Important files:
- data/gisaid_db.fas: a sequence alignment (downloaded from GISAID)
- data/md.csv: metadata for sequence alignment (also available on GISAID)
- beast/seijr0.1.0_skeleton.xml: Main results using PhyDyn package and SEIJR model
Pipeline:
- R/sampling_reference_set.R
- R/eda1.R: Exploratory data analysis and outlier detection using
treedater, producing ML and time trees, RTT regression - R/produce_xml.R
- Run PhyDyn on BEAST2 using xmls
- R/process_BEAST_output.R
- R/produce_epidemic_plots.R
- R/produce_trees.R