v3.3.0

.gitignore

@@ -38,9 +38,11 @@
 inst/doc
 doc
 Meta
-*.png
 *.lock
 
 /vignettes/*.html
 /vignettes/*.R
-/vignettes/*.md
+/vignettes/*.md
+/vignettes/*.png
+/vignettes/figure
+/plots/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: akgfmaps
 Type: Package
 Title: Alaska Groundfish and Ecosystem Survey Area Mapping
-Version: 3.2.0
+Version: 3.3.0
 Authors@R: c(person("Sean", "Rohan", email = "[email protected]", role = c("aut", "cre")),
     person("Jason", "Conner", email = "[email protected]", role = "ctb"),
     person("Liz", "Dawson", email = "[email protected]", role = "ctb"),

NEWS

@@ -1,3 +1,58 @@
+akgfmaps 3.3.0 (October 19, 2023)
+----------------------------------------------------------------
+
+NEW FEATURE
+
+- Added an include_grid_cell argument to make_2d_grid() that
+  makes the function return columns with the center coordinates
+  (lon_plot, lat_plot) of each grid cell prior to intersecting 
+  with the user-provided sf object (passed to obj argument). 
+  Centroids for intersected grid polygons are still returned by 
+  the function for use in spatial analyses and index production 
+  (e.g. VAST, sdmTMB) because they are the center of grid cells 
+  after intersecting with stratum shapefiles. The centroid prior
+  to intersection is more useful for plotting gridded data with-
+  out prior transformation.
+
+  EXAMPLE
+
+  Grid cell centroids before intersection (regularly-spaced):
+
+                +-----------+-----------+
+                |           |           | 
+                |           |           |
+                |     x     |     x     |
+                |           |           |
+                |           |           |
+                +-----------+-----------+
+
+  Grid cell centroids after intersection (irregularly-spaced;
+  useful for analyses that require accurate distances):
+
+                +-----------+-----------+
+                |          /|           |        
+                |    x    / |           |
+                |        /  |     x     |
+                |       / x |           |
+                |      /    |           |
+                +-----------+-----------+
+
+  Grid cell centroids for plotting after intersection (still 
+  regularly-spaced):
+
+                +-----------+-----------+
+                |          /|           |        
+                |         / |           |
+                |     X  /  |     x     |
+                |       /   |           |
+                |      /    |           |
+                +-----------+-----------+
+
+  USAGE
+
+  See https://github.com/afsc-gap-products/akgfmaps/blob/main/assets/make_plot_grid.md
+
+
 akgfmaps 3.2.0 (October 6, 2023)
 ----------------------------------------------------------------
 

R/make_2d_grid.R

@@ -7,9 +7,10 @@
 #' @param output_type Type of output as a 1L character vector ("point", "raster", "polygon).
 #' @param bbox Optional. A 4L numeric vector to define the edges of the interpolation grid c(xmin, ymin, xmax, ymax).
 #' @param model Character vector indicating the geometry model to use for st_intersection boundaries. Default = "semi-open"; for details see ?s2::s2_options
+#' @param include_tile_center Should the center point of each tile be included in the output? This helps with plotting data because the center point for grid locations after intesecting with the stratum shapefile is not always the center of a grid cell since intersected cells are not always squares.
 #' @export
 
-make_2d_grid <- function(obj, resolution = c(3704, 3704), output_type = "point", bbox = NULL, model = "semi-open") {
+make_2d_grid <- function(obj, resolution = c(3704, 3704), output_type = "point", bbox = NULL, model = "semi-open", include_tile_center = FALSE) {
 
   # Extract CRS
   obj_srid <- sf::st_crs(obj, parameters = TRUE)$srid
@@ -62,7 +63,22 @@ make_2d_grid <- function(obj, resolution = c(3704, 3704), output_type = "point",
 
   # Convert to polygon and find intersection with obj
   interp_polygons <- terra::as.polygons(interp_grid) |> 
-    sf::st_as_sf(crs = obj_srid) |> 
+    sf::st_as_sf(crs = obj_srid)
+
+  # Add tile center coordinates for plotting
+  if(include_tile_center) {
+
+    coords_for_plots <- sf::st_centroid(interp_polygons) |>
+      sf::st_coordinates() |>
+      as.data.frame() |>
+      dplyr::rename(lon_plot = X, lat_plot = Y)
+
+    interp_polygons <- interp_polygons |>
+      dplyr::bind_cols(coords_for_plots)
+
+  }
+
+  interp_polygons <- interp_polygons |>
     sf::st_intersection(obj, model = model)
 
   # Convert to square kilometers

assets/make_plot_grid.md

@@ -0,0 +1,34 @@
+# Return coordinates for plotting gridded data using make_2d_grid()
+
+### _Feature added in 3.3.0 (see [NEWS](/NEWS))_
+
+This example show how to use the make_2d_grid() function to produce grid cell centroid
+coordinates that facilitate plotting data from 2d grids that are used for spatial
+analyses (e.g. using VAST or sdmTMB). Otherwise this would require post-processing 
+manipulation of gridded data.
+
+The plotting coordinate columns (lon_plot and lat_plot) should only be used for 
+visualization.
+
+``` r
+library(akgfmaps)
+
+ebs_layers <- akgfmaps::get_base_layers(select.region = "sebs",
+                                        set.crs = "EPSG:3338")
+
+ebs_grid <- akgfmaps:::make_2d_grid(obj = ebs_layers$survey.strata,
+                                    resolution = res,
+                                    bbox = vast_bbox,
+                                    output_type = "point",
+                                    include_tile_center = TRUE)
+
+p1 <- ggplot() +
+      geom_tile(data = ebs_grid,
+                mapping = aes(x = lon_plot,
+                              y = lat_plot,
+                              fill = Stratum))
+
+p1
+```
+
+![](/assets/ex_2d_grid_with_plot_centroids.png)