selPheno: Function for selecting phenotypes which occured on the arena...

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

Function for selecting phenotypes which occured on the arena from specific iterations and species

Description

The generic function selPheno selects phenotypes from specific simulation step in an Eval object.

Usage

selPheno(object, time, type, reduce = F)

## S4 method for signature 'Eval'
selPheno(object, time, type, reduce = F)

Arguments

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.

Details

The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.

Value

Returns a matrix with the substrate usage and the number of individuals using the phenotype.

See Also

Eval-class and getPhenoMat

Examples

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)

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.