BacArena (version 1.8.2)

simEnv: 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 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.

Value

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

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.

See Also

Arena-class and Eval-class

Examples

# NOT RUN {
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)
# }