Estimate Time Varying Reproduction Number Directly from Confirmed Case Counts
This repository contains the stan code for running a model that estimates the time-varying reproduction number directly from confirmed case counts.
To install this package run devtools::install_github("jhellewell14/rtconfirm")
If you clone this repository and recieve an error when building it locally, trying running pkgbuild::clean_dll() followed by pkgbuild::compile_dll() to compile the stan file using the compiler on your local machine.
To get started, try running:
library(rstan)
library(patchwork)
# If you want to run in parallel run
# options(mc.cores = parallel::detectCores())
res <- rtconfirm::run_rtconfirm(country = "Poland", cut = 10)
# Output plot
res[[1]] / res[[2]]
Country names are matched to data provided by the European Centre for Disease Control, some countries with spaces in use underscores like South_Korea, United_States_of_America, or United_Kingdom.
To get a full list of countries for which there are data available run sort(unique(NCoVUtils::get_ecdc_cases()$country))
I'm starting to put together slides of the theory behind the stan model here: https://docs.google.com/presentation/d/1wg_BDQkhYTJqAylzQVK_wCnw2v6OlFf-sUmdJOx1xvg/edit?usp=sharing