Description Usage Arguments Details Value See Also Examples

This is the base function for the simulation of deterministic and stochastic cellular automata on rectangular grids.

1 2 |

`x` |
Matrix. The cellular grid, in which each cell can have a specific state value, e.g. zero (dead cell) or one (living cell) or the age of an individual. |

`state` |
A value, whose existence is checked within the neighbourhood of each cell. |

`wdist` |
The neighbourhood weight matrix. It has to be a square matrix with an odd number of rows and columns). |

`tol` |
Tolerance value for the comparision of |

`bounds` |
A vector with either one or four values specifying the type of boundaries, where 0 means open boundaries and 1 torus-like boundaries. The values are specified in the order bottom, left, top, right. |

The performance of the function depends on the size of the matrices and the
type of the boundaries, where open boundaries are faster than torus like
boundaries. Function `eightneighbours`

is even faster.

A matrix with the same structure as `x`

with the weighted
sum of the neigbours with values between `state - tol`

and
`state + tol`

.

`seedfill`

, `eightneighbours`

, `conway`

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## ==================================================================
## Demonstration of the neighborhood function alone
## ==================================================================
## weight matrix for neighbourhood determination
wdist <- matrix(c(0.5,0.5,0.5,0.5,0.5,
0.5,1.0,1.0,1.0,0.5,
0.5,1.0,1.0,1.0,0.5,
0.5,1.0,1.0,1.0,0.5,
0.5,0.5,0.5,0.5,0.5), nrow=5)
## state matrix
n <- 20; m <- 20
x <- matrix(rep(0, m * n), nrow = n)
## set state of some cells to 1
x[10, 10] <- 1
x[1, 5] <- 1
x[n, 15] <- 1
x[5, 2] <- 1
x[15, m] <- 1
#x[n, 1] <- 1 # corner
opar <- par(mfrow = c(2, 2))
## start population
image(x)
## open boundaries
image(matrix(neighbours(x, wdist = wdist, bounds = 0), nrow = n))
## torus (donut like)
image(matrix(neighbours(x, wdist = wdist, bounds = 1), nrow = n))
## cylinder (left and right boundaries connected)
image(matrix(neighbours(x, wdist = wdist, bounds = c(0, 1, 0, 1)), nrow = n))
par(opar) # reset graphics area
## ==================================================================
## The following example demonstrates a "plain implementation" of a
## stochastic cellular automaton i.e. without the simecol structure.
##
## A simecol implementation of this can be found in
## the example directory of this package (file: stoch_ca.R).
## ==================================================================
mycolors <- function(n) {
col <- c("wheat", "darkgreen")
if (n>2) col <- c(col, heat.colors(n - 2))
col
}
pj <- 0.99 # survival probability of juveniles
pa <- 0.99 # survival probability of adults
ps <- 0.1 # survival probability of senescent
ci <- 1.0 # "seeding constant"
adult <- 5 # age of adolescence
old <- 10 # age of senescence
## Define a start population
n <- 80
m <- 80
x <- rep(0, m*n)
## stochastic seed
## x[round(runif(20,1,m*n))] <- adult
dim(x)<- c(n, m)
## rectangangular seed in the middle
x[38:42, 38:42] <- 5
## plot the start population
image(x, col = mycolors(2))
## -----------------------------------------------------------------------------
## Simulation loop (hint: increase loop count)
## -----------------------------------------------------------------------------
for (i in 1:10){
## rule 1: reproduction
## 1.1 which cells are adult? (only adults can generate)
ad <- ifelse(x >= adult & x < old, x, 0)
## 1.2 how much (weighted) adult neighbours has each cell?
nb <- neighbours(ad, wdist = wdist)
## 1.3 a proportion of the seeds develops juveniles
## simplified version, you can also use probabilities
genprob <- nb * runif(nb) * ci
xgen <- ifelse(x == 0 & genprob >= 1, 1, 0)
## rule 2: growth and survival of juveniles
xsurvj <- ifelse(x >= 1 & x < adult & runif(x) <= pj, x+1, 0)
## rule 2: growth and survival of adults
xsurva <- ifelse(x >= adult & x < old & runif(x) <= pa, x+1, 0)
## rule 2: growth and survival of senescent
xsurvs <- ifelse(x >= old & runif(x) <= ps, x+1, 0)
## make resulting grid of complete population
x <- xgen + xsurvj + xsurva + xsurvs
## plot resulting grid
image(x, col = mycolors(max(x) + 1), add = TRUE)
if (max(x) == 0) stop("extinction", call. = FALSE)
}
## modifications: pa<-pj<-0.9
## additional statistics of population structure
## with table, hist, mean, sd, ...
``` |

simecol documentation built on June 3, 2018, 5:07 p.m.

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