00_Simulate.Rmd: See the live link here
02_<package>_infections.R compares each package to infections data
02_<package>_reports.R compares each package to reporting data
03_plot.R plots data in plot_data_<package>_infections.RData objects
04_eval.R starter evaluation code
the in_progress folder contains files in progress for R0, EpiFilter, and EpiNowcast
First make sure you have the correct R installed
required_version <- "4.0.0"
if (getRversion() < required_version) {
stop(paste("Your R version is", getRversion(), ". Please update to version", required_version, "or higher."))
} else {
cat(paste("R version is sufficient:", getRversion(), "\n"))
}
Then you need these packages
install.packages( "rmarkdown", "shiny" ,
"knitr", "plotly", "purrr" ,
"splines" , "tidyverse", "readr",
"EpiLPS", "EpiNow2",
"lubridate", "rstan" , "cmdstanr" , "R0" , "remotes" ,
"ggpubr" , "ggtext" , "lemon" , "patchwork")
remotes::install_github("dajmcdon/rtestim")
install.packages('EpiEstim', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))