Read world population from world_map in the plan (rather than hidden within a function).

src/functions.R

@@ -48,27 +48,12 @@ stringency <- function(date_range = "2020-01-01/2020-05-31"){
 
 ## get country borders for the whole world and get rid of the
 ## apostrophe in "Cote d'Ivoire"
-get_world_map <- function(){
-    ans <- readOGR(dsn = "./data/moodgaulcountrywithkos2013wpop.gpkg",
-                   layer = "moodgaulcountrywithkos2013wpop")
-    xname <- as.character(ans$ADM0_NAME)
-    pos <- grep(pattern = "Ivoire", x = xname)
-    xname[pos] <- "Cote dIvoire"
-    ans$name <- standardise_country_names(xname)
+get_world_map <- function(x){
+    ans <- readOGR(dsn = x)
+    ans$name <- standardise_country_names(ans$ADM0_NAME)
     return(ans)
 }
 
-get_world_pop <- function(){
-    ans <- readOGR(dsn = "./data/moodgaulcountrywithkos2013wpop.gpkg",
-                   layer = "moodgaulcountrywithkos2013wpop")
-    xname <- as.character(ans$ADM0_NAME)
-    pos <- grep(pattern = "Ivoire", x = xname)
-    xname[pos] <- "Cote dIvoire"
-    ans$name <- standardise_country_names(xname)
-    return(data.frame(name = ans$name,
-                      pop = ans$TOTPOP)
-                      )
-}
 
 #' Simplify a vector layer
 geosimplify <- function(x) {

src/plan.R

@@ -56,7 +56,6 @@ plan <- drake_plan(## raw_data = read_excel(
     ##     check.names = F,
     ##     quote = "\""
     ## ),
-    world_population = get_world_pop(),
 
     ## ECDC Covid19 geographic distribution data
     last_day = Sys.Date() - 1,
@@ -88,7 +87,17 @@ plan <- drake_plan(## raw_data = read_excel(
 
     ## CARTOGRAPHY ---------------------------------------------------
 
-    world_map = get_world_map(),
+    ## Coordinate Reference Systems
+    wgs84 = CRS("+proj=longlat +ellps=WGS84",
+                doCheckCRSArgs = FALSE),
+
+    merc = CRS("+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext  +no_defs",
+               doCheckCRSArgs = FALSE),
+
+    eust = "MOOD has received funding from the EU Horizon 2020 Research and Innovation programme under grant agreement No 874850.",
+
+    ## Country borders and population data
+    world_map = get_world_map(ile_in("data/moodgaulcountrywithkos2013wpop.gpkg")),
 
     ## GIS vector layer for European countries (EU 27 + UK + EFTA +
     ## candidate countries + non-EU countries). Source GADM.org
@@ -108,6 +117,15 @@ plan <- drake_plan(## raw_data = read_excel(
 
     ## DERIVED DATA ----------------------------------------
 
+
+    world_population = world_map %>%
+        as_tibble %>%
+        mutate(
+            name = standardise_country_names(ADM0_NAME)
+        ) %>%
+        select(name, pop = TOTPOP) %>%
+        filter(pop > 0),
+
     ## ## Deaths by country and date
     ## deaths_by_ctry_dt =
     ##   covid %>%
@@ -116,20 +134,7 @@ plan <- drake_plan(## raw_data = read_excel(
     ##   ungroup() %>%
     ##   mutate(date = as.Date(date)),
 
-    ## Population counts in thousands of people
-    pop_countries_2020 = subset(world_population,
-                                subset = name %in% xeurope_countries$name),
-
-    ## ## today (ANSI)
-    ## tod = format(Sys.Date(), "%Y%m%d"),
-
-    ## Coordinate Reference Systems
-    wgs84 = CRS("+proj=longlat +ellps=WGS84",
-                doCheckCRSArgs = FALSE),
-
-    merc = CRS("+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext  +no_defs",
-               doCheckCRSArgs = FALSE),
-   ## Lock-down dates and population counts by country of the european
+    ## Lock-down dates and population counts by country of the european
     ## and neighbouring countries
     xeurope_countries =
         enframe(
@@ -155,7 +160,6 @@ plan <- drake_plan(## raw_data = read_excel(
             by = "name"
         ),
 
-    eust = "MOOD has received funding from the EU Horizon 2020 Research and Innovation programme under grant agreement No 874850.",
 
     report_euro_html =
         rmarkdown::render(