BacArena (version 1.0.1)

addSubs: Add substances to the environment

Description

The generic function addSubs adds specific substances to the environment.

Usage

addSubs(object, smax = 0, mediac = object@mediac, difunc = "pde", difspeed = 6.7e-06, unit = "mmol/cell", add = T)
"addSubs"(object, smax = 0, mediac = object@mediac, difunc = "pde", difspeed = 6.7e-06, unit = "mmol/cell", add = T)

Arguments

object

An object of class Arena.

smax

A numeric vector 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).

difunc

A character vector ("pde","cpp" or "r") describing the function for diffusion.

difspeed

A number indicating the diffusion speed (given by number of cells per iteration).

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)

add

A boolean variable defining whether the amount of substance should be summed or replaced

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 changeSub

Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05,
           growthlimit=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
addOrg(arena,bac,amount=10) #add 10 organisms
addSubs(arena,20,c("EX_glc(e)","EX_o2(e)","EX_pi(e)")) #add substances glucose, oxygen and phosphate