Code for showing no community spread of omicron at present

omicron.R

library(readr)
library(dplyr)
library(ggplot2)
library(ggthemes)
library(lubridate)
source("davidise.R") # graph styling and saving at twitter size
# extract colorblind pallete in case I want to make strategic use of it
six_cols <- (colorblind_pal()(6))
# daily full demographic csvs folder
cases_folder <- list.files("daily_all_cases", pattern = "csv$", full.names = TRUE)
all_csvs <- file.info(cases_folder)
# find most recently saved csv file
latest_csv <- row.names(all_csvs)[which.max(all_csvs$ctime)]
all_cases <-  read_csv(latest_csv, col_types= cols(
  `Report Date` = col_date(format = ""),
  .default = col_character())) %>%
  filter(`Report Date` > (max(`Report Date`) - days(14))) %>%
  count(Date = `Report Date`, DHB) %>%
  group_by(DHB) %>%
  mutate(entries = n()) %>%
  ungroup() %>%
  filter(entries >1) %>%
  mutate(log2y=log(n,2),
         Date2=as.numeric(Date)) 

bookends = c(min(all_cases$Date2),max(all_cases$Date2))
bookendsD = format.Date(c(min(all_cases$Date),max(all_cases$Date)),
                        format="%b\n%d")
bookendsT = format.Date(c(min(all_cases$Date),max(all_cases$Date)),
                        format="%b %d")
leads <- all_cases %>% filter(n > 19)
if_doubling <- function(x, cvdata=leads){
  xinput <- cvdata$Date2[x]
  yinput <- cvdata$n[x]
  zinput <- cvdata$DHB[x]
  xguide = 1:1600/100
  yguide <- (2^(1/2))^(xguide-1)
  xcord <- xguide[yguide > yinput & yguide < 100]
  xcord <- xcord - min(xcord) + xinput
  ycord <- yguide[yguide > yinput & yguide < 100]
  dat <- data.frame(xcord, ycord,group_id = paste0(xinput,zinput),
                    DHB=zinput, stringsAsFactors = FALSE)
  return(dat)
}

result_guide <- bind_rows(lapply(1:nrow(leads), if_doubling))

dg <- ggplot(all_cases, aes(x=Date2, y=n)) + 
  geom_line(data=result_guide,
            aes(x=xcord,y=ycord,group=group_id),
            size=0.4, colour="#BFBFBF") +
  geom_point(size=0.6) +
  facet_wrap(~DHB, ncol=4) +
  theme_tufte() +
  scale_x_continuous(breaks = bookends,
                     labels = bookendsD) +
  labs(title="DHB daily cases with Omicron doubling time guide lines\n(Omicron doubling guides for 20+ case days)",
       subtitle=paste("for the two week period", bookendsT[1],"to",bookendsT[2]),
       y="Number of cases\n", x="")
dg 
davidise_graph(dg)