patches: Detect patches (clumps) of cells

In terra: Spatial Data Analysis

Detect patches (clumps) of cells

Description

Detect patches (clumps). Patches are groups of cells that are surrounded by cells that are NA. Set zeroAsNA to TRUE to also identify patches separated by cells with values of zero.

Usage

## S4 method for signature 'SpatRaster'
patches(x, directions=4, zeroAsNA=FALSE, allowGaps=TRUE, filename="", ...)

Arguments

x	SpatRaster
directions	integer indicating which cells are considered adjacent. Should be 8 (Queen's case) or 4 (Rook's case)
zeroAsNA	logical. If TRUE treat cells that are zero as if they were NA
allowGaps	logical. If TRUE there may be gaps in the patch IDs (e.g. you may have patch IDs 1, 2, 3 and 5, but not 4). If it is FALSE, these numbers will be recoded from 1 to the number of patches (4 in this example)
filename	character. Output filename
...	options for writing files as in writeRaster

Value

SpatRaster. Cell values are patch numbers

See Also

focal, boundaries

Examples

r <- rast(nrows=18, ncols=36, xmin=0)
r[1:2, 5:8] <- 1
r[5:8, 2:6] <- 1
r[7:12, 22:36] <- 1
r[15:16, 18:29] <- 1
p <- patches(r)

# zero as background instead of NA
r <- rast(nrows=10, ncols=10, xmin=0, vals=0)
r[3, 3] <- 10
r[4, 4] <- 10
r[5, 5:8] <- 12
r[6, 6:9] <- 12

# treat zeros as NA

p4 <- patches(r, zeroAsNA=TRUE)
p8 <- patches(r, 8, zeroAsNA=TRUE)

### patches for different values
# remove zeros manually
rr <- classify(r, cbind(0, NA))

# make layers for each value
s <- segregate(rr, keep=TRUE, other=NA)
p <- patches(s)


### patch ID values are not guaranteed to be consecutive
r <- rast(nrows=5, ncols=10, xmin=0)
set.seed(0)
values(r)<- round(runif(ncell(r))*0.7)
rp <- patches(r, directions=8, zeroAsNA=TRUE) 
plot(rp, type="classes"); text(rp)

## unless you set allowGaps=FALSE
rp <- patches(r, directions=8, zeroAsNA=TRUE, allowGaps=FALSE) 
plot(rp, type="classes"); text(rp)

### use zonal to remove small patches 
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
x <- classify(r, cbind(-Inf, 400, NA))
y <- patches(x)
# remove patches smaller than 100 ha
rz <- zonal(cellSize(y, unit="ha"), y, sum, as.raster=TRUE)
s <- ifel(rz < 250, NA, y)

terra documentation built on Oct. 14, 2024, 5:07 p.m.