Code and data for Dynamics and control of highly pathogenic H5 avian influenza in a threatened pelican population

• The main directory contains scripts for data cleaning, epidemiological modelling, estimating seroprevalence, and plotting figures.
• Folder "data" contains a metadata table of GISAID sequences used in the phylogenetic analysis. The epidemiological and demographic data of the pelican population used for epidemiological modelling is hosted on Figshare seperately.
• Folder "phylo" contains a R script for genetic data analyses, maximum likelihood trees of the full genome segments, and a BEAST xml for generating the time-scaled HA phylogeny.