Change substances in the environment
The generic function changeSub changes specific substances in the environment.
changeSub(object, smax, mediac, unit = "mmol/cell") ## S4 method for signature 'Arena' changeSub(object, smax, mediac, unit = "mmol/cell")
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) |
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.
Arena-class and addSubs
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 phosphatePlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.