I'm having a very hard time to calculate the probability of a point being in a particular area in a kernel density estimation. This will be used to show the probabilty of an animal moving around in a specific area.
Here is my sample data:
set.seed(123)
x <- runif(100,0,100)
y <- runif(100,0,100)
n <- 11
lims <- c(range(0,100), range(0,100))
f1 <- MASS::kde2d(x = x,y = y ,n = n, lims = lims)
Where f1$z holds the density estimations in a matrix. The corresponding plot is shown below:
library('plot.matrix')
plot(f1$z)
Now, my goal is to find for example the probability of a point being in the cell surrounded in blue.
I wonder, if this can be achieved be simply calculating:
library(raster)
raster <- raster(f1)
df <- as.data.frame(raster,xy=T)
df$layer / sum(df$layer)
But I assume the solution must be to integrate somehow like described in here.
Thank you!
The point surrounded in blue is the point f1$z[3, 2]
. Multiply this value by the cell size as computed in the code you link to and have
xlim <- range(f1$x)
ylim <- range(f1$y)
cell_size <- (diff(xlim) / n) * (diff(ylim) / n)
f1$z[3, 2] * cell_size
#[1] 0.003765805
To see that this will compute the probability over that cell, compute the density over all cells f1$z
. It must be equal to 1.
norm <- sum(f1$z) * cell_size # normalizing constant
sum(f1$z)*cell_size/norm
#[1] 1