simHum | R Documentation |
The generic function simHum
implements all neccessary functions for the individuals to update the complete environment.
simHum(
object,
arena,
j,
sublb,
bacnum,
sec_obj = "none",
cutoff = 1e-06,
pcut = 1e-06,
with_shadow = FALSE
)
## S4 method for signature 'Human'
simHum(
object,
arena,
j,
sublb,
bacnum,
sec_obj = "none",
cutoff = 1e-06,
pcut = 1e-06,
with_shadow = FALSE
)
object |
An object of class Human. |
arena |
An object of class Arena defining the environment. |
j |
The number of the iteration of interest. |
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). |
Human cell individuals undergo the 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 cell growth is implemented with cellgrowth
, the potential new phenotypes are added with checkPhen
, finally the conditional function lysis
is performed. Can be used as a wrapper for all important cell functions in a function similar to simEnv
.
Returns the updated enivironment of the arena
parameter with all new positions of individuals on the grid and all new substrate concentrations.
Human-class
, Arena-class
, simEnv
, constrain
, optimizeLP
, consume
, cellgrowth
, checkPhen
and lysis
NULL
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