simBac {BacArena} R Documentation

Function for one simulation iteration for objects of Bac class

Description

The generic function simBac implements all neccessary functions for the individuals to update the complete environment.

Usage

simBac(
object,
arena,
j,
sublb,
bacnum,
sec_obj = "none",
cutoff = 1e-06,
pcut = 1e-06,
)

## S4 method for signature 'Bac'
simBac(
object,
arena,
j,
sublb,
bacnum,
sec_obj = "none",
cutoff = 1e-06,
pcut = 1e-06,
)


Arguments

 object An object of class Bac. arena An object of class Arena defining the environment. j The index of the organism of interest in orgdat. sublb A vector containing the substance concentrations in the current position of the individual of interest. bacnum integer indicating the number of bacteria individuals per gridcell sec_obj character giving the secondary objective for a bi-level LP if wanted. 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 stores (default off).

Details

Bacterial individuals undergo step by step the following procedures: First the individuals are constrained with constrain to the substrate environment, then flux balance analysis is computed with optimizeLP, after this the substrate concentrations are updated with consume, then the bacterial growth is implemented with growth, the potential new phenotypes are added with checkPhen, finally the additional and conditional functions lysis, move or chemotaxis are performed. In case of many compounds in the vector of chemotaxis, the change of the position takes place by the order of the compounds in the vector of chemotaxis. Can be used as a wrapper for all important bacterial functions in a function similar to simEnv.

Value

Returns the updated enivironment of the population parameter with all new positions of individuals on the grid and all new substrate concentrations.

Bac-class, Arena-class, simEnv, constrain, optimizeLP, consume, growth, checkPhen, lysis, move and chemotaxis
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