Fix/final ant 714 (#10)

* rgeos and raster replaced by sf * change path data and maj on name attributes * replaced all deprecated functions, tested with data (inst/). * up version 0.5.0 fix strong deprecated dependencies
rte-antares-rpackage · Aug 31, 2023 · 557eaa7 · 557eaa7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: spMaps
 Type: Package
 Title: Europe SpatialPolygonsDataFrame Builder
-Version: 0.4.1
+Version: 0.5.0
 Authors@R: c(
  person("Tatiana", "Vargas", email = "[email protected]", role = c("aut", "cre")),
  person("Jalal-Edine", "ZAWAM", role = "aut"),
@@ -16,10 +16,11 @@ URL: https://github.com/rte-antares-rpackage/spMaps
 BugReports: https://github.com/rte-antares-rpackage/spMaps/issues
 License: GPL (>= 2) | file LICENSE 
 Encoding: UTF-8
-Depends: R (>= 2.10), 
- sp,
- raster,
- rgeos
+Depends: 
+ R (>= 2.10),
+ sf,
+ methods,
+ sp (>= 2.0-0)
 RoxygenNote: 7.2.2
 Suggests: testthat,
  covr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,7 +4,7 @@ export(getEuropeCountries)
 export(getEuropeReferenceTable)
 export(getEuropeStates)
 export(getSpMaps)
-import(rgeos)
 import(sp)
-importFrom(raster,aggregate)
+importFrom(methods,as)
+importFrom(sf,st_cast)
 importFrom(utils,data)
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,13 @@
+# changes in version 0.5.0 (2023-08-31)
+
+* rgeos and raster replaced by sf
+* add necessary minimal version sp (>= 2.0-0)
+
+## FIX DEPENDENCIES :
+* fixing issue #6 (dependencies on **rgdal**, **rgeos**, and/or **maptools**)
+
 # changes in version 0.4.1 (2023-08-02)
+
 * fix file "LICENCE" format to UTF-8
 * fix note on 0.4.0 (lazy data)
 

diff --git a/R/utils.R b/R/utils.R
@@ -12,13 +12,15 @@ getEuropeReferenceTable <- function(){
 #' @rdname spMaps
 #' 
 #' @export
-#' 
-#' @import rgeos
-#' @importFrom raster aggregate
+#'
+#' @importFrom sf st_cast
+#' @importFrom methods as
 getEuropeCountries <- function(mergeCountry = TRUE){
  europe_countries_10m
  if(mergeCountry){
- europe_countries <- raster::aggregate(europe_countries_10m, by = c("code", "admin"))
+ europe_sf <- sf::st_as_sf(europe_countries_10m)
+ aggregated_sf <- sf::st_cast(europe_sf, "MULTIPOLYGON", group = c("code", "admin"))
+ europe_countries <- as(aggregated_sf, "Spatial")
  europe_countries$name <- europe_countries$admin
  return(europe_countries)
  } else {

diff --git a/README.md b/README.md
@@ -5,6 +5,7 @@
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/rte-antares-rpackage/spMaps/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/rte-antares-rpackage/spMaps/actions/workflows/check-standard.yaml)
 [![Codecov test coverage](https://codecov.io/gh/rte-antares-rpackage/spMaps/branch/master/graph/badge.svg)](https://app.codecov.io/gh/rte-antares-rpackage/spMaps?branch=master)
+[![CRAN status](https://www.r-pkg.org/badges/version/spMaps)](https://CRAN.R-project.org/package=spMaps)
 <!-- badges: end -->
 
 

diff --git a/inst/dataset/build_save_data.R b/inst/dataset/build_save_data.R
@@ -1,131 +1,100 @@
-require(rgdal)
+require(sf)
 require(sp)
 
-# http://www.naturalearthdata.com/downloads/
-
-#----------------
-# countries - 50m
-#----------------
-
-# country_50m <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\50m_cultural",
-# layer = "ne_50m_admin_0_countries")
-#
-# summary(country_50m)
-#
-# # keep only Europe
-# country_50m <- country_50m[country_50m$continent%in% "Europe", ]
-#
-# # subset on some columns
-# europe_countries_50m <- country_50m[, c("name", "name_long", "admin", "adm0_a3",
-# "adm0_a3_is","adm0_a3_us", "type", "subunit",
-# "su_a3", "pop_est", "pop_year", "continent", "region_un",
-# "subregion", "sovereignt")]
-#
-# summary(europe_countries_50m)
-#
-# # save as rda
-# devtools::use_data(europe_countries_50m, overwrite = T)
-
-# saveRDS(country_50m, file = "inst/dataset/maps/europe_countries_50m.RDS", overwrite = T)
-
 #----------------
 # countries - 10m
 #----------------
 
