WCAfrica cartography: move from workflow based on script and saved files to...

WCAfrica cartography: move from workflow based on script and saved files to drake targets and functions.

src/Africa_gpkg.R

-library(rgdal)
-source("src/functions.R")
-source("src/packages.R")
-
-ctr <- c("Cameroon", "Central African Republic", "Chad", "Congo DR",
-         "Congo", "Equatorial Guinea", "Gabon", "Sao Tome and Principe",
-         "Benin", "Burkina Faso", "Cape Verde", "The Gambia", "Ghana",
-         "Guinea", "Guinea Bissau", "Cote d'Ivoire", "Liberia",
-         "Mali", "Mauritania", "Niger", "Nigeria", "Senegal",
-         "Sierra Leone", "Togo")
-ctry <- standardise_country_names(ctr)
-
-codes <- ccodes()
-Tcorresp <- subset(codes,
-                   subset = NAME %in% ctry,
-                   select = c("NAME", "ISO3"))
-world <- readOGR(dsn = "d:/gis/gadm/gadm36_levels.gpkg",
-                 layer = "level0")
-wcAfrica1 <- world[world$GID_0 %in% Tcorresp$ISO3, ]
-
-wcAfrica2 <- gSimplify(wcAfrica1,
-                   tol=.025,
-                   topologyPreserve=T)
-wcAfrica3 <- as(wcAfrica2,
-                "SpatialPolygonsDataFrame")
-wcAfrica3@data <- wcAfrica1@data
-
-e <- extend(extent(wcAfrica3), 1)
-E <- as(e, "SpatialPolygons")
-projection(E) <- projection(wcAfrica1)
-
-roi1 <- raster::intersect(world, E)
-roi2 <- gSimplify(roi1,
-                  tol=.025,
-                  topologyPreserve=T)
-roi3 <- as(roi2,
-           "SpatialPolygonsDataFrame")
-
-roi3@data <- roi1@data
-
-writeOGR(wcAfrica1,
-         dsn = "data/geoWCAfrica.gpkg",
-         layer = "geoWCAfrica",
-         driver = "GPKG", overwrite = T)
-
-writeOGR(wcAfrica3,
-         dsn = "data/geoWCAFricaLight.gpkg",
-         layer = "geoWCAfricaLight",
-         driver = "GPKG", overwrite = T)
-
-writeOGR(roi1,
-         dsn = "data/roiWCAfrica.gpkg",
-         layer = "roiWCAfrica",
-         driver = "GPKG",
-         overwrite = T)
-
-writeOGR(roi3,
-         dsn = "data/roiWCAfricaLight.gpkg",
-         layer = "roiWCAfricaLight",
-         driver = "GPKG",
-         overwrite = T)

src/functions.R

+#' Simplify a vector layer
+geosimplify <- function(x) {
+  sx <- gSimplify(x, tol=.025, topologyPreserve=T)
+  ans <- as(sx, "SpatialPolygonsDataFrame")
+  ans@data <- x@data
+  return(ans)
+}
+
+#' Extract the region of interest from a context
+#'
+#' Get a map of the extent of x from a context
+region_of_interest <- function(x, context) {
+  e <- extend(extent(x), 1)
+  E <- as(e, "SpatialPolygons")
+  projection(E) <- projection(x)
+  return(raster::intersect(context, E))
+}
+
+
+
 #' ECDC Covid19 data worldwide
 #'
 #' Returns the published file at a given date.
@@ -77,6 +97,7 @@ standardise_country_names <- function(x) {
       "Congo, DRC", "Congo DR",
       "Congo DRC", "Congo DR",
       "Congo, DR", "Congo DR",
+      "Republic of Congo", "Congo",
       "Gambia", "The Gambia",
       "Cote dIvoire", "Cote d'Ivoire",
       "Côte d'Ivoire", "Cote d'Ivoire",
@@ -100,6 +121,14 @@ standardise_country_names <- function(x) {
   )
 }
 
+#' Get ISO3 codes for a list of countries
+get_iso3 <- function(x) {
+  codes <- ccodes()
+  codes$ISO3[standardise_country_names(codes$NAME) %in%
+               standardise_country_names(x)]
+}
+
+
 #' Total population by country for a given year
 #'
 #' Population counts in thousands of people.

src/plan.R

@@ -40,7 +40,7 @@ plan <- drake_plan(
             "Georgia", "Israel", "Jordan", "Lebanon", "Libya",
             "Moldova", "Morocco",  "Syria", "Tunisia", "Ukraine"),
 
-    wcAfrica = c("Cameroon", "Central African Republic", "Chad",
+    wca = c("Cameroon", "Central African Republic", "Chad",
                  "Congo DR", "Congo", "Equatorial Guinea", "Gabon",
                  "Sao Tome and Principe", "Benin", "Burkina Faso",
                  "Cape Verde", "The Gambia", "Ghana", "Guinea",
@@ -80,6 +80,11 @@ plan <- drake_plan(
             lockdown = as.Date(lockdown)
         ),
 
+
+    # CARTOGRAPHY ---------------------------------------------------
+
+    world_map = getData("countries"),
+
     ## GIS vector layer for European countries (EU 27 + UK + EFTA +
     ## candidate countries + non-EU countries). Source GADM.org
     ## version 3.6
@@ -92,11 +97,11 @@ plan <- drake_plan(
                                layer = "roi_europe_light"),
 
     ## GIS vector layer for West and Central African countries
-    geoWCAfrica = readOGR(dsn = "data/geoWCAfricaLight.gpkg",
-                          layer = "geoWCAfricaLight"),
+    geoWCAfrica = world_map[world_map$ISO %in% get_iso3(wca),] %>%
+      geosimplify(),
 
-    roiWCAfrica = readOGR(dsn = "data/roiWCAfricaLight.gpkg",
-                          layer = "roiWCAfricaLight"),
+    roiWCAfrica = region_of_interest(geoWCAfrica, world_map) %>%
+      geosimplify(),
 
     ## DERIVED DATA ----------------------------------------