changeDiff: Change substance concentration patterns in the environment

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

Change substance concentration patterns in the environment

Description

The generic function changeDiff changes specific substance concentration patterns in the environment.

Usage

changeDiff(object, newdiffmat, mediac)

## S4 method for signature 'Arena'
changeDiff(object, newdiffmat, mediac)

Arguments

object	An object of class Arena.
newdiffmat	A matrix giving the new gradient matrix of the specific substances in the environment.
mediac	A character vector giving the names of substances, which should be added to the environment (the default takes all possible substances).

Details

This function can be used to add gradients of specific substances in the environment. The default conditions in changeSubs assumes an equal concentration in every grid cell of the environment.

See Also

Arena-class and changeSub

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,30) #add all substances with no concentrations.
gradient <- matrix(1:200,20,20)
arena <- changeDiff(arena,gradient,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.