experiment.run: Run an experiment, handling the eventual discrete events

In qBioTurin/epimod: Epidemiological modelling (epimod)

Run an experiment, handling the eventual discrete events

Description

This is an internal function generating the command line to run the solver with the appropriate configuration

Usage

experiment.run(
  id,
  cmd,
  i_time,
  f_time,
  s_time,
  atol,
  rtol,
  n_run = 1,
  seed,
  event_times = NULL,
  event_function = NULL,
  out_fname,
  FVA = F
)

Arguments

id	a numeric identifier used to format the output's file name
f_time	simulation's final time
s_time	step time at which the sover is forced to output the current configuration of the model (i.e. the number of tocken in each place)
atol	Absolute error tolerance that determine the error control performed by the LSODA solver.
rtol	Relative error tolerance that determine the error control performed by the LSODA solver.
n_run	when performing stochastic simulations this parameters controls the number of runs per each set of input parameters
event_times	controls the time at which the simulation is stopped to update the marking
event_function	specifies the rule to update the marking
out_fname	output filename prefix
FVA	Flag to enable the flux variability analysis
solver_fname	the name of the solver executable file
solver_type	a string definig what solver to apply (LSODA, HLSODA, ..)
taueps	controls the step of the approximation introduced by the tau-leap algorithm
timeout	string controlling the available time to run n_run simulations. See TIMEOUT(1) to check the syntax

Value

the name of the trace file

Author(s)

Paolo Castagno, Simone Pernice

Examples

## Not run: 
experiment.cmd(id=1, solver_fname="Solver.solver", s_time=365, f_time=730, timeout="1d", out_fname="simulation")


## End(Not run)

qBioTurin/epimod documentation built on July 4, 2025, 1:28 p.m.