changeSub: Change substances in the environment

In BacArena: Modeling Framework for Cellular Communities in their Environments

Description

The generic function changeSub changes specific substances in the environment.

Usage

changeSub(object, smax, mediac, unit = "mmol/cell")

## S4 method for signature 'Arena'
changeSub(object, smax, mediac, unit = "mmol/cell")

Arguments

object	An object of class Arena.
smax	A number or vector of numbers indicating the maximum substance concentration per grid cell.
mediac	A character vector giving the names of substances, which should be added to the environment (the default takes all possible substances).
unit	A character used as chemical unit to set the amount of the substances to be added (valid values are: mmol/cell, mmol/cm2, mmol/arena, mM)

Details

If nothing but object is given, then all possible substrates are initilized with a concentration of 0. Afterwards, changeSub can be used to modify the concentrations of specific substances.

See Also

Arena-class and addSubs

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) #add all substances with no concentrations.
arena <- changeSub(arena,20,c("EX_glc(e)","EX_o2(e)","EX_pi(e)")) 
#add substances glucose, oxygen and phosphate

Example output

Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ReacTran
Loading required package: rootSolve
Loading required package: deSolve
Loading required package: shape
BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
 Tutorials: https://bacarena.github.io
 Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
 Development and help: https://github.com/euba/bacarena
[1] "Median lower bound for non-zero and non-Inf exchanges is:-106"
Loading required package: glpkAPI
using GLPK version 4.65
Warning messages:
1: In changeSub(arena, 20, c("EX_glc(e)", "EX_o2(e)", "EX_pi(e)")) :
  DEPRECATED: Please use addSubs()
2: In `[<-`(`*tmp*`, mediac[i], value = Substance(object@n, object@m,  :
  implicit list embedding of S4 objects is deprecated

BacArena documentation built on July 2, 2020, 3:16 a.m.