Merge pull request #144 from afsc-gap-products/dev2

Fix demos

assets/demo/akgfmaps_SCRUG_20250122/ex2_get_layers.R

@@ -14,7 +14,7 @@ library(akgfmaps)
 
 # Get layers for one survey region
 ebs_layers <- akgfmaps::get_base_layers(
-  select.region = "sebs", # EBS shelf bottom traw survey regions
+  select.region = "sebs", # EBS shelf bottom trawl survey regions
   set.crs = "EPSG:3338", # Coordinate reference system, in this case Alaska Albers Equal Area
   high.resolution.coast = FALSE, # Set to TRUE when coast is used for analyses, e.g. raster masking
   design.year = NULL # Return the most recent/current survey design
@@ -92,17 +92,17 @@ goa_1984_2025_strata <- rbind(
 
 # Plot 1984 and 2025 survey strata for the WGOA
 ggplot() +
-  geom_sf(data = goa_1984$akland) +
+  geom_sf(data = goa_1984_layers$akland) +
   geom_sf(data = goa_1984_2025_strata,
           mapping = aes(color = factor(DESIGN_YEAR)),
           fill = NA,
           alpha = 0.5) +
   scale_color_manual(name = "Design year",
                      values = c("red", "black")) +
-  scale_x_continuous(limits = goa_1984$plot.boundary$x,
-                     breaks = goa_1984$lon.breaks) +
-  scale_y_continuous(limits = goa_1984$plot.boundary$y,
-                     breaks = goa_1984$lat.breaks) +
+  scale_x_continuous(limits = goa_1984_layers$plot.boundary$x,
+                     breaks = goa_1984_layers$lon.breaks) +
+  scale_y_continuous(limits = goa_1984_layers$plot.boundary$y,
+                     breaks = goa_1984_layers$lat.breaks) +
   theme_bw()
 
 goa_1984_2025_grid <- rbind(
@@ -112,17 +112,17 @@ goa_1984_2025_grid <- rbind(
 
 # Plot 1984 and 2025 survey grid for the WGOA
 ggplot() +
-  geom_sf(data = goa_1984$akland) +
+  geom_sf(data = goa_1984_layers$akland) +
   geom_sf(data = goa_1984_2025_grid,
           mapping = aes(color = factor(DESIGN_YEAR)),
           fill = NA,
           alpha = 0.5) +
   scale_color_manual(name = "Design year",
                      values = c("red", "black")) +
-  scale_x_continuous(limits = goa_1984$plot.boundary$x,
-                     breaks = goa_1984$lon.breaks) +
-  scale_y_continuous(limits = goa_1984$plot.boundary$y,
-                     breaks = goa_1984$lat.breaks) +
+  scale_x_continuous(limits = goa_1984_layers$plot.boundary$x,
+                     breaks = goa_1984_layers$lon.breaks) +
+  scale_y_continuous(limits = goa_1984_layers$plot.boundary$y,
+                     breaks = goa_1984_layers$lat.breaks) +
   theme_bw()
 
 # EBS shelf survey with corner stations for the 2023 survey

assets/demo/akgfmaps_SCRUG_20250122/ex3_make_idw_map.R

@@ -27,6 +27,8 @@ noodles_sf <- akgfmaps::NOODLES |>
   dplyr::rename(STATION = STATIONID) |>
   dplyr::mutate(Present = CPUE_KGHA > 0) # Plot presence/absence
 
+nbs_layers <- get_base_layers(select.region = "nbs", set.crs = "EPSG:3338")
+
 # spatially join survey grid polygons to noodle CPUE points data
 noodles_grid <- sf::st_join(nbs_layers$survey.grid,
                             noodles_sf)

