Created
January 13, 2022 19:28
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| library(readxl) | |
| library(curl) | |
| library(tidyverse) | |
| file = "https://www.ons.gov.uk/file?uri=%2fpeoplepopulationandcommunity%2fhealthandsocialcare%2fconditionsanddiseases%2fdatasets%2fcoronaviruscovid19antibodydatafortheuk%2f2022/20220113covid19infectionsurveydatasets1.xlsx" | |
| temp <- tempfile() | |
| temp <- curl_download(url=file, destfile=temp, quiet=FALSE, mode="wb") | |
| get_data = function(sheet, threshold ){ | |
| data<- read_excel(temp,sheet=sheet,range="A6:AT61") | |
| data[data=="*"] <- NA | |
| data = data %>% mutate(across(-`Weekly period`,as.numeric)) | |
| headings = read_excel(temp,sheet=sheet,range="A5:AT5",col_names = F) | |
| ages = unique(c(t(headings))) | |
| ages = ages[!is.na(ages)] | |
| colnames(data)[2:46] = paste(rep(ages,each=5),colnames(data)[2:46] ,sep="_") | |
| output = data %>% pivot_longer(-`Weekly period`) %>% separate(name,into=c("Age_range","Type"),sep="_") %>% separate(Type,into=c("Type"),sep="\\.\\.\\.") %>% pivot_wider(names_from=Type,values_from=value) %>% separate(`Weekly period`,into=c("from","to"),sep=" to ") %>% mutate(from=lubridate::dmy(from),to=lubridate::dmy(to), mid = from + (to-from)/2 ) %>% mutate(positivity = `Modelled % testing positive for COVID-19 antibodies`/100, lower = `95% Lower credible interval`/100,, upper = `95% Upper credible interval`/100) %>% mutate(Age_range=gsub("Age ","",Age_range)) | |
| output$threshold= threshold | |
| return (output) | |
| } | |
| lower = get_data("1c","Lower") | |
| higher = get_data("1g","Higher") | |
| both = bind_rows(lower,higher) | |
| both$threshold=factor(as.character(both$threshold),levels=c("Lower","Higher")) | |
| library(gganimate) | |
| anim_stat=ggplot(both ,aes(y=positivity,fill=threshold,x=Age_range,ymin=lower,ymax=upper,group=threshold))+geom_area(position="identity",alpha=1,color="black",lwd=0.4)+theme_minimal()+scale_fill_manual(values=c("#b5bef7","#7D8DE9"))+scale_color_manual(values=c("#b5bef7","#7D8DE9"))+scale_y_continuous(label=scales::percent)+labs(title = '{frame_time}',y="Percent testing positive for antibodies",x="Age range",fill="Level",caption="Data: anti-S antibody data from ONS CIS for England")+geom_errorbar(width=0.2,alpha=0.2,color="black")+ theme(plot.title = element_text(size=15)) | |
| anim_stat | |
| anim = anim_stat+transition_time(mid) | |
| a <- animate(anim, renderer = file_renderer("~/output_movie/"),height=500*1.5,width=800*1.5,res=180,nframes = 500) |
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