Merge pull request #60 from emlab-ucsb/dev-misc

Dev misc
emlab-ucsb · Jan 16, 2025 · 9a3060b · 9a3060b
2 parents 6dd763a + 340eeba
commit 9a3060b
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Showing 12 changed files with 68 additions and 106 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -14,6 +14,7 @@ export(get_gfw)
 export(get_grid)
 export(get_knolls)
 export(get_seamounts)
+export(remove_empty_layers)
 importFrom(graphics,legend)
 importFrom(graphics,par)
 importFrom(magrittr,"%>%")

diff --git a/R/get_features.R b/R/get_features.R
@@ -97,7 +97,7 @@ get_features <- function(spatial_grid = NULL, raw = FALSE, features = c("bathyme
   if("enviro_zones" %in% features) { 
     message("Getting environmental zones data... This could take several minutes")
     suppressMessages({
-      enviro_zones <- get_enviro_zones(spatial_grid = spatial_grid, raw = raw, show_plots = FALSE, num_clusters = enviro_clusters, max_num_clusters = max_enviro_clusters, antimeridian = antimeridian)
+      enviro_zones <- get_enviro_zones(spatial_grid = spatial_grid, raw = raw, enviro_zones = !raw, show_plots = FALSE, num_clusters = enviro_clusters, max_num_clusters = max_enviro_clusters, antimeridian = antimeridian)
     })
   }
 

diff --git a/R/utils.R b/R/utils.R
@@ -135,8 +135,8 @@ classify_layers <- function(dat, dat_breaks = NULL, classification_names = NULL)
       dplyr::select(3:ncol(.), 2) #put classification before geometry and drop original values
   }
 }
-#' Get an sf polygons in lonlat (EPSG 4326) from terra or sf input object
-#'
+#' Get an sf polygon in lonlat (EPSG 4326) from terra or sf input object
+#' 
 #' @param spatial_grid 
 #'
 #' @return `sf` polygons
@@ -169,20 +169,30 @@ polygon_in_4326 <-
       }
   }
 
-#' Remove empty layers in raster or columns with all zeroes in sf
+#' Remove empty layers in spatial object
 #'
-#' @param dat `sf` or raster object
+#' @description
+#' Removes any layers (`terra::rast` object) or columns (`sf` object) that are all zero or NA 
+#' 
+#' @param dat `sf` or `terra::rast` object
 #'
-#' @return `sf` or raster depending on input
+#' @return `sf` or `terra::rast` depending on input
 #'
-#' @noRd
+#' @export
 remove_empty_layers <- function(dat){
   if(check_sf(dat)){
-    dat %>% 
-      dplyr::select(which(!colSums(sf::st_drop_geometry(dat), na.rm = TRUE) %in% 0))
+    column_sums <- colSums(sf::st_drop_geometry(dat), na.rm = TRUE)
+
+    if(sum(column_sums) == 0){
+      stop("Only NAs and/ or zeroes in sf object")
+    }else dplyr::select(dat, which(!column_sums %in% 0))
+
   }else{
-    dat %>% 
-    terra::subset(which(terra::global(dat, "sum", na.rm = TRUE) >0))  
+    index_true_false  <- (terra::global(dat, "sum", na.rm = TRUE) >0)
+
+    if(all(index_true_false %in% c(NA, FALSE))) {
+      stop("Only NAs and/ or zeroes in raster")
+    } else terra::subset(dat, which(index_true_false))  
   }
 }
 

diff --git a/man/remove_empty_layers.Rd b/man/remove_empty_layers.Rd
diff --git a/tests/testthat/test-get_coral_habitat.R b/tests/testthat/test-get_coral_habitat.R
@@ -8,28 +8,21 @@ test_that("returns raw data for Bermuda", {
 # })
 
 test_that("returns Bermuda gridded data - raster", {
-  expect_s4_class(get_coral_habitat(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                      crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                                      resolution = 10000)), class = "SpatRaster")
+  expect_s4_class(get_coral_habitat(spatial_grid = get_bermuda_grid()), class = "SpatRaster")
 })
 
 test_that("returns gridded data for Kiribati - raster", {
-  expect_s4_class(get_coral_habitat(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"),
-                                                      crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs',
-                                                      resolution = 50000)),
+  expect_s4_class(get_coral_habitat(spatial_grid = get_kiribati_grid()),
                   class = "SpatRaster")
 })
 
