Diamond Princess COVID-19 analysis

This repository provides code to run an analysis of data collected during an outbreak of SARS-CoV-2 onboard the Diamond Princess. The analysis is based off a previous analysis from Andréoletti et al (2022) and uses the TimTam package for BEASTv2.

Model

See the ./model.org document which describes the model.

Results

Results figure	R script that generated it
fig:data	./R/preprocessing-part-3.R
fig:r0-estimates	./R/combine-ltt-and-histories.R and ./R/postprocessing-part-4.R
fig:prevalence-estimates	./R/combine-ltt-and-histories.R and ./R/postprocessing-part-4.R

Running analysis

This assumes that you have Apache Ant, R and Java installed.

Getting help

The computations are coordinated with Ant. To get a list of the various targets it knows how to build run the following:

ant -p

Setting up BEAST2

ant setuplib

Note that this will only set up the relevant BEAST tools. You will still need to install the TimTam package via BEAUti.

Running the analysis

Optional: generation of XML

ant preprocess	# proprocess data
ant beauti		# generate XML

Getting to the final XML files used is not an entirely automated process, and making it so would likely be counter productive.

MCMC

ant mcmc

WARNING: The XML reads sequences in from data/diamond.fasta which is not part of this repository. See the README in that directory for details.

Postprocessing

ant postprocess