extractMed: Function for re-constructing a medium concentrations from...

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

Function for re-constructing a medium concentrations from simulations

Description

The generic function extractMed re-constructs a list of vectors of medium concentrations from a simulation step in an Eval object.

Usage

extractMed(object, time = length(object@medlist), mediac = object@mediac)

## S4 method for signature 'Eval'
extractMed(object, time = length(object@medlist), mediac = object@mediac)

Arguments

object	An object of class Eval.
time	A number giving the simulation step of interest.
mediac	A character vector giving the names of substances, which should be added to the environment (the default takes all possible substances).

Details

Medium concentrations in slot medlist of an object of class Eval store only the changes of concentrations in the simulation process. The function extractMed reconstructs the original and uncompressed version of medium concentrations.

Value

Returns a list containing concentration vectors of all medium substances.

See Also

Eval-class and Arena-class

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)
med5 <- extractMed(eval,5)

euba/BacArena documentation built on Aug. 29, 2024, 11:15 p.m.