R语言-数据分析

Visualizing COVID-19

Link: datacamp

getwd()
setwd("C:\\Users\\PC\\Desktop\\R")

1. From epidemic to pandemic

Load the readr, ggplot2, and dplyr packages

library(readr)
library(ggplot2)
library(dplyr)

Read datasets/confirmed_cases_worldwide.csv into confirmed_cases_worldwide

confirmed_cases_worldwide <- read.csv("datasets/confirmed_cases_worldwide.csv")

Print out confirmed_cases_worldwide

confirmed_cases_worldwide

2. Confirmed cases throughout the world

Draw a line plot of cumulative cases vs. date

Label the y-axis

ggplot(confirmed_cases_worldwide, aes(date, cum_cases)) +
  geom_line() +
  ylab("Cumulative confirmed cases")

3. China compared to the rest of the world

Read in datasets/confirmed_cases_china_vs_world.csv

confirmed_cases_china_vs_world <- read.csv("datasets/confirmed_cases_china_vs_world.csv")

See the result

glimpse(confirmed_cases_china_vs_world)

Draw a line plot of cumulative cases vs. date, grouped and colored by is_china

Define aesthetics within the line geom

plt_cum_confirmed_cases_china_vs_world <- ggplot(confirmed_cases_china_vs_world) +
  geom_line(aes(date, cum_cases, group = is_china, color = is_china)) +
  ylab("Cumulative confirmed cases")

See the plot

plt_cum_confirmed_cases_china_vs_world

4. Let’s annotate!

who_events <- tribble(
  ~ date, ~ event,
  "2020-01-30", "Global health\nemergency declared",
  "2020-03-11", "Pandemic\ndeclared",
  "2020-02-13", "China reporting\nchange"
) %>%
  mutate(date = as.Date(date))

Using who_events, add vertical dashed lines with an xintercept at date

and text at date, labeled by event, and at 100000 on the y-axis

plt_cum_confirmed_cases_china_vs_world +
  geom_vline(aes(xintercept = date), data = who_events, linetype = "dashed") +
  geom_text(aes(date, label = event), data = who_events, y = 1e5)

5.Adding a trend line to China

Filter for China, from Feb 15

china_after_feb15 <- confirmed_cases_china_vs_world %>%
  filter(is_china == "China", date >= "2020-02-15")

Using china_after_feb15, draw a line plot cum_cases vs. date

Add a smooth trend line using linear regression, no error bars

ggplot(china_after_feb15, aes(date, cum_cases)) +
  geom_line() +
  geom_smooth(method = "lm", se = FALSE) +
  ylab("Cumulative confirmed cases")

6. And the rest of the world?

Filter confirmed_cases_china_vs_world for not China

not_china <- confirmed_cases_china_vs_world %>%
  filter(is_china == "Not China")

Using not_china, draw a line plot cum_cases vs. date

Add a smooth trend line using linear regression, no error bars

plt_not_china_trend_lin <- ggplot(not_china, aes(date, cum_cases)) +
  geom_line() +
  geom_smooth(method = "lm", se = FALSE) +
  ylab("Cumulative confirmed cases")

See the result

plt_not_china_trend_lin 

7. Adding a logarithmic scale

Modify the plot to use a logarithmic scale on the y-axis

plt_not_china_trend_lin + 
  scale_y_log10()

8. Which countries outside of China have been hit hardest?

Run this to get the data for each country

confirmed_cases_by_country <- read_csv("datasets/confirmed_cases_by_country.csv")
glimpse(confirmed_cases_by_country)

Group by country, summarize to calculate total cases, find the top 7

top_countries_by_total_cases <- confirmed_cases_by_country %>%
  group_by(country) %>%
  summarize(total_cases = max(cum_cases)) %>%
  top_n(7, total_cases)

See the result

top_countries_by_total_cases

9. Plotting hardest hit countries as of Mid-March 2020

Read in the dataset from datasets/confirmed_cases_top7_outside_china.csv

confirmed_cases_top7_outside_china <- read_csv("datasets/confirmed_cases_top7_outside_china.csv")

Glimpse the contents of confirmed_cases_top7_outside_china

glimpse(confirmed_cases_top7_outside_china)

Using confirmed_cases_top7_outside_china, draw a line plot of

cum_cases vs. date, grouped and colored by country

ggplot(confirmed_cases_top7_outside_china, aes(date, cum_cases, color = country, group = country)) +
  geom_line() +
  ylab("Cumulative confirmed cases")