,t,t,,,,,,,Mackenzie basin +DEAR,t,,,,,t,t,,,,,,,Mackenzie basin +DOGC,t,t,,t,t,t,,,,t,t,,, +DRIR,t,t,,,,t,,,,t,t,,, +DUNC,t,,,,t,,,,,t,,,t, +DUNE,t,,,,,,t,,,t,,,,Mackenzie basin +ELKR,t,,,,t,t,t,,,t,,,t, +EUCH,,t,,,,t,,,,t,,,, +EUCL,t,t,,,,t,,,,t,,,, +FINA,t,,,,,t,t,,,t,,,,Mackenzie basin +FINL,t,,,,,t,t,,,t,,,,Mackenzie basin +FIRE,t,,,,,t,t,,,t,,,,Mackenzie basin +FONT,t,,,,,,t,,,,,,,Mackenzie basin +FOXR,t,,,,,t,t,,,t,,,,Mackenzie basin +FRAN,t,t,,,t,t,,,,t,t,,, +FRCN,t,t,t,t,t,t,,,t,t,t,t,, +FROG,t,,,,,t,t,,,,,,,Mackenzie basin +GATA,t,,,,,,t,,,,,,,Mackenzie basin +GLAR,,t,,,,,t,,,,,,, +GOLD,,t,t,t,t,t,,,,t,t,t,, +GRAI,,t,t,t,t,t,,,t,t,t,t,, +GRNL,,,,,,,,,,t,,,,No target species observations +GUIC,t,t,,t,t,t,,,,t,,t,, +HARR,t,t,t,t,t,t,,,t,t,t,t,, +HAYR,,,,,,,,,,,,,,Mackenzie basin +HERR,t,t,,,,t,,,,t,,,, +HOLB,,,t,t,t,t,,,t,t,,t,, +HOMA,t,t,t,t,t,t,,,,t,,t,, +HORS,t,t,,t,,t,,,,t,t,,, +INGR,t,,,,,t,t,,,t,,,,Mackenzie basin +INKR,t,t,,t,t,t,t,,,t,t,t,, +ISKR,t,,,,,t,,,,t,,,,No target species observations +JENR,,t,,,t,,t,,,,,,, +JERV,t,t,t,t,t,t,,,t,t,,t,, +KAHN,,,,,,,t,,,,,,,Mackenzie basin +KAKC,,,,,,,,,,t,,,,Not accessible to target species +KCHL,,,,,,,,,,,,,,Mackenzie basin +KEEC,,,,t,,,,,,,,,, +KETL,,,,,t,,,,,t,,,t, +KHOR,t,,,,t,t,,,,t,,,t, +KHTZ,,t,t,t,t,t,,,t,t,t,t,, +KINR,t,t,,t,,t,,,,t,t,,, +KISK,t,,,,,,t,,,t,,,,Mackenzie basin +KISP,t,t,t,t,t,t,,,t,t,t,t,, +KITL,,t,t,t,t,t,,,t,t,t,t,, +KITR,t,t,t,t,t,t,,,t,t,t,t,, +KLAR,t,,,,,t,t,,,t,,,,No target species observations +KLIN,t,t,t,t,t,t,,,,t,t,t,, +KLUM,t,t,t,t,t,t,,,t,t,t,t,, +KNIG,,t,t,t,t,t,,,t,t,t,t,, +KOTL,t,,,,t,t,,t,,t,,,t, +KOTR,t,,,,t,t,,,,t,,,t, +KSHR,,t,t,t,t,t,,,t,t,,t,, +KTSU,,t,,t,t,,,,t,,t,t,,updated based on PSE spawning data +KUMR,,,t,t,t,t,,,t,t,t,,, +KUSR,,,,,,t,t,,,,,,,No target species observations +LARL,t,,,,t,t,t,,,t,,,t, +LBIR,t,t,,t,,t,,,,t,,t,, +LBTN,t,,,,,,t,,,t,,,,Mackenzie basin +LCHL,t,t,,t,,t,,,,t,,,, +LCHR,t,t,,,,t,,,,t,,t,, +LDEN,t,t,,t,t,t,,,,t,t,t,, +LEUT,,,,,,,,,,t,,,,Kenny Dam +LFRA,t,t,t,t,t,t,,,t,t,t,t,, +LFRT,,,,,,,t,,,t,,,,Mackenzie basin +LHAF,t,,,,,,t,,,t,,,,Mackenzie basin +LIAR,t,,,,,t,t,,,t,,,,Mackenzie basin +LILL,t,t,t,t,t,t,,,,t,t,t,, +LISR,t,t,t,t,t,t,t,,,t,t,t,, +LKEC,,,,,,t,t,,,,,,,Mackenzie