rar - 1 year ago 155
R Question

# Calculating number of three consecutive values above a threshold (in raster stack)

I need to compute number of three consecutive days when value of each pixel in a raster stack (

`x`
) is above a given threshold (defined by another raster
`y`
). I tried using
`rle`
for the purpose with
`calc`
as follows after stacking
`x`
and
`y`
together into new raster
`a`
:

``````library(raster)
fn<-function(a) with(rle(a), sum(lengths>=3 & values>a[[nlayers(a)]]))
calc(b,fn)
``````

However, I am getting the error:

Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) :

cannot use this function

Reproducible sample:

``````x1 <- raster(nrows=10, ncols=10)
x2=x3=x4=x5=x6=x1
x1[]= runif(ncell(x1))
x2[]= runif(ncell(x1))
x3[]= runif(ncell(x1))
x4[]= runif(ncell(x1))
x5[]= runif(ncell(x1))
x6[]= runif(ncell(x1))
x=stack(x1,x2,x3,x4,x5,x6)
y=x1
y[]= runif(ncell(x1))
a<-stack(x,y)
``````

You could try this:

`````` x1 <- raster(nrows=10, ncols=10)
x2=x3=x4=x5=x6=x1
x1[]= runif(ncell(x1))
x2[]= runif(ncell(x1))
x3[]= runif(ncell(x1))
x4[]= runif(ncell(x1))
x5[]= runif(ncell(x1))
x6[]= runif(ncell(x1))
x=stack(x1,x2,x3,x4,x5,x6)*4
y=x1
y[]= runif(ncell(x1))*2
a<-stack(x,y)

library(raster)

fn<-function(x) {
seq <- rle(as.numeric(x)>as.numeric(x)[[nlayers(a)]])
n = length(seq\$lengths > 3 & seq\$values == TRUE)
return(n)
}
calc(a,fn)

class       : RasterLayer
dimensions  : 10, 10, 100  (nrow, ncol, ncell)
resolution  : 36, 18  (x, y)
extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
data source : in memory
names       : layer
values      : 1, 7  (min, max)
``````

(note that I modified the example dataset to get some good sequences)

HTH !

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