README.md

In emmalouisedavis/TTI-branching-process: TTI COVID-19 branching process model

TTI-branching-process

1. System requirements

All results were run using RStudio 1.4.1106 and R version 4.0.3 (2020-10-10) on macOS Big Sur Version 11.2.3

1. Installation guide

Install packages using the following file: TTI-branching-process/inst/scripts/installPackages.r

Load ringbp package / source code run the following code chunk (typical install time <1min):

library(data.table) library(tidyverse) library(git2r) library(tictoc) library(ggplot2) library(patchwork) library(cowplot) library(latex2exp) library(furrr) library(sn) library(ggrepel) library(testthat) library(svglite)

devtools::load_all() #load in ringbp package manually

1. Demo

A demo can be found at: TTI-branching-process/inst/scripts/demo.R

The expected run time for this demo is ~5mins

Expected output is a 2x3 Figure with x-axis 'Contact tracing coverage' - the proportion of true contacts that are identified and traced. y-axis 'Prob. large outbreak' - the proportion of simulations that reached 2000 cases. There should be no discernible trend with changing coverage, due to the low numbers of runs in this demo. The probability of a large outbreak should roughly decrease as 'Rs' decreases (labels vertically down the RHS).

1. Instructions for use

To recreate the results from the paper run the following files: a. TTI-branching-process/inst/scripts/generateResults.R b. TTI-branching-process/inst/scripts/generatePlots.R

Running the full results is likely to take >48 hours on a standard PC.

emmalouisedavis/TTI-branching-process documentation built on Dec. 20, 2021, 5:17 a.m.