simulate_evolution: Simulate evolution of mixture by reassortment and/or mutation

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

Description

Simulate evolution of mixture by reassortment and/or mutation

Usage

simulate_evolution(iv, fitness, burst_size, n_cells, pop_size, generations,
  mutation_prob, coinfection, MOI_dependent_burst_size,
  choose_strain_by_fitness, one_strain_produced, reassort)

Arguments

iv	numeric vector of length n_strains = 4. Initial proportions of [mt, mt], [mt, wt], [wt, mt], [wt, wt].
fitness	numeric vector of length n_strains = 4. Relative fitness of the four strains.
burst_size	numeric vector of length 1. Burst size from a cell infected with one virion with fitness 1.
n_cells	numeric vector of length 1. Number of cells.
pop_size	numeric vector of length 1. Number of virions.
generations	numeric vector of length 1. Number of generations for which to run model.
mutation_prob	probability of mutation for each new virion. Assume same for pb1 and pa.
coinfection	logical. If TRUE, cells can be infected by more than one virion. If FALSE, each cell can only be infected by one virion.
MOI_dependent_burst_size	logical. If TRUE, for a cell infected with a single strain, the burst size scales with the MOI for that cell. If FALSE, the burst size is independent of the MOI.
choose_strain_by_fitness	logical. If TRUE, strain(s) producing virions in cell is/are chosen proportional to fitness and abundance, otherwise proportional to abundance only
one_strain_produced	logical. If TRUE, each cell can only produce progeny from one of its co-infecting strains. If FALSE, each cell can produce progeny for all of its coinfecting strains.
reassort	logical. If TRUE, random reassortment of segments occurs before packaging. If FALSE, each strain in the cell effectively produces pre-packaged viruses

Value

matrix of dim c(generations, n_strains). Proportion of virions of each strain for each generation.

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