Push the knit button!

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

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")

Exercise 4.1: Which plot arrangement better reveals the spike in counts?

The side-by-side bar chart reveals the spikes better. It is allowing comparison of heights because of proximity. The facetted bar chart might be better still.

Exercise 4.2: Rearrange this plot to better answer

“Is the proportion of TB incidence in males relative to females increasing with age?”

tb_oz %>% 
  filter(year == 2012) %>%
  ggplot(aes(x=1, y=count, fill=age_group)) +
  geom_bar(stat="identity", position="fill") + 
  facet_wrap(~sex, ncol=6) +
  scale_fill_brewer("", palette="Dark2") +
  xlab("") + ylab("") +
  coord_polar(theta = "y")

tb_oz %>% 
  filter(year == 2012) %>%
  mutate(age_group = as.numeric(age_group)) %>%
  ggplot(aes(x=age_group, y=count, colour=sex)) +
  geom_point() +
  geom_smooth(method="lm", se=F) +
  scale_colour_brewer("", palette="Dark2")

Exercise 4.3: This plot is missing something

By using proportions by sex, this plot lost some trend difference between the sexes over years. Fix it.

tb_oz %>% group_by(year, age_group) %>% 
  summarise(p = count[sex=="m"]/sum(count)) %>%
  ggplot(aes(x=year, y=p)) +
    geom_hline(yintercept = 0.50, colour="white", size=2) +
    geom_point() +
    geom_smooth(se=F) +
    facet_wrap(~age_group, ncol=6) +
    ylab("proportion of males")

tb_oz %>% 
    ggplot(aes(x=year, y=count, colour=sex)) +
    geom_point() +
    geom_smooth(method="lm", se=F) +
    facet_wrap(~age_group, ncol=6) +
    scale_colour_brewer("", palette="Dark2")