library(raster)
set.seed(17)                   # Seed a reproducible random sequence
nr <- 30                       # Number of rows
nc <- 50                       # Number of columns
#
# Create a zone raster for normalizing the probabilities.
#
zone <- raster(ncol=nc, nrow=nr)
zone[] <- 0
#
# Create a probability raster (for illustrating the algorithm later).
#
p <- raster(ncol=nc, nrow=nr)
p[] <- (1:(nc*nr) - 1/2) / (nc*nr) + rnorm(nc*nr, sd=0.5)
p <- abs(focal(p, ngb=5, run=mean))
z <- zonal(p, zone, stat='sum')
p <- p / z[[2]] # This normalizes p to sum to unity as required
#------------------------------------------------------------------------------#
#
# The algorithm begins here.
#
pvec <- sort(getValues(p), decreasing=TRUE) # The probabilities, sorted
d <- cumsum(pvec)                           # Cumulative probabilities
dpos <- d[d <= 0.95]                        # Position to stop
region <- p                                 # Initialize the output
region[p < pvec[length(dpos)]] <- NA        # Exclude the last 5% of the probability
plot(region)                                # Display the result