-country_10m_map <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\10m_cultural\\10m_cultural",
- layer = "ne_10m_admin_0_map_units")
+
+country_10m_map <- sf::st_read(dsn = "D:\\Users\\mahoudiabd\\Downloads\\Datastorm",
+ layer = "ne_10m_ADMIN_0_map_units")
 # 
 # country_10m_ref <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\10m_cultural\\10m_cultural",
-# layer = "ne_10m_admin_0_countries")
+# layer = "ne_10m_ADMIN_0_countries")
 
-country_10m_map <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\50m_cultural",
- layer = "ne_50m_admin_0_map_units")
+country_10m_map <- sf::st_read(dsn = "D:\\Users\\mahoudiabd\\Downloads\\Datastorm",
+  layer = "ne_50m_ADMIN_0_map_units")
 
-# country_10m_ref <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\50m_cultural",
-# layer = "ne_50m_admin_0_countries")
+# country_10m_ref <- st_read(dsn = "C:\\Users\\Datastorm\\Downloads\\50m_cultural",
+# layer = "ne_50m_ADMIN_0_countries")
 # keep only Europe + Turquie
-country_10m <- country_10m_map[country_10m_map$continent%in% "Europe" | 
- country_10m_map$name_long %in% c("Turkey", "Cyprus"), ]
+country_10m <- country_10m_map[country_10m_map$CONTINENT %in% "Europe" |
+ country_10m_map$NAME_LONG %in% c("Turkey", "Cyprus"), ]
 summary(country_10m)
 
 plot(country_10m)
-plot(country_10m[country_10m$name_long %in% "Cyprus",])
+plot(country_10m[country_10m$NAME_LONG %in% "Cyprus",])
 
 # chypre : fusion avec la chypre du nors
-country_10m_cyprus <- country_10m_map[country_10m_map$name_long %in% c("Cyprus", "Northern Cyprus"), ]
-country_10m_cyprus <- raster::aggregate(country_10m_cyprus, by = c("adm0_a3_is"))
-plot(country_10m_cyprus)
-
-slot(country_10m, "polygons")[[which(country_10m$name_long %in% "Cyprus")]] <- slot(country_10m_cyprus, "polygons")[[1]]
-plot(country_10m[country_10m$name_long %in% "Cyprus",])
-
-# remove canaries from spain
-# plot(country_10m[country_10m$adm0_a3 %in% "ESP",])
-
-pols_esp <- slot(country_10m, "polygons")[[which(country_10m$adm0_a3 %in% "ESP")]]
+########
 
-sum_area <- 0
-# min_lat <- NA
-# max_lat <- NA
-# min_lon <- NA
-# max_lon <- NA
-keep_polygons <- sapply(country_10m[country_10m$adm0_a3 %in% "ESP", ]@polygons[[1]]@Polygons, function(x){
- # canaries : lattitude < 30
- if(x@labpt[2] > 30){
- sum_area <<- sum_area + x@area
- # min_lon <<- min(min_lon, x@coords[, 1], na.rm = T)
- # min_lat <<- min(min_lat, x@coords[, 2], na.rm = T)
- # max_lon <<- max(max_lon, x@coords[, 1], na.rm = T)
- # max_lat <<- max(max_lat, x@coords[, 2], na.rm = T) 
- }
- x@labpt[2]>30
-})
+# Subset data
+country_cyprus <- country_10m_map[country_10m_map$NAME_LONG %in% c("Cyprus", "Northern Cyprus"), ]# Perform a union of geometries
+union_geometry <- st_union(country_cyprus$geometry)# Replace the geometry of the "Cyprus" feature in the original dataset
+country_10m[country_10m$NAME_LONG == "Cyprus", "geometry"] <- union_geometry
 
-# new_bbox <- matrix(c(min_lon, max_lon, min_lat, max_lat), nrow = 2, ncol = 2, byrow = T, 
-# dimnames = list(c("x", "y"), c("min", "max")))
+# Plot the updated dataset
+plot(country_10m[country_10m$NAME_LONG %in% "Cyprus", ])
 
-new_order <- country_10m[country_10m$adm0_a3 %in% "ESP", ]@polygons[[1]]@plotOrder[which(keep_polygons)] 
-new_order[order(new_order)] <- 1:length(new_order)
 
-slot(pols_esp, "area") <- sum_area
-slot(pols_esp, "plotOrder") <- new_order
-slot(pols_esp, "Polygons") <- country_10m[country_10m$adm0_a3 %in% "ESP", ]@polygons[[1]]@Polygons[which(keep_polygons)] 
+###########
 
-# bug leaflet : have to reset comment...
-comment(pols_esp) <- rgeos::createPolygonsComment(pols_esp)
+#slot(country_10m, "polygons")[[which(country_10m$NAME_LONG %in% "Cyprus")]] <- slot(country_10m_cyprus, "polygons")[[1]]
 
