changeSub: Change substances in the environment

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

Change substances in the environment

Description

The generic function changeSub changes specific substances in the environment.

Usage

changeSub(object, smax, mediac, unit = "mmol/cell")

## S4 method for signature 'Arena'
changeSub(object, smax, mediac, unit = "mmol/cell")

Arguments

object	An object of class Arena.
smax	A number or vector of numbers indicating the maximum substance concentration per grid cell.
mediac	A character vector giving the names of substances, which should be added to the environment (the default takes all possible substances).
unit	A character used as chemical unit to set the amount of the substances to be added (valid values are: mmol/cell, mmol/cm2, mmol/arena, mM)

Details

If nothing but object is given, then all possible substrates are initilized with a concentration of 0. Afterwards, changeSub can be used to modify the concentrations of specific substances.

See Also

Arena-class and addSubs

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) #add all substances with no concentrations.
arena <- changeSub(arena,20,c("EX_glc(e)","EX_o2(e)","EX_pi(e)")) 
#add substances glucose, oxygen and phosphate

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.