addOrg {BacArena}R Documentation

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

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)


[Package BacArena version 1.8.2 Index]