scripts/timing.R

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

run_timing <- function() {
  set.seed(2)
  iv <- c(95,0,0,5) #mt,mt  mt,wt  wt,mt   wt,wt
  fitness <- c(1,0,1.1,1)
  n_cells <- 1e4
  pop_size <- 1000
  mutation_prob <- .09#2e-5 #Russell et al. (2012)
  burst_size <- 10
  generations <- 20
  
  sim_wrapper <- function(iv, fitness, burst_size, n_cells, pop_size,
                          generations) {
    function(mutation_prob,
             coinfection,
             MOI_dependent_burst_size,
             choose_strain_by_fitness,
             one_strain_produced,
             reassort, filename)  {
      results <- 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)
      invisible(results)
    }
  }
  
  sim_fn <- sim_wrapper(iv, fitness, burst_size, n_cells, pop_size,
                        generations)
  
  sim_fn(mutation_prob = 0,
         coinfection = TRUE,
         MOI_dependent_burst_size = TRUE,
         choose_strain_by_fitness = FALSE,
         one_strain_produced = FALSE,
         reassort = TRUE,
         filename = "results_mutate_MOI_dependent")
}