Description Usage Arguments Details See Also Examples
The generic function changeDiff
changes specific substance concentration patterns in the environment.
1 2 3 4 | 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
1 2 3 4 5 6 7 8 9 | 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
|
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ReacTran
Loading required package: rootSolve
Loading required package: deSolve
Loading required package: shape
BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
Tutorials: https://bacarena.github.io
Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
Development and help: https://github.com/euba/bacarena
[1] "Median lower bound for non-zero and non-Inf exchanges is:-106"
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