 test_that("returns gridded data for Bermuda - sf", {
-  expect_s3_class(get_coral_habitat(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                            crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                            resolution = 10000, 
-                                                            output = "sf_square")), class = "sf")
+  expect_s3_class(get_coral_habitat(spatial_grid = get_bermuda_grid(output = "sf_square")), 
+                  class = "sf")
 })
 
 test_that("returns extra columns as well as coral data for sf grid", {
-  expect_equal(get_boundary(name = "Bermuda") |> 
-                 get_grid(resolution = 10000, crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', output = "sf_square") |> 
+  expect_equal(get_bermuda_grid(output = "sf_square") |> 
                  dplyr::mutate(extracol1 = 1, extracol2 = 2, .before = 1) |> 
                  get_coral_habitat() |>
                  ncol(), 6)

diff --git a/tests/testthat/test-get_dist.R b/tests/testthat/test-get_dist.R
@@ -1,23 +1,15 @@
 test_that("returns gridded Bermuda distance to shore - raster", {
-  expect_s4_class(suppressWarnings(get_dist(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                      crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                                      resolution = 10000))), 
+  expect_s4_class(suppressWarnings(get_dist(spatial_grid = get_bermuda_grid())), 
                   class = "SpatRaster")
 })
 
 test_that("returns gridded distance to shore for Kiribati - sf", {
-  expect_s3_class(suppressWarnings(get_dist(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"), 
-                                                                      crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs', 
-                                                                      resolution = 50000, 
-                                                                      output = "sf_hex"))), 
+  expect_s3_class(suppressWarnings(get_dist(spatial_grid = get_kiribati_grid(output = "sf_hex"))), 
                   class = "sf")
 })
 
 test_that("returns gridded distance to port for Kiribati - raster", {
-  expect_s3_class(suppressWarnings(get_dist(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"), 
-                                                                    crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs', 
-                                                                    resolution = 50000, 
-                                                                    output = "sf_hex"), dist_to = "ports")), 
+  expect_s3_class(suppressWarnings(get_dist(spatial_grid = get_kiribati_grid(output = "sf_hex"), dist_to = "ports")), 
                   class = "sf")
 })
 

diff --git a/tests/testthat/test-get_ecoregion.R b/tests/testthat/test-get_ecoregion.R
@@ -8,30 +8,20 @@ test_that("returns 6 ecoregions for Kiribati - sf", {
 })
 
 test_that("returns Bermuda gridded data - raster", {
-  expect_s4_class(get_ecoregion(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                            crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                            resolution = 10000, 
-                                                        output = "raster"), type = "MEOW"), class = "SpatRaster")
+  expect_s4_class(get_ecoregion(spatial_grid = get_bermuda_grid(), type = "MEOW"), class = "SpatRaster")
 })
 
 test_that("returns Bermuda gridded data for no data - raster", {
-  expect_s4_class(get_ecoregion(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                        crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                        resolution = 10000, 
-                                                        output = "raster"), type = "LME"), class = "SpatRaster")
+  expect_s4_class(get_ecoregion(spatial_grid = get_bermuda_grid(), type = "LME"), class = "SpatRaster")
 })
 
 test_that("returns gridded data for Kiribati - sf", {
-  expect_s3_class(get_ecoregion(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"),
-                                                            crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs',
-                                                            resolution = 50000, 
-                                                          output = "sf_square"), type = "Longhurst"),
+  expect_s3_class(get_ecoregion(spatial_grid = get_kiribati_grid(output = "sf_square"), type = "Longhurst"),
                   class = "sf")
 })
 
 test_that("returns extra columns as well as empty data for sf grid", {
-  expect_equal(get_boundary(name = "Bermuda") |> 
-                 get_grid(resolution = 10000, crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', output = "sf_square") |> 
+  expect_equal(get_bermuda_grid(output = "sf_square") |> 
                  dplyr::mutate(extracol1 = 1, extracol2 = 2, .before = 1) |> 
                  get_ecoregion(type = "LME") |>
                  ncol(), 4)