assets/demo/akgfmaps_SCRUG_20250122/ex4_geopackages.R

@@ -0,0 +1,78 @@
+# Example: Access data directly from a geopackage
+# SCRUG, akgfmaps, January 22, 2025
+# Created by Sean Rohan (GitHub: sean-rohan-noaa)
+
+# akgfmaps installs layer files locally
+# Layers used to include a variety of formats; starting with akgfmaps v4, layers will be included in
+# geopackage (.gpkg) files.
+list.files(system.file("extdata", package = "akgfmaps"),
+           full.names = TRUE)
+
+# Loading layers directly from built-in Geopackage
+# Geopackages are an open, standards-based, platform-independent format for storing geospatial data.
+# They are based on SQLite, can store multiple layers and data types in one file.
+
+library(akgfmaps)
+library(dplyr)
+
+# Filepath to geopackage with AFSC bottom trawl survey layers
+gpkg_fpath <- system.file("extdata", "afsc_bottom_trawl_surveys.gpkg", package = "akgfmaps")
+
+# Inpsect the layers at the dsn (data source name).
+# There are four layers in individual tables (called 'layers' in sf)
+sf::st_layers(dsn = gpkg_fpath)
+
+# Load all of of the features from the survey_area layer
+survey_areas <- sf::st_read(dsn = gpkg_fpath,
+                            layer = "survey_area")
+
+survey_areas
+
+# Plot the survey areas
+ggplot() +
+  geom_sf(data = survey_areas,
+          mapping = aes(color = SURVEY_NAME),
+          fill = NA) +
+  facet_wrap(~DESIGN_YEAR) +
+  theme(legend.position = "bottom")
+
+# Filter to retreive the NBS survey area
+nbs_area <- dplyr::filter(survey_areas, SURVEY_DEFINITION_ID == 143)
+
+ggplot() +
+  geom_sf(data = nbs_area,
+          mapping = aes(color = SURVEY_NAME)) +
+  facet_wrap(~DESIGN_YEAR) +
+  theme(legend.position = "bottom")
+
+# Alternatively, we can retrieve features from the geopackage using a SQLite query.
+# In this case, retrieve GOA stratum polygons for the 1984 and 2025 design years.
+goa_strata <- sf::st_read(dsn = gpkg_fpath,
+                          query =
+                          "SELECT
+                            AREA_TYPE,
+                            SURVEY_DEFINITION_ID,
+                            DESIGN_YEAR,
+                            AREA_ID AS STRATUM,
+                            AREA_M2,
+                            GEOM
+                            FROM SURVEY_STRATA
+                            WHERE SURVEY_DEFINITION_ID = 47"
+                          )
+
+head(goa_strata)
+table(goa_strata$DESIGN_YEAR)
+
+# Plotting the 1984 and 2025 GOA survey strata
+ggplot() +
+  geom_sf(data = goa_strata,
+          mapping = aes(fill = factor(STRATUM)),
+          color = NA) +
+  scale_fill_viridis_d(option = "H") +
+  facet_wrap(~DESIGN_YEAR, nrow = 2) +
+  theme(legend.position = "none",
+        axis.title = element_blank())
+
+
+# Land layers
+sf::st_layers(dsn = system.file("extdata", "land_layers.gpkg", package = "akgfmaps"))

assets/demo/akgfmaps_SCRUG_20250122/ex5_get_layers_old_version.R

@@ -0,0 +1,75 @@
+# Example: Using the old get_base_layers() function
+# SCRUG, akgfmaps, January 22, 2025
+# Created by Sean Rohan (GitHub: sean-rohan-noaa)
+
+# Through the end of 2025, an option will be provided to use the old interface and layers using
+# get_base_layers_v3(). The function is limited to the functionality and layers that were avaialble
+# in akgfmaps v 3.6.2
+#
+# The old version has the following limitations:
+# - No access to design years (e.g., the most recent GOA BT survey stratum shapefile will be 1984)
+# - Cannot select multiple regions at the same time
+# - Field names differ among shapefiles
+# - No correspondence with GAP_PRODUCTS
+# - Access to longline
+
+# Recommendation: Don't use this version unless you can't replace with the new version due to time
+# and reliance on fields in specific shapefiles.
+
+library(akgfmaps)
+
+# Arguments differ between function versions
+?get_base_layers
+?get_base_layers_v3
+
+# Retrieve and plot GOA and EBS/NBS strata
+goa_1984_v3 <- akgfmaps::get_base_layers_v3(
+  select.region = "goa",
+  set.crs = "EPSG:3338",
+  high.resolution.coast = FALSE
+)
+
+ebs_nbs_2024_v3 <- akgfmaps::get_base_layers_v3(
+  select.region = "ebs",
+  set.crs = "EPSG:3338",
+  high.resolution.coast = FALSE
+)
+
+ggplot() +
+  geom_sf(data = goa_1984_v3$akland) +
+  geom_sf(data = goa_1984_v3$survey.strata,
+          mapping = aes(
+            fill = factor(STRATUM)
+          )
+  ) +
+  scale_x_continuous(limits = goa_1984_v3$plot.boundary$x,
+                     breaks = goa_1984_v3$lon.breaks) +
+  scale_y_continuous(limits = goa_1984_v3$plot.boundary$y,
+                     breaks = goa_1984_v3$lat.breaks) +
+  theme_bw() +
+  scale_fill_viridis_d(option = "H") +
+  theme(legend.position = "none")
+
+ggplot() +
+  geom_sf(data = ebs_nbs_2024_v3$akland) +
+  geom_sf(data = ebs_nbs_2024_v3$survey.strata,
+          mapping = aes(
+            fill = factor(Stratum)
+          )
+  ) +
+  scale_x_continuous(limits = ebs_nbs_2024_v3$plot.boundary$x,
+                     breaks = ebs_nbs_2024_v3$lon.breaks) +
+  scale_y_continuous(limits = ebs_nbs_2024_v3$plot.boundary$y,
+                     breaks = ebs_nbs_2024_v3$lat.breaks) +
+  scale_fill_viridis_d(option = "H") +
+  theme_bw() +
+  theme(legend.position = "none")
+
+# Note that the field names do not match within or between regions.
+head(goa_1984_v3$survey.area)
+head(goa_1984_v3$survey.strata)
+head(goa_1984_v3$survey.grid)
+
+head(ebs_nbs_2024_v3$survey.area)
+head(ebs_nbs_2024_v3$survey.strata)
+head(ebs_nbs_2024_v3$survey.grid)