東京都の年代別COVID-19陽性者数の分析

covid19tokyo.R

#library
library(tidyverse)
library(incidence)
library(lubridate)
library(scales)
library(ggsci)
library(ggthemes)
library(glue)
library(patchwork)
library(jsonlite)
library(curl)

##東京都年代別------------------------------------------
##https://stopcovid19.metro.tokyo.lg.jp/

URL = "https://stopcovid19.metro.tokyo.lg.jp/data/130001_tokyo_covid19_patients.csv"
tokyo <- read_csv(URL,na = c("NA","","'-"))
tail(tokyo)
tokyo$患者_年代 <- fct_relevel(tokyo$患者_年代, "10歳未満","10代","20代","30代","40代","50代","60代","70代","80代","90代","100歳以上","不明")
tokyo <- tokyo %>% rename(age="患者_年代", date="公表_年月日")
#mutate(tokyo, age = na_if(age, "'-"))

tokyo <- tokyo %>% mutate(age2 = case_when(
  age == "10歳未満"~"10代以下", 
  age =="10代"~"10代以下",
  age =="20代"~"20-30代",
  age =="30代"~"20-30代",
  age == "40代" ~ "40-50代",
  age == "50代" ~ "40-50代",
  age =="60代"~"60-70代",
  age =="70代"~"60-70代",
  age =="80代"~"80代以上",
  age =="90代"~"80代以上",
  age =="100歳以上"~"80代以上")) %>% dplyr::filter(Date>="2020-02-24")

tokyo <- tokyo %>% mutate(age3 = case_when(
  age == "10歳未満"~"30代以下", 
  age =="10代"~"30代以下",
  age =="20代"~"30代以下",
  age =="30代"~"30代以下",
  age == "40代" ~ "40-60代",
  age == "50代" ~ "40-60代",
  age =="60代"~"40-60代",
  age =="70代"~"70代以上",
  age =="80代"~"70代以上",
  age =="90代"~"70代以上",
  age =="100歳以上"~"70代以上"))

tokyo <- tokyo %>% dplyr::filter(!is.na(age3))

#incidence確認
dat <- tokyo$date
class(dat)
i <- incidence(dat)
i
plot(i)



##年代別陽性者数　日別------------------------------------------
i.7.age <- incidence(dat, interval = "1 day", groups = tokyo$age3)
i.7.age

#日付など
today <- lubridate::today()
date_last <- length(i.7.age$dates)
date_start_fit <- date_last-13

#直近の倍加時間
f <- incidence::fit(i.7.age[date_start_fit:date_last])
f

##倍加時間抽出------------------------------------------
##増加局面
#DT_30 <- round(f$info$doubling["30代以下"], digits = 1)
#DT_40to60 <- round(f$info$doubling["40-60代"], digits = 1)
#DT_70 <- round(f$info$doubling["70代以上"], digits = 1)

#倍加時間抽出,30代以下のみ減少
DT_30 <- round(f$info$halving["30代以下"], digits = 1)
DT_40to60 <- -round(f$info$halving["40-60代"], digits = 1)
DT_70 <- -round(f$info$halving["70代以上"], digits = 1)

#フォント指定
font_family = "HiraginoSans-W4" # Macの場合
windowsFonts(font_family = windowsFont("Meiryo")) # Windowsの場合

#グラフ描画
lims <- as.Date(strptime(c("2020-03-20","2020-09-30"), format = "%Y-%m-%d"))  
p <- plot(i.7.age, stack = FALSE, fit=f)+
  scale_x_date(limits = lims, date_breaks  = "5 days", labels = date_format(format = "%B%d日"))+
  annotate("text", hjust=0, x=today+1, y=150, label=glue("半減期：{DT_30}日"), family=font_family, size=5,colour="#00468BFF")+
  annotate("text", hjust=0, x=today+1, y=80, label=glue("倍加時間：{DT_40to60}日"), family=font_family, size=5,colour="#ED0000FF")+
  annotate("text", hjust=0, x=today+1, y=30, label=glue("倍加時間：{DT_70}日"), family=font_family, size=5, colour="#42B540FF")+
  labs(title="東京都 COVID-19 年代別陽性者数推移",
       subtitle = "COVID-19 Confirmed Cases by Age Groups in Tokyo, Japan", 
       x="", y="New Reported Cases", 
       caption = "（ヽ´ん`）@kenmomd \nDATA：東京都福祉保健局",
       fill = "Age",
       colour = "Age")+
  theme_bw(base_size = 13, base_family = font_family)+
  scale_y_continuous(expand = c(0,0), limits = c(0,400))+
  scale_fill_lancet()+
  scale_color_lancet()+
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
p
ggsave(filename = "./Tokyo-Age_Daiy_c.png", plot=p, width=15, height=9, dpi = 180)

tokyo_age3_daily.csv

tokyo_age3_weekly.csv