The analysis pipelne assumes the stability of the file locations. To recover the results: 1.) (Optional) Run the Mathematica files in GeneticViremicAnalysis to (re)generate the HDF5 summary of the genetic and viremic results and estimate mut target size. Make sure to run "snp_analysis.nb" first, since this file sets the site information used in the genetic analysis. In case you don't have access to Mathematica, the .h5 files have been provided so you can test the Julia code which follows (Julia is free). 2.) Run Julia scripts to do the heavy lifting. I run these sequentially in VSCode but it should be possible to run them from the command line. These call packages EscapeSimulator, and the auxiliary functions defined in file_access.jl that make it easy to simulate using fitted paramters.

bayes_posterior.jl to generate posterior on the fiteness cost function. This is stored in the same file snpanalysis.h5

fit_reservoir.jl to perform the fitting of the reservoir. You should be able to recover ξ = 2.1. Also generates the statistics used in the hypothesis testing

simulate_therapy.jl to simulate the result of viral rebounds in trials

therapy_ranking.jl to compare and rank therapies with arbitrary number of combinations of antibodies.

linkage_simulations.jl to test the inference procedure (calls the Tomoko.jl package which runs longer genomes with symmetric mutation rates)

Tested with Julia 1.61. 3.) Finally we include some (Mathematica-based) plotting functions in the Plotting folder. This includes a file of helper functions PlotFunctions.nb

and a file for figure generation.

PlotGeneration.nb

Please feel free to file an issues if something is confusing or needs explanation.