Description Usage Arguments Details Value See Also Examples
The generic function simHum
implements all neccessary functions for the individuals to update the complete environment.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 |
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
1 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.