changeDiff: Change substance concentration patterns in the environment

Description Usage Arguments Details See Also Examples

Description

The generic function changeDiff changes specific substance concentration patterns in the environment.

Usage

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changeDiff(object, newdiffmat, mediac)

## S4 method for signature 'Arena'
changeDiff(object, newdiffmat, mediac)

Arguments

object

An object of class Arena.

newdiffmat

A matrix giving the new gradient matrix of the specific substances in the environment.

mediac

A character vector giving the names of substances, which should be added to the environment (the default takes all possible substances).

Details

This function can be used to add gradients of specific substances in the environment. The default conditions in changeSubs assumes an equal concentration in every grid cell of the environment.

See Also

Arena-class and changeSub

Examples

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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,30) #add all substances with no concentrations.
gradient <- matrix(1:200,20,20)
arena <- changeDiff(arena,gradient,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

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