basin +LKEL,t,t,t,t,t,t,,,t,t,,t,, +LMUS,t,,,,,t,t,,,t,,,,Mackenzie basin +LNAR,t,t,t,t,t,t,,,t,t,,t,, +LNIC,t,t,,t,t,t,,,t,t,,t,, +LNRS,,,,,t,,,,,t,,,, +LNTH,t,t,,t,t,t,,,t,t,t,,, +LOMI,t,,,,,t,t,,,t,,,,Mackenzie basin +LPCE,t,,,,,,t,,,t,,,,Mackenzie basin +LPET,,,,,,,t,,,,,,,Mackenzie basin +LPRO,t,,,,,t,t,,,t,,,,Mackenzie basin +LRAN,t,,,,,t,t,,,,,,,Mackenzie basin +LRDO,,,t,t,t,t,,,t,t,t,t,, +LSAL,,t,,,,t,,,,t,,,, +LSIK,,,,,,,t,,,,,,,Mackenzie basin +LSKE,t,t,t,t,t,t,,,t,t,t,t,, +LSTR,,t,,t,t,t,,,,t,t,,, +LTRE,t,t,,,t,,,,,t,t,,, +MAHD,t,t,,,,t,,,,t,,,, +MBNK,,,,t,t,t,,,,,,,, +MCGR,t,t,,,,t,,,,t,,,, +MDEA,t,,,,,t,t,,,t,,,,Mackenzie basin +MESC,,t,,,,,,,,t,,,, +MESI,t,,,,,t,t,,,t,,,,Mackenzie basin +MFRA,,t,,,,,,,,t,,,, +MFRT,,,,,,,t,,,,,,,Mackenzie basin +MIDR,t,t,,,,t,,,,t,t,,, +MILL,,,,,,,t,,,,,,,Mackenzie basin +MMUS,t,,,,,t,t,,,t,,,,Mackenzie basin +MORI,,,t,t,t,t,,,t,t,t,t,, +MORK,t,t,,,,t,,,,t,,,, +MORR,t,t,,t,t,t,,,t,t,t,t,, +MPRO,t,,,,,t,t,,,t,,,,Mackenzie basin +MSKE,t,t,,t,t,t,t,,,t,t,t,, +MSTR,t,,,,,t,t,,,t,,t,, +MURR,t,,,,t,t,t,,,t,,,,Mackenzie basin +MURT,,,,,,,,,,t,,,, +MUSK,,,,,,t,,,,t,,,, +NAHR,,t,,,,t,t,,,t,,,, +NAKR,,t,,t,,t,t,,,t,t,,, +NARC,t,t,,,,t,,,t,t,,,, +NASC,,,t,t,t,t,,,t,t,t,t,, +NASR,t,t,,t,t,t,,,,t,t,t,, +NATR,t,,,,,t,t,t,,t,,,,Mackenzie basin +NAZR,,t,,,,,,,,t,,,, +NBNK,,,,t,t,t,,,,,t,,, +NECL,,,t,t,t,t,,,t,t,t,t,, +NECR,t,t,,t,,t,,,,t,t,,, +NEVI,,,t,t,t,t,,,t,t,t,t,, +NICL,,t,,t,,,,,,t,,,, +NIEL,,t,t,t,t,t,,,t,t,t,t,, +NIMP,,t,t,t,t,t,,,t,t,t,t,, +OKAN,t,t,,,t,t,,,,t,t,,, +OSPK,t,,,,,t,t,,,t,,,,Mackenzie basin +OWIK,,t,t,t,t,t,,,t,t,t,t,, +PARA,t,,,,,t,t,,,t,,,,Mackenzie basin +PARK,t,t,t,t,t,t,,,t,t,,t,, +PARS,t,,,,,t,t,t,,t,,,,Mackenzie basin +PCEA,t,,,,,t,t,,,t,,,,Mackenzie basin +PINE,t,,,,,t,t,,,t,,,,Mackenzie basin +PITR,,,,,,t,,,,t,,,,No target species observations +PORI,,,t,t,t,t,,,t,t,,t,, +QUES,t,t,,t,,t,,,t,t,t,,, +REVL,t,,,,t,t,,,,t,,,t, +SAHD,,,,,,,t,,,,,,,Mackenzie basin +SAHT,,,,,,,,,,,,,,Mackenzie basin +SAJR,,,,t,,,,,t,t,t,,, +SALM,,t,t,t,t,t,,,t,t,,t,, +SALR,,t,,,,t,,,,t,,,, +SANJ,,t,t,t,t,t,,,t,t,t,t,, +SETN,t,t,t,t,t,t,,,t,t,t,t,, +SEYM,,t,t,t,t,t,,,t,t,,t,, +SHEK,,,,,,,,,,,,,,Mackenzie basin +SHER,,t,,t,t,t,,,,t,,t,, +SHUL,t,t,,t,t,t,,,t,t,t,,t, +SIML,t,,,,t,t,,,,t,,,,No