-slot(country_10m, "polygons")[[which(country_10m$adm0_a3 %in% "ESP")]] <- pols_esp 
-
-plot(country_10m[country_10m$adm0_a3 %in% "ESP",])
+# remove canaries from spain
+# plot(country_10m[country_10m$ADM0_A3 %in% "ESP",])
+
+pols_esp <- country_10m[country_10m$ADM0_A3 == "ESP", ]
+
+#########
+
+# Assuming country_10m is your sf object
+spain <- country_10m[country_10m$ADM0_A3 %in% "ESP", ]
+# Extract the geometries and calculate sum area
+spain_polygons <- spain$geometry
+sum_area <- sum(st_area(spain_polygons[st_coordinates(st_centroid(spain_polygons))[ ,2] > 30]))
+# Calculate new order
+new_order <- seq_along(spain_polygons[st_coordinates(st_centroid(spain_polygons))[ ,2] > 30])
+# Update the order of the geometries
+spain_polygons[st_coordinates(st_centroid(spain_polygons))[ ,2] > 30] <- spain_polygons[new_order]
+# Update the area attribute
+spain$area <- sum_area
+# Update the geometry
+spain$geometry <- spain_polygons
+# Plot the modified polygons
+plot(spain)
+
+#########
 
 # subset on columns
-europe_countries_10m <- country_10m[, c("name", "admin", "adm0_a3",
- "adm0_a3_is","adm0_a3_us",
- "type", "subunit",
- "continent", "region_un",
- "subregion", "sovereignt")]
+europe_countries_10m <- country_10m[, c("NAME", "ADMIN", "ADM0_A3",
+ "ADM0_A3_US",
+ "TYPE", "SUBUNIT",
+ "CONTINENT", "REGION_UN",
+ "SUBREGION", "SOVEREIGNT")]
 summary(europe_countries_10m)
 plot(europe_countries_10m)
 
-names(europe_countries_10m) <- gsub("^adm0_a3$", "code", names(europe_countries_10m))
+names(europe_countries_10m) <- gsub("^ADM0_A3$", "CODE", names(europe_countries_10m))
 
 # ref table
-europe_countries_ref <- unique(data.frame(europe_countries_10m[, c("admin", "code")],
+europe_countries_ref <- unique(data.frame(europe_countries_10m[, c("ADMIN", "CODE")],
  stringsAsFactors = F))
-colnames(europe_countries_ref) <- c("name", "code")
+colnames(europe_countries_ref) <- c("NAME", "CODE")
 
 
 #----------------
 # states - 10m
 #----------------
 #
-# states_10m <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\10m_cultural\\10m_cultural",
-# layer = "ne_10m_admin_1_states_provinces_shp")
+# states_10m <- st_read(dsn = "C:\\Users\\Datastorm\\Downloads\\10m_cultural\\10m_cultural",
+# layer = "ne_10m_ADMIN_1_states_provinces_shp")
 
-states_10m <- readOGR(dsn = "C:\\Users\\Datastorm\\Downloads\\10m_cultural\\10m_cultural",
- layer = "ne_10m_admin_1_states_provinces_lakes_shp")
+states_10m <- st_read(dsn = "D:\\Users\\mahoudiabd\\Downloads\\Datastorm",
+ layer = "ne_10m_ADMIN_1_states_provinces_lakes")
 # subset on Europe
-states_10m_europe <- states_10m[states_10m$sr_adm0_a3%in% europe_countries_10m$code | 
+
+states_10m_europe <- states_10m[states_10m$adm0_a3%in% europe_countries_10m$CODE | 
  states_10m$admin %in% c("Cyprus", "Northern Cyprus"), ]
 summary(states_10m_europe)
 
@@ -139,45 +108,41 @@ summary(states_10m_europe[states_10m_europe$admin %in% c("Cyprus", "Northern Cyp
 
 # chypre : fusion avec la chypre du nors
 levels(states_10m_europe$admin) <- gsub("Northern Cyprus", "Cyprus", levels(states_10m_europe$admin))
-levels(states_10m_europe$sr_adm0_a3) <- gsub("^CYN$", "CYP", levels(states_10m_europe$sr_adm0_a3))
+levels(states_10m_europe$adm0_a3) <- gsub("^CYN$", "CYP", levels(states_10m_europe$adm0_a3))
 
 plot(states_10m_europe[states_10m_europe$admin %in% c("Cyprus"), ])
 
