gistfile1.txt

library(readxl)
library(ggplot2)
library(viridis)
library(tidyverse)
UK <- read_excel("referencetable.xlsx", sheet = "Table 7", skip = 4, n_max = 350)
UK$Mortality.age.std=as.numeric(UK$Mortality.age.std)
UK$Lower.limit=as.numeric(UK$Lower.limit)
UK$Upper.limit=as.numeric(UK$Upper.limit)
mynamestheme=theme(plot.title=element_text(face="bold",size=(15)))
UK.covid <- read_excel("referencetable.xlsx", sheet = "Table 5", skip = 4, n_max = 350)
UK.covid$Mortality.age.std=as.numeric(UK.covid$Mortality.age.std)
UK.covid$Lower.limit=as.numeric(UK.covid$Lower.limit)
UK.covid$Upper.limit=as.numeric(UK.covid$Upper.limit)
UK.non.covid <- read_excel("referencetable.xlsx", sheet = "Table 6", skip = 4, n_max = 350)
UK.non.covid$Mortality.age.std=as.numeric(UK.non.covid$Mortality.age.std)
UK.non.covid$Lower.limit=as.numeric(UK.non.covid$Lower.limit)
UK.non.covid$Upper.limit=as.numeric(UK.non.covid$Upper.limit)
UK[UK$Number.deaths=="<3",]$Number.deaths=1.5
UK[UK$Number.deaths=="1.5",]$Unreliable="u"
UK$Number.deaths=as.numeric(UK$Number.deaths)
select=UK$Vaccination.status!="Unvaccinated"
UK_all_deaths=aggregate(UK[select,]$Number.deaths,by=list(Age.group=UK[select,]$Age.group,Month=UK[select,]$Month), FUN=sum)
UK_all_person.years=aggregate(UK[select,]$Person.years,by=list(Age.group=UK[select,]$Age.group,Month=UK[select,]$Month), FUN=sum)
UK_all_vax=UK_all_deaths
UK_all_vax$Number.deaths=UK_all_vax$x
UK_all_vax$Person.years=UK_all_person.years$x
UK_all_vax$Mortality.std=UK_all_vax$Number.deaths/UK_all_vax$Person.years*100000
UK$Mortality.std=UK$Number.deaths/UK$Person.years*100000
UK_all_vax$Unvaccinated.Mortality.std=UK[UK$Vaccination.status=="Unvaccinated",]$Mortality.std
UK_all_vax$Unvaccinated.Person.years=UK[UK$Vaccination.status=="Unvaccinated",]$Person.years
UK.non.covid$Covid="No"
UK.covid$Covid="Yes"
UK.combined<-rbind(UK.non.covid,UK.covid)
UK.combined.sum<-UK.combined %>%
  group_by(Age.group,Vaccination.status,Covid) %>%
  summarize(mean_mort = sum(Mortality.age.std, na.rm = TRUE))
ggplot(UK.combined.sum, aes(x=Age.group,                            
               fill=as.numeric(mean_mort), 
               y=Vaccination.status))+
  facet_wrap(~Covid)+
  scale_fill_viridis_c(option="C")+
  geom_tile() + theme_bw() + guides(fill=guide_legend(title="Mortality Age Standard"))