run_default_pars: Simulate evolution of mixture by reassortment and/or...

In ada-w-yan/reassortment: Modelling Evolution of Strain Mixtures Including Reassortment

Description

Simulate evolution of mixture by reassortment and/or mutation, for many replicates

Usage

run_default_pars(MOI = 1, iv = c(95, 0, 0, 5), fitness_MW = 0,
  fitness_WM = 1.25, fitness_MM = 1, mutation_prob = 2e-04,
  reassort = TRUE, pop_size = 1e+06, burst_size = 10,
  MOI_dependent_burst_size = TRUE, choose_strain_by_fitness = FALSE,
  sim_name, hash)

Arguments

MOI	multiplicity of infection = number of virions/number of cells
iv	numeric vector of length n_strains = 4. Initial proportions of [mt, mt], [mt, wt], [wt, mt], [wt, wt].
fitness_MW	fitness of the PB1 mutant
fitness_WM	fitness of the PA mutant
fitness_MM	fitness of the double mutant
mutation_prob	probability of mutation for each new virion. Assume same for pb1 and pa.
reassort	logical. If TRUE, random reassortment of segments occurs before packaging. If FALSE, each strain in the cell effectively produces pre-packaged viruses
pop_size	numeric vector of length 1. Number of virions.
burst_size	numeric vector of length 1. Burst size from a cell infected with one virion with fitness 1.
sim_name	character vector for naming of output file
hash	character vector: git hash for tagging run

Value

matrix of dim c(generations * n_replicates, n_strains + 1). Concatenated simulation results for n_replicates simulations with the above model parameters.

ada-w-yan/reassortment documentation built on April 10, 2021, 12:03 a.m.