covid_uk_omicron

# Total Cases: https://coronavirus.data.gov.uk/ (updated after 4PM at minimum)
# Omicron split: https://www.gov.uk/government/publications/covid-19-omicron-daily-overview (updated at ?)

library(data.table)
library(ggplot2)

yc <- fread(
        'https://api.coronavirus.data.gov.uk/v2/data?areaType=region&metric=newCasesBySpecimenDate&format=csv', 
        select = c(2, 4, 5)
)
setnames(yc, c('RGN', 'sdate', 'n'))
y <- fread(
        paste0(
            'https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1041217/sgtf_regionepicurve_',
            (Sys.Date() - 1),
            '.csv'
        ),
        select = 1:5
)
setnames(y, c('RGN', 'sdate', 'n_sgtf', 'p_sgtf', 'sgtf'))
y <- y[grepl('SGTF', sgtf)][, sgtf := NULL]
y[RGN == 'Yorkshire and Humber', RGN := 'Yorkshire and The Humber']
y[, sdate := as.IDate(sdate, '%d/%m/%Y')]
y <- yc[y, on = c('RGN', 'sdate')]
y[, omicron := as.integer(n * p_sgtf / 100)][, others := n - omicron]   
y <- melt(y[, .(RGN, sdate, omicron, others)], id.vars = 1:2, variable.name = 'variant', value.name = 'cases')

ggplot(y, aes(sdate, cases, color = variant)) + 
    geom_line() +
    facet_wrap(~RGN) +
    labs(x = 'Specimen Date', y = 'Cases') +
    theme_minimal() +
    theme(axis.text.x=element_text(angle = 45, hjust = 1)) +
    scale_x_date(date_breaks = '1 week', date_labels = '%d %b') +
    scale_y_continuous(label = scales::comma)