addOrg: Add individuals to the environment

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

Add individuals to the environment

Description

The generic function addOrg adds individuals to the environment.

Usage

addOrg(
  object,
  specI,
  amount = 1,
  x = NULL,
  y = NULL,
  posmat = NULL,
  biomass = NA,
  n0 = NULL,
  n = NULL,
  m0 = NULL,
  m = NULL
)

## S4 method for signature 'Arena'
addOrg(
  object,
  specI,
  amount = 1,
  x = NULL,
  y = NULL,
  posmat = NULL,
  biomass = NA,
  n0 = NULL,
  n = NULL,
  m0 = NULL,
  m = NULL
)

Arguments

object	An object of class Arena.
specI	An object of class Organism.
amount	A numeric number giving the number of individuals to add.
x	A numeric vector giving the x positions of individuals on the grid.
y	A numeric vector giving the y positions of individuals on the grid.
posmat	A As an alternative to parameter x, y, a matrix with corrdinates an be specified (matrix entries with a '1' indicate an organism to be added)
biomass	A numeric vector giving the starting biomass of the individuals. (unit: fg)
n0	Start column of matrix to take free positions from (default 1)
n	End column of matrix to take free positions from (default arena@m)
m0	Start row of matrix to take free positions from (default 1)
m	End row of matrix to take free positions from (default arena@n)

Details

The arguments x and y should be in the same length as the number of organisms added (given by the argument amount).

See Also

Arena-class and Bac-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

# Alternative way: adding organisms by giving matrix with positions
arena <- Arena(n=20,m=20)
mat <- matrix(sample(c(0,1), 400, replace = TRUE), nrow = 20, ncol = 20)
bac <- Bac(Ec_core)
arena <- addOrg(arena, specI=bac, posmat = mat)

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