Change basemap data to comply with CRAN

To comply with CRAN policy, the high resolution basemap originally distributed with mapmixture v1.1.1 has been replaced with the medium resolution basemap distributed with the `rnaturalearthdata` package, which `mapmixture` now imports as default for the `mapmixture()` function. See the `mapmixture` GitHub example page for the single line of code needed to import the high resolution basemap from the `rnaturalearthhires` package.

NEWS.md

@@ -1,3 +1,9 @@
-# mapmixture 1.1.1
+## mapmixture 1.1.2
 
-* Initial CRAN submission.
+* To comply with CRAN policy, the high resolution basemap originally distributed with mapmixture v1.1.1 has been replaced with the medium resolution basemap distributed with the `rnaturalearthdata` package, which `mapmixture` now imports as default for the `mapmixture()` function. See the `mapmixture` GitHub example page for the single line of code needed to import the high resolution basemap from the `rnaturalearthhires` package.
+* Added extra arguments to customise scatter plot site divider lines.
+* Minor updates to documentation.
+
+## mapmixture 1.1.1
+
+* First release on CRAN.

R/func_mapmixture.R

@@ -65,7 +65,7 @@
 #' mapmixture(
 #'   admixture_df = admixture1,
 #'   coords_df = coordinates,
-#'   cluster_cols = c("blue","green"),
+#'   cluster_cols = c("#f1a340","#998ec3"),
 #'   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),
@@ -103,19 +103,19 @@ mapmixture <- function(
 
   # 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.")
-  })
+  # 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 ----
@@ -140,10 +140,12 @@ mapmixture <- function(
 
   # Read in world boundaries
   # world_boundaries <- sf::st_read(system.file("extdata", "world.gpkg", package = "mapmixture"), quiet = TRUE)
-  load(system.file("extdata", "countries10.rda", package = "mapmixture"))
+  # load(system.file("extdata", "countries10.rda", package = "mapmixture"))
+  world_boundaries <- rnaturalearthdata::countries50[, c("geometry")]
 
   # Transform world boundaries to CRS
-  world_boundaries <- sf::st_transform(get("countries10"), crs = crs)
+  # world_boundaries <- sf::st_transform(get("countries10"), crs = crs)
+  world_boundaries <- sf::st_transform(world_boundaries, crs = crs)
 
   # Transform coordinates in admix_coords object to CRS
   admix_coords <- transform_df_coords(admix_coords, crs = crs)

README.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/Tom-Jenkins/mapmixture/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Tom-Jenkins/mapmixture/actions/workflows/R-CMD-check.yaml)
 [![cran](https://www.r-pkg.org/badges/version/mapmixture)](https://CRAN.R-project.org/package=mapmixture)
+[![download](https://cranlogs.r-pkg.org/badges/grand-total/mapmixture)](https://CRAN.R-project.org/package=mapmixture)
 <!-- [![Codecov test coverage](https://codecov.io/gh/Tom-Jenkins/mapmixture/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Tom-Jenkins/mapmixture?branch=main) -->
 <!-- badges: end -->
 
@@ -80,16 +81,20 @@ map1
 ```
 
 
-#### Customised usage of mapmixture
+#### Customised usage of mapmixture with a high resolution map
 
 <details markdown="1">
 <summary>Code</summary>
 ```{r dpi=300}
-# Load package
+# Load packages
 library(mapmixture)
+library(rnaturalearthhires)
 
-# Read in admixture file format 3
-file <- system.file("extdata", "admixture3.csv", package = "mapmixture")
+# Install rnaturalearthhires package using:
+# install.packages("rnaturalearthhires", repos = "https://ropensci.r-universe.dev", type = "source")
+
+# Read in admixture file format 1
+file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
 admixture3 <- read.csv(file)
 
 # Read in coordinates file
@@ -98,11 +103,12 @@ coordinates <- read.csv(file)
 
 # Run mapmixture
 map2 <- mapmixture(
-  admixture_df = admixture3,
+  admixture_df = admixture1,
   coords_df = coordinates,
-  cluster_cols = c("green","blue"),
+  cluster_cols = c("#f1a340","#998ec3"),
   cluster_names = c("Group A","Group B"),
   crs = 3035,
+  basemap = rnaturalearthhires::countries10[, c("geometry")],
   boundary = c(xmin=-15, xmax=16, ymin=40, ymax=62),
   pie_size = 1,
   pie_border = 0.3,
@@ -128,6 +134,31 @@ map2 <- mapmixture(
 map2
 ```
 
+#### Admixture map with single coloured circles
+
+<details markdown="1">
+<summary>Code</summary>
+```{r dpi=300}
+# Load package
+library(mapmixture)
+
+# Read in admixture file format 3
+file <- system.file("extdata", "admixture3.csv", package = "mapmixture")
+admixture1 <- read.csv(file)
+
+# Read in coordinates file
+file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
+coordinates <- read.csv(file)
+
+# Run mapmixture
+map3 <- mapmixture(admixture1, coordinates, crs = 3035)
+# map3
+```
+</details>
+```{r dpi=300, echo=FALSE}
+map3
+```
+
 
 #### Add additional geoms or theme options to mapmixture ggplot object
 
@@ -147,7 +178,7 @@ file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
 coordinates <- read.csv(file)
 
 # Run mapmixture
-map3 <- mapmixture(
+map4 <- mapmixture(
   admixture_df = admixture1,
   coords_df = coordinates,
   cluster_cols = c("#f1a340","#998ec3"),
@@ -177,11 +208,11 @@ map3 <- mapmixture(
   )+
   # Adjust the size of the legend keys
   guides(fill = guide_legend(override.aes = list(size = 5, alpha = 1)))
-# map3
+# map4
 ```
 </details>
 ```{r dpi=300, echo=FALSE}
-map3
+map4
 ```
 
