Function for selecting phenotypes which occured on the arena from specific iterations and species
The generic function selPheno selects phenotypes from specific simulation step in an Eval object.
selPheno(object, time, type, reduce = F) ## S4 method for signature 'Eval' selPheno(object, time, type, reduce = F)
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.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.