diff --git a/tests/testthat/test-get_enviro_zones.R b/tests/testthat/test-get_enviro_zones.R
@@ -4,43 +4,29 @@ test_that("returns raw Bio-Oracle data - 11 layer raster", {
 
 test_that("returns gridded Bermuda Bio-Oracle data - raster", {
   set.seed(500)
-  expect_s4_class(get_boundary(name = "Bermuda") |> 
-                    get_grid(crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                             resolution = 20000)|> 
+  expect_s4_class(get_bermuda_grid()|> 
                     get_enviro_zones(raw = FALSE, enviro_zones = FALSE), class = "SpatRaster")
 })
 
 test_that("returns gridded Bermuda Bio-Oracle data - sf", {
   set.seed(500)
-  expect_s3_class(get_boundary(name = "Bermuda") |> 
-                    get_grid(crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                             resolution = 20000,
-                             output = "sf_square")|> 
+  expect_s3_class(get_bermuda_grid(output = "sf_square")|> 
                     get_enviro_zones(raw = FALSE, enviro_zones = FALSE), class = "sf")
 })
 
 test_that("returns gridded Bermuda envirozones - raster", {
-  expect_s4_class(get_boundary(name = "Bermuda") |> 
-                    get_grid(crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                             resolution = 20000,
-                             output = "raster")|> 
+  expect_s4_class(get_bermuda_grid()|> 
                     get_enviro_zones(raw = FALSE, enviro_zones = TRUE, num_clusters = 3), class = "SpatRaster")
 })
 
 test_that("returns gridded Kiribati envirozones - sf", {
-  expect_s3_class(get_boundary(name = "Kiribati", country_type = "sovereign") |> 
-                    get_grid(crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs', 
-                             resolution = 50000,
-                             output = "sf_square") |>
+  expect_s3_class(get_kiribati_grid(output = "sf_square") |>
                     get_enviro_zones(raw = FALSE, enviro_zones = TRUE, num_clusters = 3), class = "sf")
 })
 
 test_that("returns gridded Bermuda envirozones data with extra input columns - sf", {
   set.seed(500)
-  expect_equal(get_boundary(name = "Bermuda") |> 
-                    get_grid(crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                             resolution = 20000,
-                             output = "sf_square") |> 
+  expect_equal(get_bermuda_grid(output = "sf_square") |> 
                     dplyr::mutate(extracol1 = 1, extracol2 = 2, .before = 1) |>
                     get_enviro_zones(raw = FALSE, enviro_zones = TRUE, show_plots = TRUE) |>
                  ncol(), 6)

diff --git a/tests/testthat/test-get_features.R b/tests/testthat/test-get_features.R
@@ -5,20 +5,15 @@ test_that("returns raw Bermuda data as list", {
 
 test_that("returns gridded Bermuda features - raster", {
   set.seed(500)
-  expect_s4_class(suppressWarnings(get_features(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                                        crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                                                        resolution = 20000))),
+  expect_s4_class(suppressWarnings(get_features(spatial_grid = get_bermuda_grid())),
                   class = "SpatRaster")
 })
 
 test_that("returns gridded Kiribati features - sf with extra cols", {
   set.seed(1234)
-  expect_equal(suppressWarnings(get_boundary(name = "Kiribati", country_type = "sovereign") |>
-                                     get_grid(crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs',
-                                              resolution = 50000, 
-                                              output = "sf_square") |>
+  expect_equal(suppressWarnings(get_kiribati_grid(output = "sf_square") |>
                                      dplyr::mutate(extracol1 = 1, extracol2 = 2, .before = 1) |>
                                      get_features(antimeridian = TRUE) |>
                                   ncol()), 
-               39)
+               41)
 })
diff --git a/tests/testthat/test-get_geomorphology.R b/tests/testthat/test-get_geomorphology.R
@@ -4,17 +4,12 @@ test_that("return raw data for Bermuda - sf", {
 })
 
 test_that("return gridded data for Bermuda - raster", {
-  expect_s4_class(get_geomorphology(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                      crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs',
-                                                                      resolution = 20000)), 
+  expect_s4_class(get_geomorphology(spatial_grid = get_bermuda_grid()), 
                   class = "SpatRaster")
 })
 
 test_that("return gridded data for Bermuda - sf", {
-  expect_s3_class(get_geomorphology(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                            crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs',
-                                                            resolution = 20000,
-                                                            output = "sf_hex")), 
+  expect_s3_class(get_geomorphology(spatial_grid = get_bermuda_grid(output = "sf_hex")), 
                   class = "sf")
 })
 
