Commit 7accfd41 authored by Facundo Muñoz's avatar Facundo Muñoz ®️
Browse files

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

parent 4ead19b1
...@@ -48,27 +48,12 @@ stringency <- function(date_range = "2020-01-01/2020-05-31"){ ...@@ -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 ## get country borders for the whole world and get rid of the
## apostrophe in "Cote d'Ivoire" ## apostrophe in "Cote d'Ivoire"
get_world_map <- function(){ get_world_map <- function(x){
ans <- readOGR(dsn = "./data/moodgaulcountrywithkos2013wpop.gpkg", ans <- readOGR(dsn = x)
layer = "moodgaulcountrywithkos2013wpop") ans$name <- standardise_country_names(ans$ADM0_NAME)
xname <- as.character(ans$ADM0_NAME)
pos <- grep(pattern = "Ivoire", x = xname)
xname[pos] <- "Cote dIvoire"
ans$name <- standardise_country_names(xname)
return(ans) 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 #' Simplify a vector layer
geosimplify <- function(x) { geosimplify <- function(x) {
......
...@@ -56,7 +56,6 @@ plan <- drake_plan(## raw_data = read_excel( ...@@ -56,7 +56,6 @@ plan <- drake_plan(## raw_data = read_excel(
## check.names = F, ## check.names = F,
## quote = "\"" ## quote = "\""
## ), ## ),
world_population = get_world_pop(),
## ECDC Covid19 geographic distribution data ## ECDC Covid19 geographic distribution data
last_day = Sys.Date() - 1, last_day = Sys.Date() - 1,
...@@ -88,7 +87,17 @@ plan <- drake_plan(## raw_data = read_excel( ...@@ -88,7 +87,17 @@ plan <- drake_plan(## raw_data = read_excel(
## CARTOGRAPHY --------------------------------------------------- ## 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 + ## GIS vector layer for European countries (EU 27 + UK + EFTA +
## candidate countries + non-EU countries). Source GADM.org ## candidate countries + non-EU countries). Source GADM.org
...@@ -108,6 +117,15 @@ plan <- drake_plan(## raw_data = read_excel( ...@@ -108,6 +117,15 @@ plan <- drake_plan(## raw_data = read_excel(
## DERIVED DATA ---------------------------------------- ## 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 country and date
## deaths_by_ctry_dt = ## deaths_by_ctry_dt =
## covid %>% ## covid %>%
...@@ -116,19 +134,6 @@ plan <- drake_plan(## raw_data = read_excel( ...@@ -116,19 +134,6 @@ plan <- drake_plan(## raw_data = read_excel(
## ungroup() %>% ## ungroup() %>%
## mutate(date = as.Date(date)), ## 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 ## and neighbouring countries
xeurope_countries = xeurope_countries =
...@@ -155,7 +160,6 @@ plan <- drake_plan(## raw_data = read_excel( ...@@ -155,7 +160,6 @@ plan <- drake_plan(## raw_data = read_excel(
by = "name" by = "name"
), ),
eust = "MOOD has received funding from the EU Horizon 2020 Research and Innovation programme under grant agreement No 874850.",
report_euro_html = report_euro_html =
rmarkdown::render( rmarkdown::render(
......
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