Push the knit button!

library(tidyverse) # contains ggplot2, dplyr, tidyr, etc
library(ggthemes)
library(ggmap)

tuberculosis dataset

tb <- read_csv(here::here("data/TB_notifications_2020-07-01.csv")) %>% 
  dplyr::select(country, iso3, year, new_sp_m04:new_sp_fu) %>%
  pivot_longer(cols=new_sp_m04:new_sp_fu, names_to="sexage", values_to="count") %>%
  mutate(sexage = str_replace(sexage, "new_sp_", "")) %>%
  mutate(sex=substr(sexage, 1, 1), 
         age=substr(sexage, 2, length(sexage))) %>%
  dplyr::select(-sexage) %>%
  filter(!(age %in% c("04", "014", "514", "u"))) %>%
  filter(year > 1996, year < 2013) %>%
  mutate(age_group = factor(age, 
                            labels = c("15-24", "25-34", "35-44", 
                                       "45-54", "55-64", "65-"))) %>%
  dplyr::select(country, year, age_group, sex, count)

# Filter Australia
tb_oz <- tb %>% 
  filter(country == "Australia") 

# Fix names for map joining
tb_fixed <- tb %>% 
  mutate(region=recode(country, 
                       "United States of America"="USA", 
                       "United Kingdom of Great Britain and Northern Ireland"="UK",
                       "Russian Federation"="Russia",
                       "Viet Nam"="Vietnam",
                       "Venezuela (Bolivarian Republic of)"="Venezuela",
                       "Bolivia (Plurinational State of)"="Bolivia",
                       "Czechia"="Czech Republic",
                       "Iran (Islamic Republic of)"="Iran",
                       "Lao People's Democratic Republic"="Laos",
                       "Democratic People's Republic of Korea"="North Korea",
                       "Republic of Korea"="South Korea",
                       "United Republic of Tanzania"="Tanzania",
                       "Congo"="Republic of Congo"))
tb_2012 <- tb_fixed %>% #<<
  filter(year == 2012) %>%
  group_by(region) %>%
  summarise(count = sum(count))

platypus dataset

load(here::here("data/platypus.rda"))
oz_bbox <- c(112.9, # min long
              -45, # min lat
              159, # max long
              -10) # max lat
oz_map <- get_map(location = oz_bbox, source = "osm")

Exercise 2.1: Polygon fill colour

world_map <- map_data("world")
oz <- world_map %>% 
  filter(region == "Australia")

ggplot(oz, aes(x=long, y=lat, 
               group=group)) + 
  geom_polygon(fill = "orange") + #<<
  coord_map() +
  theme_map()

Exercise 2.2: Change the color palette

tb_2012_map <- world_map %>% left_join(tb_2012) #<<
ggplot(tb_2012_map, aes(x=long, y=lat, group=group)) + 
    geom_polygon(aes(fill=count), #<<
             color="grey70", size=0.1, na.rm=TRUE) +  #<<
    expand_limits(x = world_map$long*1.1, y = world_map$lat*1.1) +
    scale_fill_distiller("Count", palette="YlGnBu") +
    theme_map()

Exercise 2.3: Density plot on map

ggmap(oz_map) + 
  geom_density2d(data=platypus, 
             aes(x=Longitude, y=Latitude), 
     colour="purple") + 
  theme_map()