 # remove islands from france
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "FRA", ])
-states_10m_europe <- states_10m_europe[!(states_10m_europe$sr_adm0_a3 %in% "FRA" & !states_10m_europe$type_en %in% "Region"), ]
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "FRA", ])
+plot(states_10m_europe[states_10m_europe$adm0_a3 %in% "FRA", ])
+states_10m_europe <- states_10m_europe[!(states_10m_europe$adm0_a3 %in% "FRA" & !states_10m_europe$type_en %in% "Region"), ]
+plot(states_10m_europe[states_10m_europe$adm0_a3 %in% "FRA", ])
 
 # N0R
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "NOR", ])
-states_10m_europe <- states_10m_europe[!(states_10m_europe$sr_adm0_a3 %in% "NOR" & !states_10m_europe$type_en %in% "County"), ]
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "NOR", ])
+plot(states_10m_europe[states_10m_europe$adm0_a3 %in% "NOR", ])
+states_10m_europe <- states_10m_europe[!(states_10m_europe$adm0_a3 %in% "NOR" & !states_10m_europe$type_en %in% "County"), ]
+plot(states_10m_europe[states_10m_europe$adm0_a3 %in% "NOR", ])
 
 # NLD
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "NLD", ])
-states_10m_europe <- states_10m_europe[!(states_10m_europe$sr_adm0_a3 %in% "NLD" & !states_10m_europe$type_en %in% "Province"), ]
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "NLD", ])
-
-# ESP
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "ESP", ])
-states_10m_europe <- states_10m_europe[!(states_10m_europe$sr_adm0_a3 %in% "ESP" & states_10m_europe$name %in% "ESP-00 (Canary Is. aggregation)"), ]
-plot(states_10m_europe[states_10m_europe$sr_adm0_a3 %in% "ESP", ])
+plot(states_10m_europe[states_10m_europe$adm0_a3 %in% "NLD", ])
+states_10m_europe <- states_10m_europe[!(states_10m_europe$adm0_a3 %in% "NLD" & !states_10m_europe$type_en %in% "Province"), ]
+plot(states_10m_europe[states_10m_europe$adm0_a3 %in% "NLD", ])
 
-# for(co in europe_countries_ref$code){
+# for(co in europe_countries_ref$CODE){
 # print(co)
 # par(ask = T)
-# plot(states_10m_europe[!states_10m_europe$sr_adm0_a3 %in% co, ])
+# plot(states_10m_europe[!states_10m_europe$adm0_a3 %in% co, ])
 # }
 
 # subset on columns
-europe_states_provinces_10m <- states_10m_europe[, c("admin", "sr_adm0_a3", "sr_sov_a3", "adm1_code",
+europe_states_provinces_10m <- states_10m_europe[, c("admin", "adm0_a3", "sov_a3", "adm1_code",
  "name", "type", "type_en", "region")]
 summary(europe_states_provinces_10m)
 
-names(europe_states_provinces_10m) <- gsub("^sr_adm0_a3$", "code", names(europe_states_provinces_10m))
+names(europe_states_provinces_10m) <- gsub("^adm0_a3$", "code", names(europe_states_provinces_10m))
 
-devtools::use_data(europe_countries_10m, europe_countries_ref, 
- europe_states_provinces_10m, internal = TRUE, overwrite = T)
+
+## Export des tables vers le dossier inst, ne pas lancer si on ne souhaite pas écraser les données.
+#devtools::use_data(europe_countries_10m, europe_countries_ref, europe_states_provinces_10m, internal = TRUE, overwrite = T)
 
 
 #------------------------------------------------------------------------------------------#
@@ -193,39 +158,4 @@ myData1<-readAntares(areas = "all", links = "all")
 ml<-mapLayout(readLayout())
 plotMap(myData1, ml)
 
-plotMapLayout(ml)
-
-#-------------------
-# Identify leaflet bug with Spain
-#-------------------
-
-# require(leaflet)
-# 
-# map=getSpMaps(countries = c("ESP"))
-# 
-# str(map[map$name %in% 'France',])
-# str(map[map$name %in% 'Spain',])
-# 
-# s <- sp::polygons(map)
-# 
-# plot(s)
-# leaflet(map) %>% addPolygons()
-# 
-# leaflet:::derivePolygons
-# leaflet:::polygonData.SpatialPolygons
-# leaflet:::polygonData(s)
-# 
-# leaflet:::sp_bbox(s)
-# leaflet:::to_multipolygon_list.SpatialPolygons
-# 
-# pgons <- s@polygons[[1]]
-# comment(pgons)
-# rgeos::createPolygonsComment(pgons)
-# leaflet:::to_multipolygon.Polygons
-# lapply(pgons@polygons, to_multipolygon)
-# 
-# str(s)
-# s@polygons
-# pgons = leaflet:::derivePolygons(map, lng = NULL, lat = NULL, T, T, 
-# "addPolygons")
-# 
+plotMapLayout(ml)