人类的发展史就是和各种疾病争斗的发展史。新冠肺炎对我们的工作和生活产生巨大的影响，通过数据分析，来了解下疫情的发展情况如何。数据来源于这个github仓库。

library(tidyverse)
library(lubridate)
library(maps)
library(viridis)
library(ggrepel)
library(paletteer)
library(shadowtext)
library(showtext)
showtext_auto()

1 读取数据

df <- read_csv("D:/Myblog/datas/time_series_covid19_confirmed_global.csv")
df %>% 
  slice_head(n = 6)

# A tibble: 6 × 74
  `Province/State` `Country/Region`     Lat   Long `1/22/20` `1/23/20` `1/24/20`
  <chr>            <chr>              <dbl>  <dbl>     <dbl>     <dbl>     <dbl>
1 <NA>             Afghanistan         33    65            0         0         0
2 <NA>             Albania             41.2  20.2          0         0         0
3 <NA>             Algeria             28.0   1.66         0         0         0
4 <NA>             Andorra             42.5   1.52         0         0         0
5 <NA>             Angola             -11.2  17.9          0         0         0
6 <NA>             Antigua and Barbu…  17.1 -61.8          0         0         0
# ℹ 67 more variables: `1/25/20` <dbl>, `1/26/20` <dbl>, `1/27/20` <dbl>,
#   `1/28/20` <dbl>, `1/29/20` <dbl>, `1/30/20` <dbl>, `1/31/20` <dbl>,
#   `2/1/20` <dbl>, `2/2/20` <dbl>, `2/3/20` <dbl>, `2/4/20` <dbl>,
#   `2/5/20` <dbl>, `2/6/20` <dbl>, `2/7/20` <dbl>, `2/8/20` <dbl>,
#   `2/9/20` <dbl>, `2/10/20` <dbl>, `2/11/20` <dbl>, `2/12/20` <dbl>,
#   `2/13/20` <dbl>, `2/14/20` <dbl>, `2/15/20` <dbl>, `2/16/20` <dbl>,
#   `2/17/20` <dbl>, `2/18/20` <dbl>, `2/19/20` <dbl>, `2/20/20` <dbl>, …