@@ -24,8 +19,6 @@ test_that("return raw data for Kiribati - sf", {
 })
 
 test_that("return gridded data for Kiribati  - raster", {
-  expect_s4_class(get_geomorphology(spatial_grid = get_grid(get_boundary(name = "Kiribati", country_type = "sovereign"),
-                                                            crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs',
-                                                            resolution = 50000)), 
+  expect_s4_class(get_geomorphology(spatial_grid = get_kiribati_grid()), 
                   class = "SpatRaster")
 })
diff --git a/tests/testthat/test-get_knolls.R b/tests/testthat/test-get_knolls.R
@@ -4,9 +4,7 @@ test_that("returns raw knolls data for Bermuda - sf", {
 })
 
 test_that("returns gridded Bermuda data - raster", {
-  expect_s4_class(suppressWarnings(get_knolls(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                                crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                                                resolution = 10000))), 
+  expect_s4_class(suppressWarnings(get_knolls(spatial_grid = get_bermuda_grid())), 
                   class = "SpatRaster")
 })
 
@@ -18,10 +16,7 @@ test_that("returns raw data for Kiribati - sf", {
 })
 
 test_that("returns gridded data for Kiribati - sf", {
-  expect_s3_class(suppressWarnings(get_knolls(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"), 
-                                                                                crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs', 
-                                                                                resolution = 50000, 
-                                                                      output = "sf_hex"), 
+  expect_s3_class(suppressWarnings(get_knolls(spatial_grid = get_kiribati_grid(output = "sf_hex"), 
                                               antimeridian = TRUE)), 
                   class = "sf")
 })
diff --git a/tests/testthat/test-get_seamounts.R b/tests/testthat/test-get_seamounts.R
@@ -24,39 +24,29 @@ test_that("returns Kiribati raw peaks data buffered - sf", {
 })
 
 test_that("returns buffered gridded Bermuda seamounts - raster", {
-  expect_s4_class(suppressWarnings(get_seamounts(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                         crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                                         resolution = 20000),
+  expect_s4_class(suppressWarnings(get_seamounts(spatial_grid = get_bermuda_grid(),
                                                  raw = FALSE,
                                                  buffer = 30000)),
                   class = "SpatRaster")
 })
 
 test_that("returns buffered gridded Kiribati seamounts - raster", {
-  expect_s4_class(suppressWarnings(get_seamounts(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"), 
-                                                                                        crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs', 
-                                                                                        resolution = 50000),
+  expect_s4_class(suppressWarnings(get_seamounts(spatial_grid = get_kiribati_grid(),
                                    raw = FALSE, 
                                    buffer = 30000, 
                                    antimeridian = TRUE)), 
                   class = "SpatRaster")
 })
 
 test_that("returns buffered gridded Bermuda seamounts - sf", {
-  expect_s3_class(suppressWarnings(get_seamounts(spatial_grid = get_grid(boundary = get_boundary(name = "Bermuda"), 
-                                                                         crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', 
-                                                                         resolution = 20000, 
-                                                                         output = "sf_square"),
+  expect_s3_class(suppressWarnings(get_seamounts(spatial_grid = get_bermuda_grid(output = "sf_square"),
                                                  raw = FALSE,
                                                  buffer = 30000)),
                   class = "sf")
 })
 
 test_that("returns buffered gridded Kiribati seamounts - sf", {
-  expect_s3_class(suppressWarnings(get_seamounts(spatial_grid = get_grid(boundary = get_boundary(name = "Kiribati", country_type = "sovereign"), 
-                                                                         crs = '+proj=laea +lon_0=-159.609375 +lat_0=0 +datum=WGS84 +units=m +no_defs', 
-                                                                         resolution = 50000,
-                                                                         output = "sf_hex"),
+  expect_s3_class(suppressWarnings(get_seamounts(spatial_grid = get_kiribati_grid(output = "sf_hex"),
                                                  raw = FALSE, 
                                                  buffer = 30000, 
                                                  antimeridian = TRUE)),