Push the knit button!

library(tidyverse) # contains ggplot2, dplyr, tidyr, etc
library(leaflet)
library(lubridate)
library(plotly)
library(gganimate)
library(viridis)
library(ggthemes)

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",
                       "Iran (Islamic Republic of)"="Laos",
                       "Democratic People's Republic of Korea"="North Korea",
                       "Republic of Korea"="South Korea",
                       "United Republic of Tanzania"="Tanzania",
                       "Congo"="Republic of Congo"))

# Aggregate by year
tb_yearly <- tb_fixed %>%
group_by(year, region) %>%
summarise(count = sum(count))

platypus dataset

load(here::here("data/platypus.rda"))
platypus <- platypus %>%
  rename(eventDate = `Event Date - parsed`) %>%
  filter(!is.na(Latitude), !is.na(Longitude), !is.na(eventDate)) %>%
  filter(year(eventDate) > 2018) 

Exercise 1.1: Leaflet with different colour