branch_lengths

Code and data associated with the manuscript "A simple method of estimating rabies outbreak sizes from phylogenies". Authors: Rowan Durrant, Christina Cobbold, Elaine Ferguson, Criselda Bautista, Kirstyn Brunker, Katie Hampson, Jonathan Dushoff.

NOTE: some FASTA and tree files are too big for GitHub!

input

Branching process simulation output (EF); Cosmopolitan AF1b dataset for site-specific rate and transversion rate parameter estimation.

code

• mutations_function_time_sites.R: simulates viral evolution.

• simulate_branches_time_sites.R: applies above function to epi model output.

• subsampling.R: downsamples datasets from full outbreak simulations.

• make_trees.sh: mass generate phylogenetic trees using IQTREE.

• plot_equation_curve.R: look at relationship between the sequencing probability and the tree length.

• estimate_function.R: function to estimate outbreak sizes using our method.

• accuracy_quadratic.R: see how accurate our method is.

• romblon_calcs.R: estimate the size of the ongoing outbreak in Romblon province, Philippines.

• romblon_figure.R: figure for this section.

• overdispersion.R, subsampling_overdispersion.R, accuracy_overdispersion.R: testing the effect of an overdispersed secondary case distribution.

• subsampling_time_biased.R, accuracy_time_biased.R: testing the effect of sequencing delays.

• test_annual_estimates.R: can we get annual estimates of case numbers, and are they as accurate as the full outbreak size estimate?

• z_testing.R: how can we make this method more applicable to other diseases? (not in current manuscript- work in progress!)

output

Some output files/folders have not been uploaded as their contents are absolutely massive- these will need to be re-generated locally using the scripts above (simulate_branches_time_sites.R and subsampling.R) if you would like to use them.

Simulation_trees/, time_biased_trees/ and overdispersion_trees/ contains the phylogenies from these simulated outbreaks.

romblon-data

Contains a Philippines-wide rabies BEAST log file (CB); sequences and phylogenies for Romblon outbreak; transmission tree reconstruction table with estimated generation intervals.