Description Usage Arguments Details Value See Also Examples
The generic function selPheno
selects phenotypes from specific simulation step in an Eval
object.
1 2 3 4 |
object |
An object of class Eval. |
time |
A numeric vector giving the simulation steps which should be plotted. |
type |
A names indicating the species of interest in the arena. |
reduce |
A boolean variable indicating if the resulting matrix should be reduced. |
The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.
Returns a matrix with the substrate usage and the number of individuals using the phenotype.
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,40) #add all possible substances
eval <- simEnv(arena,5)
selPheno(eval,time=5,type='ecoli_core_model',reduce=TRUE)
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