Vax data for @davehawkinsSOA

A quick reproduction script for @davehawkinsSOA

Get latest data from ONS

setup/requirements

library(tidyverse)
library(hrbrthemes)
library(janitor)
library(readxl)
options(dplyr.summarise.inform = FALSE)

fetch file

latest_file_url='https://www.ons.gov.uk/file?uri=/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/deathsbyvaccinationstatusengland/deathsoccurringbetween1january2021and31may2022/referencetable06072022accessible.xlsx'

onsdl=tempfile(fileext='.xlsx')

download.file(url=latest_file_url,destfile=onsdl,mode='wb',quiet=T)

parse file and process data

tbl2=read_xlsx(onsdl,sheet='Table 2',skip=3) %>%
  clean_names() %>%
  mutate(
    date=as.Date.character(sprintf("%s 1, %d",month,year),"%B %d, %Y"),
    rate=as.numeric(age_standardised_mortality_rate_100_000_person_years),
    rate_lo=as.numeric(lower_confidence_limit),
    rate_hi=as.numeric(upper_confidence_limit),
    count_of_deaths=as.numeric(count_of_deaths),
    vaxgrp=ifelse(vaccination_status=='Unvaccinated','Unvaccinated','Any vaccination level')
  )

tbl2_agg=tbl2 %>%
  group_by(cause_of_death,date,age_group,vaxgrp) %>%
  summarise(
    rate_adj=weighted.mean(rate,w=person_years,na.rm=T), # get weighted average of ONS's ASMR
    count_of_deaths=sum(count_of_deaths,na.rm=T),
    person_years=sum(person_years,na.rm=T)    
  ) %>%
  ungroup() %>%
  mutate(
    rate_crude=count_of_deaths/person_years*1e5,
    se=rate_adj/sqrt(count_of_deaths),
    ci=1.96*se,
    rate_lo=rate_adj-ci,
    rate_hi=rate_adj+ci
  )  

quick plot

tbl2_agg %>%
  filter(
    cause_of_death=='All causes',
    age_group!= '18-39'
  ) %>%
  ggplot(aes(date,rate_adj,color=vaxgrp)) +
      geom_ribbon(aes(ymin=rate_lo,ymax=rate_hi),alpha=0.5) +
      geom_line(size=1) +
      #scale_y_log10() +
      #annotation_logticks(sides='lr')  +
      facet_wrap(~age_group,scale='free_y') +
      theme_ipsum() +
      labs(
        title='Monthly age-standardised mortality rates for all cause deaths by age group and vax status',
        color=NULL,
        y='Age-standardised all cause deaths per 100,000',
        caption='source: UK ONS, Deaths by vaccination status, England\nhttps://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/deathsbyvaccinationstatusengland'
      ) +
      theme(
        legend.position='bottom',
        panel.grid.minor = element_blank(),
        axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
        panel.spacing = unit(.2, "lines")
      )