In terminological/uk-covid-datatools: Functions for sourcing, cleaning and calculating Rt for uk covid timeseries data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

devtools::load_all("~/Git/uk-covid-datatools/")
#devtools::install_github("terminological/uk-covid-datatools", force = TRUE)
ukcovidtools::setup()

Get data and cleanse:

testData = dpc$datasets$getPHEApi(areaType = "nation")

timeseries has UK region, England NHS region, and England Unitary Authority

Calculate groupwise Rt (data is already grouped on uk_region)

tsp$plotIncidenceQuantiles(testData,colour = statistic)+facet_wrap(vars(name))+scale_y_continuous(trans="log1p", breaks = ukcovidtools::breaks_log1p(n = 6))

# switch the serial interval
tn = SerialIntervalProvider$resampledSerialInterval(dpc)
tsp$serial = tn

testData %>% tsp$estimateRt() %>% tsp$plotRt(colour=name, rtlim = c(0,2.5), dates = "2020-03-01")+facet_wrap(vars(statistic),ncol=1)

terminological/uk-covid-datatools documentation built on June 24, 2021, 8:16 p.m.