aug2021graph.R

# Data
# https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coronavirus/covid-19-data-and-statistics/covid-19-case-demographics#case-details
library(readr)
library(dplyr)
library(ggplot2)
library(ggthemes)
library(lubridate)
library(patchwork)

# you need to provide csv name
file_name <- "covid_cases_2021-08-22.csv"
update_date = as.Date(gsub("[^1234567890-]","",file_name))
# update date needed because any current day info is partial
# rather than complete

MoH <- read_csv(file_name, 
                col_types = cols(
  `Report Date` = col_date(format = ""),
  `Case Status` = col_character(),
  Sex = col_character(),
  `Age group` = col_character(),
  DHB = col_character(),
  `Overseas travel` = col_character(),
  Historical = col_character()))

complete_sequence <- data.frame(case_date = seq.Date(from=as.Date("2020-08-11"), 
                                                    to=as.Date("2020-09-30"), 
                                                    by="day"), n=0)
Aug_Ref <- MoH %>%
  filter(`Overseas travel` != "Yes",
         DHB != "Managed Isolation & Quarantine",
         `Report Date` >= as.Date("2020-08-01"),
         `Report Date` < as.Date("2020-10-01"),
         is.na(Historical)) %>%
  count(case_date = `Report Date`) %>%
  bind_rows(complete_sequence) %>%
  arrange(desc(n)) %>%
  group_by(case_date) %>%
  slice(1) %>%
  ungroup() %>%
  mutate(outbreak_day = as.numeric(difftime(case_date, 
                                            as.Date("2020-08-10"),
                                            units="day")),
         outbreak = "aug 2020") %>% 
  select(outbreak_day, n, outbreak)

current_sequence <- data.frame(case_date = seq.Date(from=as.Date("2021-08-17"), 
                                                     to=Sys.Date() - days(1), 
                                                     by="day"), n=0)

graphdaily <- MoH %>%
  filter(`Overseas travel` != "Yes",
         DHB != "Managed Isolation & Quarantine",
         `Report Date` >= as.Date("2021-08-10"),
         is.na(Historical)) %>%
  count(case_date = `Report Date`) %>%
  bind_rows(current_sequence) %>%
  arrange(desc(n)) %>%
  group_by(case_date) %>%
  slice(1) %>%
  ungroup() %>%
  mutate(outbreak_day = as.numeric(difftime(case_date,
                                            as.Date("2021-08-16"),
                                            units="day")),
         outbreak = "current",
         Day = ifelse(case_date ==update_date, "Partial", "Complete")) %>%
  select(outbreak_day, n, outbreak, Day)

  


top <- ggplot(graphdaily,aes(x=outbreak_day, y=n)) + 
  geom_point(size=1) + theme_minimal() + 
  geom_segment(aes(xend=outbreak_day, yend=0, linetype=Day)) +
  geom_line(data=Aug_Ref, colour="orange", alpha=0.7) +
  geom_point(data=Aug_Ref, colour="orange", size=0.8, alpha=0.7) +
  ylab("Daily new\ncases") + xlab("") +
  ggtitle("Current NZ outbreak (black) vs Aug 2020 non-Delta outbreak (orange).
Note:this doesn't show who was in isolation while infectious") +
  theme(legend.position = "bottom", axis.title.x = element_blank())

top

place0 <- data.frame(outbreak_day = c(0,0),
                     n = c(0,0),
                     outbreak = c("aug 2020", "current"),
                     Day = c("Complete", "Complete"))
graphcumul <- graphdaily %>%
  bind_rows(Aug_Ref, place0) %>%
  arrange(outbreak, outbreak_day) %>%
  group_by(outbreak) %>%
  mutate(cummulative_cases = cumsum(n),
         prev_cases=lag(cummulative_cases),
         prev_outbreak_day = lag(outbreak_day),
         Day = ifelse(is.na(Day), "Complete", Day)) %>%
  ungroup() %>%
  filter(!is.na(prev_cases))


bottom <- ggplot(graphcumul,aes(x=outbreak_day, y=cummulative_cases,
                 colour=outbreak)) + 
  geom_point(size=0.3) + theme_minimal() + 
  geom_segment(aes(xend=prev_outbreak_day, yend=prev_cases, linetype=Day)) +
  scale_colour_manual(values=c("orange","black")) +
  ylab("Cummulative\nCases") + xlab("Day of outbreak")+
  theme(legend.position = "none")
bottom
grf <- top / bottom
ggsave(filename="~/Desktop/ouput.png", plot=grf,dpi=72, units="in",
       height = 5.556, width=9.877)
grf