Description Usage Arguments Details See Also Examples
The generic function changeSub
changes specific substances in the environment.
1 2 3 4 |
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
1 2 3 4 5 6 7 8 | 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 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"
Loading required package: glpkAPI
using GLPK version 4.65
Warning messages:
1: In changeSub(arena, 20, c("EX_glc(e)", "EX_o2(e)", "EX_pi(e)")) :
DEPRECATED: Please use addSubs()
2: In `[<-`(`*tmp*`, mediac[i], value = Substance(object@n, object@m, :
implicit list embedding of S4 objects is deprecated
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