run_simulation_cpp: Interface to the entire C++ driftSim simulation

In jameshay218/driftSim: Short-sighted evolution of influenza cellular receptor binding avidity shapes influenza epidemic dynamics

Description

Interface to the entire C++ driftSim simulation

Usage

run_simulation_cpp(flags, hostPopn, virusPars, deltaVMat, iniKs, day,
  final_day, input_files, output_files, VERBOSE, scenario, callback)

Arguments

flags	set of boolean flags for simulation output. See run_simulation
hostPopn	vector of parameters related to the host population. See run_simulation
virusPars	vector of parameters related to the influenza virions. See run_simulation
deltaVMat	matrix of gradients for use in simulating adaptive binding avidity.
iniKs	data frame of initial K values
day	integer of simulation starting day
final_day	integer of simulation final day (steps of 1 day)
input_files	vector of input file names, as in run_simulation
output_files	vector of output file names, as in run_simulation
VERBOSE	boolean to indicate how much console output the simulation should have
scenario	integer 1 to 4, indicating which version of the model is being run. See scenario_descriptions for a description of each scenario
callback	pointer to enable call backs to R. Pretty much just for progress bar in the shiny app

Value

the final virus ID from the simulation

jameshay218/driftSim documentation built on Jan. 24, 2020, 6:14 p.m.