Jonathan Lisic - 1 year ago 79

R Question

I am trying to calculate local quantiles with the raster R package. But am not able to generate sensible results.

This is a minimal example that produces the odd results:

`library(raster)`

set.seed(100)

n <- 5

# create a raster object

r <- raster::raster( matrix(rnorm(n^2),n,n))

# create a weight matrix

W <- matrix(1,nrow=3,ncol=3)

# create a weight matrix

rLocalKDE2 <- raster::focal(r,W,fun=stats::quantile,probs=0.3)

The

`as.matrix`

`> as.matrix(r)`

[,1] [,2] [,3] [,4] [,5]

[1,] 1.449469 19.5963292 -2.4142891 -1.7028303 -8.851035

[2,] 1.049408 -0.6686213 -0.3880794 0.7489177 -1.282491

[3,] -6.028731 2.3172630 1.2115319 2.0829121 -8.260212

[4,] 0.179009 -6.7879331 3.0286532 2.1160440 -1.006479

[5,] 10.087954 0.5925101 -0.9240929 -1.4685703 3.899903

> as.matrix(rLocalKDE2)

[,1] [,2] [,3] [,4] [,5]

[1,] NA NA NA NA NA

[2,] NA -6.028731 -2.414289 -8.851035 NA

[3,] NA -6.787933 -6.787933 -8.260212 NA

[4,] NA -6.787933 -6.787933 -8.260212 NA

[5,] NA NA NA NA NA

This result seems quite odd, given that

`stats::quantile(as.matrix(r)[2:4,2:4],probs=0.3)`

I am running R 3.3.1 from brew on OS X 10.11.6 with raster 2.5-8.

Answer Source

Your formulation of the function is not correct, as the `probs`

argument is defined outside the function and passed on as additional argument to focal and ignored. In effect you got the 0 percentile returned. See below for a corrected version:

```
library(raster)
set.seed(100)
n <- 5
r <- raster::raster( matrix(rnorm(n^2),n,n))
W <- matrix(1,nrow=3,ncol=3)
# create a weight matrix
k <- raster::focal(r, W, fun=function(x) stats::quantile(x,probs=0.3))
as.matrix(k)
[,1] [,2] [,3] [,4] [,5]
[1,] NA NA NA NA NA
[2,] NA -0.1525472 -0.1327071 -0.13270706 NA
[3,] NA -0.1525472 -0.5046161 -0.08247059 NA
[4,] NA -0.1525472 -0.2965709 -0.07162857 NA
[5,] NA NA NA NA NA
>
```