# 查看数据结构
glimpse(df)

Rows: 256
Columns: 74
$ `Province/State` <chr> NA, NA, NA, NA, NA, NA, NA, NA, "Australian Capital T…
$ `Country/Region` <chr> "Afghanistan", "Albania", "Algeria", "Andorra", "Ango…
$ Lat              <dbl> 33.0000, 41.1533, 28.0339, 42.5063, -11.2027, 17.0608…
$ Long             <dbl> 65.0000, 20.1683, 1.6596, 1.5218, 17.8739, -61.7964, …
$ `1/22/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `1/23/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `1/24/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `1/25/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `1/26/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 1, 0, 0, 0,…
$ `1/27/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 1, 0, 0, 0,…
$ `1/28/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 1, 0, 0, 0,…
$ `1/29/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 1, 0, 0, 1, 0, 0, 0,…
$ `1/30/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 3, 0, 0, 2, 0, 0, 0,…
$ `1/31/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 2, 0, 0, 3, 0, 0, 0,…
$ `2/1/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 3, 1, 0, 4, 0, 0, 0,…
$ `2/2/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 2, 2, 0, 4, 0, 0, 0,…
$ `2/3/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 2, 2, 0, 4, 0, 0, 0,…
$ `2/4/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 3, 2, 0, 4, 0, 0, 0,…
$ `2/5/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 3, 2, 0, 4, 0, 0, 0,…
$ `2/6/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 4, 2, 0, 4, 0, 0, 0,…
$ `2/7/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/8/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/9/20`         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/10/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/11/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/12/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/13/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/14/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/15/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/16/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/17/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/18/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/19/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/20/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/21/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/22/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/23/20`        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/24/20`        <dbl> 1, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 0, 0,…
$ `2/25/20`        <dbl> 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 2, 0,…
$ `2/26/20`        <dbl> 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 2, 0,…
$ `2/27/20`        <dbl> 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 3, 0,…
$ `2/28/20`        <dbl> 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 5, 2, 0, 4, 0, 3, 0,…
$ `2/29/20`        <dbl> 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 9, 3, 0, 7, 2, 9, 0,…
$ `3/1/20`         <dbl> 1, 0, 1, 0, 0, 0, 0, 1, 0, 6, 0, 9, 3, 0, 7, 2, 14, 3…
$ `3/2/20`         <dbl> 1, 0, 3, 1, 0, 0, 0, 1, 0, 6, 0, 9, 3, 1, 9, 2, 18, 3…
$ `3/3/20`         <dbl> 1, 0, 5, 1, 0, 0, 1, 1, 0, 13, 0, 11, 3, 1, 9, 2, 21,…
$ `3/4/20`         <dbl> 1, 0, 12, 1, 0, 0, 1, 1, 0, 22, 1, 11, 5, 1, 10, 2, 2…
$ `3/5/20`         <dbl> 1, 0, 12, 1, 0, 0, 1, 1, 0, 22, 1, 13, 5, 1, 10, 3, 4…
$ `3/6/20`         <dbl> 1, 0, 17, 1, 0, 0, 2, 1, 0, 26, 0, 13, 7, 1, 10, 3, 5…
$ `3/7/20`         <dbl> 1, 0, 17, 1, 0, 0, 8, 1, 0, 28, 0, 13, 7, 1, 11, 3, 7…
$ `3/8/20`         <dbl> 4, 0, 19, 1, 0, 0, 12, 1, 0, 38, 0, 15, 7, 2, 11, 3, …
$ `3/9/20`         <dbl> 4, 2, 20, 1, 0, 0, 12, 1, 0, 48, 0, 15, 7, 2, 15, 4, …
$ `3/10/20`        <dbl> 5, 10, 20, 1, 0, 0, 17, 1, 0, 55, 1, 18, 7, 2, 18, 6,…
$ `3/11/20`        <dbl> 7, 12, 20, 1, 0, 0, 19, 1, 0, 65, 1, 20, 9, 3, 21, 9,…
$ `3/12/20`        <dbl> 7, 23, 24, 1, 0, 0, 19, 4, 0, 65, 1, 20, 9, 3, 21, 9,…
$ `3/13/20`        <dbl> 7, 33, 26, 1, 0, 1, 31, 8, 1, 92, 1, 35, 16, 5, 36, 1…
$ `3/14/20`        <dbl> 11, 38, 37, 1, 0, 1, 34, 18, 1, 112, 1, 46, 19, 5, 49…
$ `3/15/20`        <dbl> 16, 42, 48, 1, 0, 1, 45, 26, 1, 134, 1, 61, 20, 6, 57…
$ `3/16/20`        <dbl> 21, 51, 54, 2, 0, 1, 56, 52, 2, 171, 1, 68, 29, 7, 71…
$ `3/17/20`        <dbl> 22, 55, 60, 39, 0, 1, 68, 78, 2, 210, 1, 78, 29, 7, 9…
$ `3/18/20`        <dbl> 22, 59, 74, 39, 0, 1, 79, 84, 3, 267, 1, 94, 37, 10, …
$ `3/19/20`        <dbl> 22, 64, 87, 53, 0, 1, 97, 115, 4, 307, 1, 144, 42, 10…
$ `3/20/20`        <dbl> 24, 70, 90, 75, 1, 1, 128, 136, 6, 353, 3, 184, 50, 1…
$ `3/21/20`        <dbl> 24, 76, 139, 88, 2, 1, 158, 160, 9, 436, 3, 221, 67, …
$ `3/22/20`        <dbl> 40, 89, 201, 113, 2, 1, 266, 194, 19, 669, 5, 259, 10…
$ `3/23/20`        <dbl> 40, 104, 230, 133, 3, 3, 301, 235, 32, 669, 5, 319, 1…
$ `3/24/20`        <dbl> 74, 123, 264, 164, 3, 3, 387, 249, 39, 818, 6, 397, 1…
$ `3/25/20`        <dbl> 84, 146, 302, 188, 3, 3, 387, 265, 39, 1029, 6, 443, …
$ `3/26/20`        <dbl> 94, 174, 367, 224, 4, 7, 502, 290, 53, 1219, 12, 493,…
$ `3/27/20`        <dbl> 110, 186, 409, 267, 4, 7, 589, 329, 62, 1405, 12, 555…
$ `3/28/20`        <dbl> 110, 197, 454, 308, 5, 7, 690, 407, 71, 1617, 15, 625…
$ `3/29/20`        <dbl> 120, 212, 511, 334, 7, 7, 745, 424, 77, 1791, 15, 656…
$ `3/30/20`        <dbl> 170, 223, 584, 370, 7, 7, 820, 482, 78, 2032, 15, 689…
$ `3/31/20`        <dbl> 174, 243, 716, 376, 7, 7, 1054, 532, 80, 2032, 17, 74…

观察发现，数据集中存在缺失值、列名不好理解等问题。

2 数据清洗

除1-4列外，其余列名都是日期。
我们希望将数据清洗成两列，第一列为日期，第二列为该日期的确诊病例数。

根据此思路，我们对数据进行整理。

df1 <- df %>%
  pivot_longer(
    cols = 5:ncol(.),
    names_to = "date",
    values_to = "cases"
  ) %>%
  mutate(date = lubridate::mdy(date)) %>%
  janitor::clean_names() %>%
  group_by(country_region, date) %>%
  summarise(cases = sum(cases)) %>%
  ungroup()
df1

# A tibble: 12,600 × 3
   country_region date       cases
   <chr>          <date>     <dbl>
 1 Afghanistan    2020-01-22     0
 2 Afghanistan    2020-01-23     0
 3 Afghanistan    2020-01-24     0
 4 Afghanistan    2020-01-25     0
 5 Afghanistan    2020-01-26     0
 6 Afghanistan    2020-01-27     0
 7 Afghanistan    2020-01-28     0
 8 Afghanistan    2020-01-29     0
 9 Afghanistan    2020-01-30     0
10 Afghanistan    2020-01-31     0
# ℹ 12,590 more rows