target species observations +SKGT,t,,,,t,t,,,,t,,,, +SLOC,t,,,,t,t,,,,t,,,t, +SMAR,t,,,,t,t,,,,t,,,t, +SMOK,t,,,,t,t,t,,,t,,,,Mackenzie basin +SPAT,t,,,,,t,t,,,t,,,,No target species observations +SQAM,t,t,t,t,t,t,,,t,t,t,t,, +STHM,t,t,,t,t,t,,,t,t,t,,, +STIR,,t,,t,t,t,t,,,t,t,,, +STUL,,t,,,t,t,,,,t,t,,, +STUR,t,t,,,,t,,,,t,t,,, +SUST,t,t,t,t,,t,,,,t,t,t,, +SWIR,t,t,,,,t,t,,,,,,, +TABR,t,t,,,,t,,,,t,,,, +TAHR,t,,,,t,t,,,,t,t,t,, +TAHS,,t,t,t,t,t,,,t,t,t,t,, +TAKL,t,t,,,,t,,,,t,t,,, +TASR,t,t,,,,t,,,,t,t,,, +TATR,,t,,,,t,t,,,t,t,,, +TAYR,t,,,,,t,,,,t,,t,, +TESR,,t,,,,,t,,,t,,,, +THOM,t,t,,t,t,t,,,t,t,t,t,, +TOAD,t,,,,,t,t,,,,,,,Mackenzie basin +TOBA,,t,t,t,t,t,,,t,t,t,t,, +TOOD,t,,,,,t,t,,,t,,,,Mackenzie basin +TSAY,,t,t,t,t,t,,,t,t,,t,, +TSEA,,,,,,,t,,,,,,,Mackenzie basin +TSIT,,t,t,t,t,t,,,t,t,,t,, +TURN,t,,,,,t,t,,,t,,,,Mackenzie basin +TUTR,,,,,,,t,,,,,,, +TUYR,t,,,,,,t,,,,,,,Blockage near mouth of Tuya River +TWAC,t,t,,,,t,,,,t,,,, +UARL,t,,,,t,t,,,,t,,,t, +UBIR,t,t,,t,,t,,,,t,,,, +UBTN,t,,,,,,t,,,t,,,,Mackenzie basin +UCHR,t,t,,,,,,,,t,,t,, +UDEN,t,t,t,t,,t,,,t,t,t,t,,salmon/steelhead added as test for Ulkatcho +UEUT,t,,,,t,t,,,,t,,,, +UFRA,t,t,,,,t,,,,t,,,, +UFRT,,,,,,,t,,,,,,,Mackenzie basin +UHAF,t,,,,,,t,,,t,,,,Mackenzie basin +UISR,,,,,,t,,,,t,,,,Forrest Kerr Generating Station +UJER,,t,,,,,t,,,,,,, +UKEC,t,,,,,t,t,,,t,,,,Mackenzie basin +ULRD,t,,,,,t,t,,,t,,,,Mackenzie basin +UMUS,t,,,,,t,t,,,t,,,,Mackenzie basin +UNAR,t,t,,,t,t,,,,t,,t,, +UNRS,t,,,,,t,,,,t,,,, +UNTH,t,t,,t,t,t,,,,t,,,, +UNUR,t,,,t,t,t,,,,t,,,, +UOMI,t,,,,,t,t,,,t,,,,Mackenzie basin +UPCE,t,,,,t,t,t,,,t,,,,Mackenzie basin +UPET,,,,,,,t,,,t,,,,Mackenzie basin +UPRO,t,,,,,,t,,,t,,,,Mackenzie basin +USHU,t,t,,t,t,t,,,t,t,t,,t, +USIK,t,,,,,,t,,,t,,,,Mackenzie basin +USKE,t,t,,t,,t,,,,t,t,t,, +USTK,,,,,t,t,t,,,t,,t,, +UTRE,t,,,,,t,,,,t,t,,, +VICT,,t,t,t,t,t,,,,t,,t,, +WILL,t,t,,t,t,t,,,,t,,,, +WORC,,t,t,t,t,t,,,t,t,,t,, +ZYMO,t,t,,t,t,t,,,,t,,t,, diff --git a/inst/extdata/configs/default/parameters_fresh.csv b/inst/extdata/configs/default/parameters_fresh.csv index 7cf6b27..d7855ad 100644 --- a/inst/extdata/configs/default/parameters_fresh.csv +++ b/inst/extdata/configs/default/parameters_fresh.csv @@ -1,12 +1,14 @@ -"species_code","access_gradient_max","spawn_gradient_min","rear_gradient_min","cluster_rearing","cluster_direction","cluster_bridge_gradient","cluster_bridge_distance","cluster_confluence_m","cluster_spawning","cluster_spawn_direction","cluster_spawn_bridge_gradient","cluster_spawn_bridge_distance","cluster_spawn_confluence_m","observation_threshold","observation_date_min","observation_buffer_m","observation_species","observation_control_apply" -"BT",0.25,0,0,TRUE,"both",0.05,10000,10,FALSE,"",NA,NA,NA,1,"1900-01-01",20,"BT;CH;CO;SK;PK;CM;ST",FALSE -"CH",0.15,0,0,TRUE,"both",0.05,10000,10,FALSE,"",NA,NA,NA,5,"1990-01-01",20,"CH;CM;CO;PK;SK",TRUE -"CM",0.15,0,0,FALSE,"",NA,NA,NA,FALSE,"",NA,NA,NA,5,"1990-01-01",20,"CH;CM;CO;PK;SK",TRUE -"CO",0.15,0,0,TRUE,"both",0.05,10000,10,FALSE,"",NA,NA,NA,5,"1990-01-01",20,"CH;CM;CO;PK;SK",TRUE -"CT",0.25,0,0,FALSE,"",NA,NA,NA,FALSE,"",NA,NA,NA,NA,NA,NA,NA,NA -"DV",0.25,0,0,FALSE,"",NA,NA,NA,FALSE,"",NA,NA,NA,NA,NA,NA,NA,NA -"PK",0.15,0,0,FALSE,"",NA,NA,NA,FALSE,"",NA,NA,NA,5,"1990-01-01",20,"CH;CM;CO;PK;SK",TRUE -"RB",0.25,0,0,FALSE,"",NA,NA,NA,FALSE,"",NA,NA,NA,NA,NA,NA,NA,NA -"SK",0.15,0,0,TRUE,"both",0.05,10000,10,TRUE,"both",0.05,3000,10,5,"1990-01-01",20,"CH;CM;CO;PK;SK",TRUE -"ST",0.2,0,0,TRUE,"both",0.05,10000,10,FALSE,"",NA,NA,NA,5,"1990-01-01",20,"CH;CM;CO;PK;SK;ST",TRUE -"WCT",0.2,0,0,TRUE,"both",0.05,10000,10,FALSE,"",NA,NA,NA,1,"1900-01-01",20,"WCT",FALSE +species_code,access_gradient_max,spawn_gradient_min,rear_gradient_min,cluster_rearing,cluster_direction,cluster_bridge_gradient,cluster_bridge_distance,cluster_confluence_m,cluster_spawning,cluster_spawn_direction,cluster_spawn_bridge_gradient,cluster_spawn_bridge_distance,cluster_spawn_confluence_m,observation_threshold,observation_date_min,observation_buffer_m,observation_species,observation_control_apply +BT,0.25,0,0,TRUE,both,0.05,10000,10,FALSE,,NA,NA,NA,1,NA,20,BT;DV,FALSE +CH,0.15,0,0,TRUE,both,0.05,10000,10,FALSE,,NA,NA,NA,5,1990-01-01,20,CH;CM;CO;PK;SK,TRUE +CM,0.15,0,0,FALSE,,NA,NA,NA,FALSE,,NA,NA,NA,5,1990-01-01,20,CH;CM;CO;PK;SK,TRUE +CO,0.15,0,0,TRUE,both,0.05,10000,10,FALSE,,NA,NA,NA,5,1990-01-01,20,CH;CM;CO;PK;SK,TRUE +CT,0.25,0,0,FALSE,,NA,NA,NA,FALSE,,NA,NA,NA,NA,NA,NA,NA,NA +DV,0.25,0,0,FALSE,,NA,NA,NA,FALSE,,NA,NA,NA,NA,NA,NA,NA,NA +PK,0.15,0,0,FALSE,,NA,NA,NA,FALSE,,NA,NA,NA,5,1990-01-01,20,CH;CM;CO;PK;SK,TRUE +RB,0.25,0,0,FALSE,,NA,NA,NA,FALSE,,NA,NA,NA,NA,NA,NA,NA,NA +SK,0.15,0,0,TRUE,both,0.05,10000,10,TRUE,both,0.05,3000,10,5,1990-01-01,20,CH;CM;CO;PK;SK,TRUE +ST,0.2,0,0,TRUE,both,0.05,10000,10,FALSE,,NA,NA,NA,5,1990-01-01,20,CH;CM;CO;PK;SK;ST,TRUE +WCT,0.2,0,0,TRUE,both,0.05,10000,10,FALSE,,NA,NA,NA,1,1900-01-01,20,WCT,FALSE +GR,0.15,0,0,TRUE,both,0.05,10000,10,FALSE,,NA,NA,NA,5,1990-01-01,20,GR,TRUE +KO,0.15,0,0,TRUE,both,0.05,10000,10,TRUE,both,0.05,3000,10,5,1990-01-01,20,KO,TRUE \ No newline at end of file diff --git a/tests/testthat/test-lnk_pipeline_species.R b/tests/testthat/test-lnk_pipeline_species.R index e98ceb8..9fe1493 100644 --- a/tests/testthat/test-lnk_pipeline_species.R +++ b/tests/testthat/test-lnk_pipeline_species.R @@ -33,6 +33,41 @@ test_that("lnk_pipeline_species intersects cfg$species with AOI presence", { c("BT", "WCT")) }) +test_that("lnk_pipeline_species picks up species columns added to the CSV (link#106)", { + # Drives the column list from the CSV header — adding a new species + # (gr, ko) propagates without a code edit. + cfg_stub <- structure(list( + species = c("BT", "GR", "KO", "ST") + ), class = c("lnk_config", "list")) + loaded_stub <- list( + wsg_species_presence = data.frame( + watershed_group_code = "PARS", + bt = "t", ch = "f", cm = "f", co = "f", ct = "f", dv = "f", + gr = "t", ko = "t", + pk = "f", rb = "f", sk = "f", st = "f", wct = "f", + stringsAsFactors = FALSE + ) + ) + expect_setequal(lnk_pipeline_species(cfg_stub, loaded_stub, "PARS"), + c("BT", "GR", "KO")) +}) + +test_that("lnk_pipeline_species ignores notes column", { + cfg_stub <- structure(list( + species = c("BT") + ), class = c("lnk_config", "list")) + loaded_stub <- list( + wsg_species_presence = data.frame( + watershed_group_code = "PARS", + bt = "t", + notes = "t", # would falsely register as a species under naive logic + stringsAsFactors = FALSE + ) + ) + expect_setequal(lnk_pipeline_species(cfg_stub, loaded_stub, "PARS"), + c("BT")) +}) + test_that("lnk_pipeline_species returns empty when AOI not in WSG table", { cfg_stub <- structure(list( species = c("BT", "CH")