Function for re-constructing a medium concentrations from simulations
The generic function extractMed re-constructs a list of vectors of medium concentrations from a simulation step in an Eval object.
extractMed(object, time = length(object@medlist), mediac = object@mediac) ## S4 method for signature 'Eval' extractMed(object, time = length(object@medlist), mediac = object@mediac)
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). |
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.
Returns a list containing concentration vectors of all medium substances.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.