continue_driver_process_sim: Restarts a multiple driver scenario

In NickWilliamsSanger/rsimpop: Simulates Cellular Evolution using a Continous Time Birth Death Model

Restarts a multiple driver scenario

Description

The user specifies the rate at which drivers are introduced and the distribution the selective coefficients are drawn from. Note that unlike in run_selection_sim the drivers are allowed to stochastically die out. The drivers at the specified rate with the gap between successive introductions exponentially distributed.

Usage

continue_driver_process_sim(insim, nyears, fitnessGen)

Arguments

insim	Result of previous sim
nyears	Total number of years to run the simulation
final_division_rate	Rate of symmetric cell division once population equilibrium is reached.
target_pop_size	Size of target population
drivers_per_year	The expected number of drivers per year
bForceReseed	Whether to reseed.
offset	time offset for choosing seed.

Value

simpop object.

Examples

fitnessGen=function(){
 trials=rexp(100,rate=30)
 idx=which(trials>0.05)
 if(length(idx)==0){
  fitnessGen()
 }else{
  trials[idx[1]]
 }
}
dps=run_driver_process_sim(0.1,1/(2*190),target_pop_size = 1e5,nyears = 30,fitness=fitnessGen,drivers_per_year = 5)
## Do stuff - subsample, plot trees etc and the restart to simulate the next 10 years:
dps2=continue_driver_process_sim(dps,40,fitnessGen = fitnessGen)
## Do stuff and simulation the next 10 years
dps2=continue_driver_process_sim(dps2,50,fitnessGen = fitnessGen)

NickWilliamsSanger/rsimpop documentation built on Sept. 6, 2024, 12:42 a.m.