 
@@ -204,7 +235,7 @@ file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
 coordinates <- read.csv(file)
 
 # Run mapmixture
-map4 <- mapmixture(
+map5 <- mapmixture(
   admixture_df = admixture1,
   coords_df = coordinates,
   cluster_cols = c("#f1a340","#998ec3"),
@@ -245,11 +276,11 @@ structure_barplot <- structure_plot(
   )
 
 # Arrange plots
-# grid.arrange(map4, structure_barplot, nrow = 2, heights = c(4,1))
+# grid.arrange(map5, structure_barplot, nrow = 2, heights = c(4,1))
 ```
 </details>
 ```{r dpi=300, echo=FALSE, }
-grid.arrange(map4, structure_barplot, nrow = 2, heights = c(4,1))
+grid.arrange(map5, structure_barplot, nrow = 2, heights = c(4,1))
 ```
 
 <details markdown="1">
@@ -269,7 +300,7 @@ file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
 coordinates <- read.csv(file)
 
 # Run mapmixture
-map4 <- mapmixture(
+map6 <- mapmixture(
   admixture_df = admixture1,
   coords_df = coordinates,
   cluster_cols = c("#f1a340","#998ec3"),
@@ -300,11 +331,11 @@ facet_barplot <- structure_plot(admixture1,
   )
 
 # Arrange plots
-# grid.arrange(map4, facet_barplot, ncol = 2, widths = c(3,2))
+# grid.arrange(map6, facet_barplot, ncol = 2, widths = c(3,2))
 ```
 </details>
 ```{r dpi=300, echo=FALSE, }
-grid.arrange(map4, facet_barplot, ncol = 2, widths = c(3,2))
+grid.arrange(map6, facet_barplot, ncol = 2, widths = c(3,2))
 ```
 
 
@@ -331,12 +362,12 @@ file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
 coordinates <- read.csv(file)
 
 # Run mapmixture
-map5 <- mapmixture(admixture1, coordinates, crs = 3035, basemap = earth)
-# map5
+map7 <- mapmixture(admixture1, coordinates, crs = 3035, basemap = earth)
+# map7
 ```
 </details>
 ```{r dpi=300, echo=FALSE}
-map5
+map7
 ```
 
 
@@ -349,6 +380,7 @@ The vector data (shapefile) used in the example below was downloaded from the Na
 ```{r dpi=300}
 # Load packages
 library(mapmixture)
+library(rnaturalearthhires)
 library(ggplot2)
 library(dplyr)
 library(sf)
@@ -366,8 +398,8 @@ crs <- 3035
 boundary <- c(xmin=-11, xmax=13, ymin=50, ymax=60) |> transform_bbox(bbox = _, 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)
+world <- rnaturalearthhires::countries10[, c("geometry")]
+world <- st_transform(world, crs = crs)
 
 # Read in Marine Conservation Zones shapefile
 # Extract polygons for Western Channel, Offshore Brighton and Swallow Sand
@@ -382,7 +414,7 @@ coords_df <- standardise_data(coordinates, type = "coordinates")
 admix_coords <- merge_coords_data(coords_df, admixture_df) |> transform_df_coords(df = _, crs = crs)
 
 # Plot map and add pie charts
-map6 <- ggplot()+
+map8 <- ggplot()+
   geom_sf(data = world, colour = "black", fill = "#d9d9d9", size = 0.1)+
   geom_sf(data = mczs, aes(fill = "MCZs"), linewidth = 0.3)+
   scale_fill_manual(values = c("yellow"))+
@@ -402,11 +434,11 @@ map6 <- ggplot()+
   theme(
     legend.title = element_blank(),
   )
-# map6
+# map8
 ```
 </details>
 ```{r dpi=300, echo=FALSE}
-map6
+map8
 ```
 
 
@@ -545,7 +577,7 @@ library(mapmixture)
 launch_mapmixture()
 
 # Tested with the following package versions:
-# shiny v1.8.0
+# shiny v1.8.0 (important)
 # shinyFeedback v0.4.0
 # shinyjs v2.1.0
 # shinyWidgets 0.8.4