simEnv: Main function for simulating all processes in the environment

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

Main function for simulating all processes in the environment

Description

The generic function simEnv for a simple simulation of the environment.

Usage

simEnv(
  object,
  time,
  lrw = NULL,
  continue = FALSE,
  reduce = FALSE,
  diffusion = TRUE,
  diff_par = FALSE,
  cl_size = 2,
  sec_obj = "none",
  cutoff = 1e-06,
  pcut = 1e-06,
  with_shadow = TRUE,
  verbose = TRUE
)

## S4 method for signature 'Arena'
simEnv(
  object,
  time,
  lrw = NULL,
  continue = FALSE,
  reduce = FALSE,
  diffusion = TRUE,
  diff_par = FALSE,
  cl_size = 2,
  sec_obj = "none",
  cutoff = 1e-06,
  pcut = 1e-06,
  with_shadow = TRUE,
  verbose = TRUE
)

Arguments

object	An object of class Arena or Eval.
time	A number giving the number of iterations to perform for the simulation
lrw	A numeric value needed by solver to estimate array size (by default lwr is estimated in the simEnv() by the function estimate_lrw())
continue	A boolean indicating whether the simulation should be continued or restarted.
reduce	A boolean indicating if the resulting Eval object should be reduced
diffusion	True if diffusion should be done (default on).
diff_par	True if diffusion should be run in parallel (default off).
cl_size	If diff_par is true then cl_size defines the number of cores to be used in parallelized diffusion.
sec_obj	character giving the secondary objective for a bi-level LP if wanted. Use "mtf" for minimizing total flux, "opt_rxn" for optimizing a random reaction, "opt_ex" for optimizing a random exchange reaction, and "sumex" for optimizing the sum of all exchange fluxes.
cutoff	value used to define numeric accuracy
pcut	A number giving the cutoff value by which value of objective function is considered greater than 0.
with_shadow	True if shadow cost should be stored.
verbose	Set to false if no status messages should be printed.

Details

The returned object itself can be used for a subsequent simulation, due to the inheritance between Eval and Arena. The parameter for sec_obj can be used to optimize a bi-level LP with a secondary objective if wanted. This can be helpful to subselect the solution space and create less alternative optimal solution. The secondary objective can be set to "mtf" to minimize the total flux, to simulate minimal enzyme usage of an organisms. If set to "opt_rxn" or "opt_ex", the secondary objective is picked as a random reaction or exchange reaction respectively everytime a fba is performed. This means that every individual of a population will select a different secondary reaction to optimize. The "sumex" option maximizes the secretion of products.

Value

Returns an object of class Eval which can be used for subsequent analysis steps.

See Also

Arena-class and Eval-class

Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05,
           minweight=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
arena <- addOrg(arena,bac,amount=10) #add 10 organisms
arena <- addSubs(arena,40) #add all possible substances
eval <- simEnv(arena,5)

euba/BacArena documentation built on Aug. 29, 2024, 11:15 p.m.