计算每日确诊病例

df1 %>% 
  group_by(date) %>% 
  summarise(confirmed = sum(cases)) %>% 
  ggplot(aes(x = date, y = confirmed)) + 
    geom_point() +
    scale_x_date(
      date_labels = "%m-%d",
      date_breaks = "week"
    ) +
    scale_y_continuous(
      breaks = c(0, 50000, 100000, 200000, 300000, 500000, 900000),
      labels = scales::comma  # 不使用科学计数法 
    ) +
    theme_bw()

看图说话，从2020年1月20日至3月底，新冠肺炎确诊病例呈快速增长的趋势，而且越来越快。看看咱们国家的情况。

df1 %>% 
  filter(country_region == "China")  %>% 
  ggplot(aes(x = date, y = cases)) +
    geom_point() +
    scale_x_date(
      date_breaks = "week",
      date_labels = "%m-%d"
    )

我国在经历短暂病例数增加的后，疫情马上稳定了下来。

df1 %>% 
  group_by(country_region) %>% 
  filter(max(cases) >= 20000)  %>% 
  ungroup() %>% 
  ggplot(aes(x = date, y = cases, color = country_region)) + 
    geom_point() +
    scale_x_date(
      date_labels = "%m-%d",
      date_breaks = "week"
    ) +
    scale_y_log10() +
    facet_wrap("country_region", ncol = 2) +
    theme(
      axis.text.x = element_text(angle = 45, hjust = 1),
      legend.position = "none"
    )

在最大病例数超过20000例的国家中，除我国外，其他国家的病例数都经历了一个断崖式的增长。

3 可视化探索

想要在图形中显示出现100个病例后，各国确认人数的爆发趋势：

横坐标为日期，即在出现100个病例后的第几天。
纵坐标是累积确诊人数。

要达到这个这个效果，我们需要针对时间轴做一些变形：

按国家分组
筛选累积确诊数超过100的国家
找到所有case超过100的日期，并找到最早达到100病例数的日期（第0天），将其设置为0
构建新列，为当前日期与第0天的差值，即从100个病例开始至今过了多少天，并将这列转变为数值。

df2 <- df1 %>%
  group_by(country_region) %>%
  filter(max(cases) >= 100) %>%
  mutate(
    days_since_100 = date - min(date[cases >= 100])
  ) %>%
  mutate(days_since_100 = as.numeric(days_since_100)) %>%
  filter(days_since_100 >= 0) %>%
  ungroup()
df2

# A tibble: 1,710 × 4
   country_region date       cases days_since_100
   <chr>          <date>     <dbl>          <dbl>
 1 Afghanistan    2020-03-27   110              0
 2 Afghanistan    2020-03-28   110              1
 3 Afghanistan    2020-03-29   120              2
 4 Afghanistan    2020-03-30   170              3
 5 Afghanistan    2020-03-31   174              4
 6 Albania        2020-03-23   104              0
 7 Albania        2020-03-24   123              1
 8 Albania        2020-03-25   146              2
 9 Albania        2020-03-26   174              3
10 Albania        2020-03-27   186              4
# ℹ 1,700 more rows

df2_most <- df2 %>% 
  group_by(country_region) %>% 
  slice_max(days_since_100, n = 1) %>% 
  filter(cases >= 10000) %>% 
  ungroup() %>% 
  arrange(desc(cases))

highlight <- df2 %>% 
  group_by(country_region) %>% 
  slice_max(days_since_100, n = 1) %>% 
  ungroup() %>% 
  arrange(desc(cases)) %>% 
  slice_max(days_since_100, n = 10) %>% 
  pull(country_region)

df2 %>%
  bind_rows(
    tibble(country = "33% daily rise", days_since_100 = 0:30) %>%
      mutate(cases = 100 * 1.33^days_since_100)
  ) %>%
  
  ggplot(aes(days_since_100, cases, color = country_region)) +
    geom_hline(yintercept = 100) +
    geom_vline(xintercept = 0) +
    geom_line(size = 0.8) +
    geom_point(pch = 21, size = 1) +
    scale_y_continuous(
      labels = scales::comma_format(accuracy = 1),
      breaks = 10^seq(2, 8),
      trans = "log10"
    ) +
    theme_minimal() +
    scale_color_manual(values = c(prismatic::clr_darken(paletteer_d("ggsci::category20_d3"), 0.2)[1:length(highlight)],
                                  "gray70")) +
    theme(legend.position = "none",
          panel.grid.minor = element_blank(),
          panel.background = element_rect(fill = "#FFF1E6"),
          panel.spacing = margin(3, 15, 3, 15, "mm")) +
    labs(x = "Number of days since 100th case",
         y = "",
         title = "Country by country: how coronavirus case trajectories compare",
         subtitle = "Cumulative number of cases, by Number of days since 100th case",
         caption = "data source from @www.ft.com") +
    gghighlight::gghighlight(country_region %in% highlight,
      label_key = country_region, use_direct_label = TRUE,
      label_params = list(segment.color = NA, nudge_x = 1),
      use_group_by = FALSE
  )