Change substance concentration patterns in the environment
The generic function changeDiff changes specific substance concentration patterns in the environment.
changeDiff(object, newdiffmat, mediac) ## S4 method for signature 'Arena' changeDiff(object, newdiffmat, mediac)
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). |
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.
Arena-class and changeSub
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 phosphatePlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.