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update-rt-estimate.R
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update-rt-estimate.R
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# Run Rt estimates for different data sources
# remotes::install_github("epiforecasts/covidregionaldata")
library(EpiNow2)
# Update delays
# source(here::here("rt-estimate", "delays", "public-linelist-delays.R"))
# Get delays and fresh UK data; set up cores
source(here::here("rt-estimate", "utils", "rt-data-defaults.R"))
# Get function for Rts
# - This functions runs using EpiNow2 v1.2 as used in the paper
source(here::here("rt-estimate", "utils", "run-rt-estimate.R"))
# Set min/max dates for data
data <- data[data$date >= as.Date("2020-03-19") & data$date <= max(data$date)-1,]
# regional data only available after 19 March; this trims England data to same
# hospital admissions always 1 day more delayed than other data
# Set root for saving estimates
save_loc <- "rt-estimate/estimate-all-time/"
# Run estimates -----------------------------------------------------------
# Run everything everywhere
# Cases - by test date
run_rt_estimate(data = data,
save_loc = save_loc,
count_variable = c("cases_test"),
reporting_delay = cases_delay,
burn_in = 0,
no_cores = no_cores,
future = FALSE)
# Hospital admissions
run_rt_estimate(data = data,
save_loc = save_loc,
count_variable = c("cases_hosp"),
reporting_delay = cases_delay,
burn_in = 0,
no_cores = no_cores,
future = FALSE)
# Deaths - by date of death
run_rt_estimate(data = data,
save_loc = save_loc,
count_variable = c("deaths_death"),
reporting_delay = deaths_delay,
burn_in = 0,
no_cores = no_cores,
future = FALSE)
# Run specific regions ----------------------------------------------------
# # Cases - by test date
# run_rt_estimate(data = data[data$region %in% c("North West"),],
# save_loc = save_loc,
# count_variable = c("cases_test"),
# reporting_delay = cases_delay,
# burn_in = 0,
# future = FALSE)
# # Hospital admissions
# run_rt_estimate(data = data[data$region %in% c("England", "East of England"),],
# save_loc = save_loc,
# count_variable = c("cases_hosp"),
# reporting_delay = cases_delay,
# burn_in = 0,
# future = FALSE)
# # Deaths - by date of death
# run_rt_estimate(data = data[data$region %in% c("Midlands"),],
# save_loc = save_loc,
# count_variable = c("deaths_death"),
# reporting_delay = deaths_delay,
# burn_in = 0,
# future = FALSE)
# EpiNow2 v 1.3 -----------------------------------------------------------
# - Alternatively use EpiNow2 v1.3 (current development version as of 16/11/20)
# source(here::here("rt-estimate", "utils", "run-rt-estimate-epinow2-v1-3.R"))
#
# # Data & settings
# source(here::here("rt-estimate", "utils", "rt-data-defaults.R"))
# data <- data[data$date >= as.Date("2020-03-19") & data$date <= max(data$date)-1,]
# save_loc <- "rt-estimate/estimate-all-time/"
#
# run_rt_estimate(data = data,
# save_loc = save_loc,
# count_variable = c("cases_test"),
# reporting_delay = cases_delay,
# burn_in = 0,
# no_cores = no_cores)
# # Hospital admissions
# run_rt_estimate(data = data,
# save_loc = save_loc,
# count_variable = c("cases_hosp"),
# reporting_delay = cases_delay,
# burn_in = 0,
# no_cores = no_cores)
# # Deaths - by date of death
# run_rt_estimate(data = data,
# save_loc = save_loc,
# count_variable = c("deaths_death"),
# reporting_delay = deaths_delay,
# burn_in = 0,
# no_cores = no_cores)