This repository contains the BEAST 2 XML files and R scripts needed to replicate the analyses presented in the manuscript "Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data".
The files are organized as follows:
sequences/ contains details of which SARS-CoV-2 genomes were used
from GISAID, including the table of acknowledgements listing the
contributing individuals, labs and organizations.
To reproduce analyses, the appropriate sequence data must be included
in this folder. (For details, see the README.md file in this folder.)
XMLs/ contains the BEAST 2 XML input files necessary to replicate
the analyses. These analysis files require BEAST 2.6.7 to run
correctly. (For further details, see the README.md file in this folder.)
R_scripts/ contains the R scripts used for post-processing and
generating the figures presented in the manuscript. (For further details,
see the README.md in this folder.)