Country polygons now downloaded to extdata directory

The world country polygons are downloaded from Natural Earth and placed in the extdata directory. The mapmixture() function checks the data is present before execution.

NEWS.md

@@ -1,3 +1,3 @@
-# mapmixture 1.1.0
+# mapmixture 1.1.1
 
 * Initial CRAN submission.

R/func_mapmixture.R

@@ -59,31 +59,31 @@
 #' mapmixture(admixture1, coordinates)
 #'
 #' # Plot using the ETRS89-extended / LAEA Europe coordinate reference system
-#' mapmixture(admixture1, coordinates, crs = 3035)
+#' # mapmixture(admixture1, coordinates, crs = 3035)
 #'
 #' # Plot using custom parameters
-#' mapmixture(admixture1, coordinates,
-#'   cluster_cols = c("blue","green"),
-#'   cluster_names = c("Group 1","Group 2"),
-#'   crs = "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +units=m",
-#'   boundary = c(xmin=-15, xmax=16, ymin=40, ymax=62),
-#'   pie_size = 1.5,
-#'   pie_border = 0.2,
-#'   pie_opacity = 1,
-#'   land_colour = "#d9d9d9",
-#'   sea_colour = "#deebf7",
-#'   expand = FALSE,
-#'   arrow = TRUE,
-#'   arrow_size = 1,
-#'   arrow_position = "tl",
-#'   scalebar = TRUE,
-#'   scalebar_size = 1,
-#'   scalebar_position = "tl",
-#'   plot_title = "Mapmixture Figure",
-#'   plot_title_size = 15,
-#'   axis_title_size = 12,
-#'   axis_text_size = 10
-#' )
+#' # mapmixture(admixture1, coordinates,
+#' #   cluster_cols = c("blue","green"),
+#' #   cluster_names = c("Group 1","Group 2"),
+#' #   crs = "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +units=m",
+#' #   boundary = c(xmin=-15, xmax=16, ymin=40, ymax=62),
+#' #   pie_size = 1.5,
+#' #   pie_border = 0.2,
+#' #   pie_opacity = 1,
+#' #   land_colour = "#d9d9d9",
+#' #   sea_colour = "#deebf7",
+#' #   expand = FALSE,
+#' #   arrow = TRUE,
+#' #   arrow_size = 1,
+#' #   arrow_position = "tl",
+#' #   scalebar = TRUE,
+#' #   scalebar_size = 1,
+#' #   scalebar_position = "tl",
+#' #   plot_title = "Mapmixture Figure",
+#' #   plot_title_size = 15,
+#' #   axis_title_size = 12,
+#' #   axis_text_size = 10
+#' # )
 mapmixture <- function(
   # Data input
   admixture_df, coords_df,
@@ -98,7 +98,25 @@ mapmixture <- function(
   plot_title = "", plot_title_size = 12,
   axis_title_size = 10, axis_text_size = 8) {
 
-  # Standarise input data ----
+
+  # Download countries10.rda file to mapmixture extdata directory if not present
+  # https://github.com/ropensci/rnaturalearthhires
+  tryCatch({
+    filepath <- system.file("extdata", "countries10.rda", package = "mapmixture")
+    if (filepath == "") {
+      message("Downloading countries10 data from Natural Earth...")
+      url <- "https://github.com/ropensci/rnaturalearthhires/raw/master/data/countries10.rda"
+      desfile <- paste0(system.file("extdata", package = "mapmixture"), "/countries10.rda")
+      utils::download.file(url, destfile = desfile, mode = "wb")
+      message("Data downloaded to 'mapmixture/inst/extdata' folder.")
+      }
+    }, error = function(err) {
+      # Print error message if an error occurs from downloading
+      stop("Error downloading data from Natural Earth. Please check internet connection.")
+  })
+
+
+  # Standardise input data ----
   tryCatch({
     admixture_df <- standardise_data(admixture_df, type = "admixture")
     coords_df <- standardise_data(coords_df, type = "coordinates")
@@ -119,10 +137,11 @@ mapmixture <- function(
   admix_coords <- merge_coords_data(coords_df, admixture_df)
 
   # Read in world boundaries
-  world_boundaries <- sf::st_read(system.file("extdata", "world.gpkg", package = "mapmixture"), quiet = TRUE)
+  # world_boundaries <- sf::st_read(system.file("extdata", "world.gpkg", package = "mapmixture"), quiet = TRUE)
+  load(system.file("extdata", "countries10.rda", package = "mapmixture"))
 
   # Transform world boundaries to CRS
-  world_boundaries <- sf::st_transform(world_boundaries, crs = crs)
+  world_boundaries <- sf::st_transform(get("countries10"), crs = crs)
 
   # Transform coordinates in admix_coords object to CRS
   admix_coords <- transform_df_coords(admix_coords, crs = crs)

README.Rmd

@@ -359,9 +359,9 @@ coordinates <- read.csv(file)
 crs <- 3035
 boundary <- c(xmin=-11, xmax=13, ymin=50, ymax=60) |> transform_bbox(bbox = _, crs)
 
-# Read in world coastlines and transform to CRS
-file <- system.file("extdata", "world.gpkg", package = "mapmixture")
-world <- st_read(file, quiet = TRUE) |> st_transform(x = _, crs = crs)
+# Read in world countries from Natural Earth and transform to CRS
+load(system.file("extdata", "countries10.rda", package = "mapmixture"))
+world <- st_transform(get("countries10"), crs = crs)
 
 # Read in Marine Conservation Zones shapefile
 # Extract polygons for Western Channel, Offshore Brighton and Swallow Sand

README.md

@@ -380,9 +380,9 @@ coordinates <- read.csv(file)
 crs <- 3035
 boundary <- c(xmin=-11, xmax=13, ymin=50, ymax=60) |> transform_bbox(bbox = _, crs)
 
-# Read in world coastlines and transform to CRS
-file <- system.file("extdata", "world.gpkg", package = "mapmixture")
-world <- st_read(file, quiet = TRUE) |> st_transform(x = _, crs = crs)
+# Read in world countries from Natural Earth and transform to CRS
+load(system.file("extdata", "countries10.rda", package = "mapmixture"))
+world <- st_transform(get("countries10"), crs = crs)
 
 # Read in Marine Conservation Zones shapefile
 # Extract polygons for Western Channel, Offshore Brighton and Swallow Sand