+title: 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 [[https://doi.org/10.1093/sysbio/syac037][Andréoletti /et al/ (2022)]] and uses the [[https://aezarebski.github.io/timtam/][TimTam]] package for BEASTv2.

• Data

See the [[file:./data/readme.org]] document which describes the sequence and case data used in this analysis.

• Model

See the [[file:./model.org]] document which describes the model.

• Results

+caption: Figures and files

+name: tbl:figure-script

| 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]] |

+caption: Data

+name: fig:data

+attr_org: :width 500px

+attr_html: :width 400px

[[./out/manuscript/data-plot.png]]

+caption: R0 estimates

+name: fig:r0-estimates

+attr_org: :width 500px

+attr_html: :width 400px

[[./out/manuscript/r0-estimates.png]]

+caption: Prevalence estimates

+name: fig:prevalence-estimates

+attr_org: :width 500px

+attr_html: :width 400px

[[./out/manuscript/prevalence-estimates.png]]

• Running analysis

This assumes that you have [[https://ant.apache.org/][Apache Ant]], [[https://cran.r-project.org/][R]] and [[https://www.java.com/en/][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:

+begin_src sh

ant -p

+end_src

** Setting up BEAST2

+begin_src sh

ant setuplib

+end_src

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

+begin_src sh

ant preprocess # proprocess data ant beauti # generate XML

+end_src

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

*** MCMC

+begin_src sh

ant mcmc

+end_src

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

*** Postprocessing

+begin_src sh

ant postprocess

+end_src