diff --git a/R/get_base_layers.R b/R/get_base_layers.R index af47006..d462d22 100644 --- a/R/get_base_layers.R +++ b/R/get_base_layers.R @@ -214,7 +214,7 @@ get_base_layers <- function(select.region, survey.strata <- sf::st_read(system.file("extdata", "ebs_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- survey.strata[survey.strata$STRATUM %in% c(10, 20, 31, 32, 41, 42, 43, 50, 61, 62, 82, 90), ] + survey.strata <- survey.strata[survey.strata$Stratum %in% c(10, 20, 31, 32, 41, 42, 43, 50, 61, 62, 82, 90), ] survey.grid <- sf::st_read(system.file("extdata", grid.file, package = "akgfmaps"), quiet = TRUE) @@ -229,7 +229,6 @@ get_base_layers <- function(select.region, quiet = TRUE) survey.strata <- sf::st_read(system.file("extdata", "ebs_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.grid <- sf::st_read(system.file("extdata", grid.file, package = "akgfmaps"), quiet = TRUE) @@ -247,7 +246,7 @@ get_base_layers <- function(select.region, survey.strata <- sf::st_read(system.file("extdata", "ebs_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- survey.strata[survey.strata$STRATUM %in% c(81, 70, 71), ] + survey.strata <- survey.strata[survey.strata$Stratum %in% c(81,70,71), ] survey.grid <- sf::st_read(system.file("extdata", "bs_grid_w_corners.shp", package = "akgfmaps"), quiet = TRUE) @@ -308,6 +307,9 @@ get_base_layers <- function(select.region, survey.strata <- sf::st_read(system.file("extdata", "ai_strata.shp", package = "akgfmaps"), quiet = TRUE) survey.grid <- sf::st_read(system.file("extdata", "ai_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM < 800 & survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM < 800 & survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "ai", set.crs = set.crs) lon.breaks <- c(170, 175, -180, -175, -170, -165, -160) @@ -320,6 +322,9 @@ get_base_layers <- function(select.region, survey.strata <- sf::st_read(system.file("extdata", "ai_strata.shp", package = "akgfmaps"), quiet = TRUE) survey.grid <- sf::st_read(system.file("extdata", "ai_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM < 800 & survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM < 800 & survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "ai", set.crs = set.crs) lon.breaks <- seq(-176, -164, 2) @@ -329,11 +334,12 @@ get_base_layers <- function(select.region, # Aleutian Islands - Central --------------------------------------------------------------------- if(select.region[1] == "ai.central") { survey.area <- sf::st_read(system.file("extdata", "ai_area.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- sf::st_read(system.file("extdata", "ai_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.grid <- sf::st_read(system.file("extdata", "ai_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM < 800 & survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM < 800 & survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "ai", set.crs = set.crs) lon.breaks <- c(176, 178, 180, seq(-178, -170, 2)) @@ -343,11 +349,12 @@ get_base_layers <- function(select.region, # Aleutian Islands - West --------------------------------------------------------------------- if(select.region[1] == "ai.west") { survey.area <- sf::st_read(system.file("extdata", "ai_area.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- sf::st_read(system.file("extdata", "ai_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.grid <- sf::st_read(system.file("extdata", "ai_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM < 800 & survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM < 800 & survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "ai", set.crs = set.crs) lon.breaks <- seq(168, 180, 2) @@ -358,11 +365,12 @@ get_base_layers <- function(select.region, # Gulf of Alaska --------------------------------------------------------------------------------- if(select.region[1] == "goa") { survey.area <- sf::st_read(system.file("extdata", "goa_area.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- sf::st_read(system.file("extdata", "goa_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.grid <- sf::st_read(system.file("extdata", "goa_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "goa", set.crs = set.crs) lon.breaks <- seq(-175, -130, 5) @@ -372,11 +380,12 @@ get_base_layers <- function(select.region, # Gulf of Alaska - West -------------------------------------------------------------------------- if(select.region[1] == "goa.west") { survey.area <- sf::st_read(system.file("extdata", "goa_area.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- sf::st_read(system.file("extdata", "goa_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.grid <- sf::st_read(system.file("extdata", "goa_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "goa", set.crs = set.crs) lon.breaks <- seq(-174, -144, 2) @@ -386,11 +395,12 @@ get_base_layers <- function(select.region, # Gulf of Alaska - East -------------------------------------------------------------------------- if(select.region[1] == "goa.east") { survey.area <- sf::st_read(system.file("extdata", "goa_area.shp", package = "akgfmaps"), quiet = TRUE) - survey.strata <- sf::st_read(system.file("extdata", "goa_strata.shp", package = "akgfmaps"), quiet = TRUE) - survey.grid <- sf::st_read(system.file("extdata", "goa_grid.shp", package = "akgfmaps"), quiet = TRUE) + survey.strata <- survey.strata[survey.strata$STRATUM > 0, ] + survey.grid <- survey.grid[survey.grid$STRATUM > 0, ] + inpfc.strata <- get_inpfc_strata(select.region = "goa", set.crs = set.crs) lon.breaks <- seq(-160, -124, 2) @@ -549,23 +559,23 @@ get_base_layers <- function(select.region, "Exploitabl", "Active"), names(survey.grid) - ) - ] <- c("STATION_NUMBER", - "REGION", - "STATION_TYPE", - "STATION_DEPTH", - "GEOGRAPHIC_AREA", - "GEOGRAPHIC_AREA_NUMBER", - "NPFMC_MANAGEMENT_AREA", - "NPFMC_SABLEFISH_AREA", - "REP_AREA", - "FMP_MANAGEMENT_AREA", - "INPFC_MANAGEMENT_AREA", - "HABITAT_TYPE", - "LAT", - "LONG", - "EXPLOITABLE", - "ACTIVE") + ) + ] <- c("STATION_NUMBER", + "REGION", + "STATION_TYPE", + "STATION_DEPTH", + "GEOGRAPHIC_AREA", + "GEOGRAPHIC_AREA_NUMBER", + "NPFMC_MANAGEMENT_AREA", + "NPFMC_SABLEFISH_AREA", + "REP_AREA", + "FMP_MANAGEMENT_AREA", + "INPFC_MANAGEMENT_AREA", + "HABITAT_TYPE", + "LAT", + "LONG", + "EXPLOITABLE", + "ACTIVE") survey.area <- survey.strata[, "geometry"] |> sf::st_union(by_feature = FALSE) |> @@ -719,7 +729,7 @@ get_base_layers <- function(select.region, place.labels <- akgfmaps::transform_data_frame_crs(place.labels, out.crs = set.crs) - # Correct remaining degenerate geometry and dateline wrapping issues ----------------------------- + # Attempt to correct any remaining degenerate geometry and dateline wrapping issues -------------- if(fix.invalid.geom) { akland <- fix_geometry(x = akland)