addOrg {BacArena} | R Documentation |
The generic function addOrg
adds individuals to the environment.
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 )
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) |
The arguments x
and y
should be in the same length as the number of organisms added (given by the argument amount
).
Arena-class
and Bac-class
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)