Jenks classification for raster representation

Arnaud,

You can (directly) do the same with Raster* objects what Roger did with sp
objects:

library(raster)
t<-raster(ncol = 10, nrow = 10)
t[1:2,] <- seq(1,10,1)
t[3:5,1:5] <- seq(1,5,1)
t[6:8,6:10] <- ?seq(6,10,1)
t[9:10,] <- seq(1,10,1)
plot(t)

library(classInt)
zClass <- classIntervals(values(t), n=5,style="jenks")

# image
image(t, breaks=zClass$brks, col=colorRampPalette(c("red", "yellow"))(5) )

# or spplot
spplot(t, "values", at=zClass$brks, col.regions=colorRampPalette(c("red",
"yellow"))(5))

# or plot, after an adjustment to zClass that won't be needed in the future
(versions > 1.9-13)
zClass$brks[1] <- zClass$brks[1] - 1
plot(t, breaks=zClass$brks, col=colorRampPalette(c("red", "yellow"))(5) )


# The ?only additional consideration is that classIntervals will fail, or be
very slow, for very large rasters.
# To avoid that, you can take a sample:

zClass <- classIntervals(na.omit(sampleRegular(t, 100000)),
n=5,style="jenks")
zClass$brks[1] <- zClass$brks[1] - 1

plot(t, breaks=zClass$brks, col=colorRampPalette(c("red", "yellow"))(5))


Robert


On Fri, Sep 16, 2011 at 12:58 PM, Arnaud Mosnier <a.mosnier at gmail.com>wrote:

Dear list,

In order to allow others benefiting from my errors, see below a
presentation
of a problem and it's solution by Roger Bivand (Thanks !).

######################################

I want to use natural breaks (jenks) method to find class intervals into
raster's values in order to plot it with an adapted color range.
I know that the package "classInt" allows to do exactly what I want but I
do
not achieve to use it correctly.

Here is a small script that represent my case

# here a raster with some NAs

library(raster)
t<-raster(ncol = 10, nrow = 10)
t[1:2,] <- seq(1,10,1)
t[3:5,1:5] <- seq(1,5,1)
t[6:8,6:10] <- ?seq(6,10,1)
t[9:10,] <- seq(1,10,1)
plot(t)

# Then I tried to use classIntervals and findColours function

library(classInt)
zClass <- classIntervals(as.data.frame(t)[!is.na(as.data.frame(t))], n=5,
style="jenks") ?# I have to remove NAs
plot(t, col = findColours(zClass, pal = c("red", "yellow"))) # I do not
understand the result both in the plot and in the legend !

I would be pleased if you can give me tips about this.

########################################

I do not think that the plot method for RasterLayer objects lets you pass a
vector of breaks, nor does the image.plot from fields that maybe is the
source of the legend. If you do things simply, it works:

tSG <- as(t, "SpatialGridDataFrame")
spplot(tSG, "values", at=zClass$brks,
?col.regions=colorRampPalette(
c("red", "yellow"))(5))

or

image(tSG, "values", breaks=zClass$brks,
?col=colorRampPalette(c("red", "yellow"))(5))

or using graphics::image

image(as.image.SpatialGridDataFrame(tSG), breaks=zClass$brks,
?col=colorRampPalette(c("red", "yellow"))(5))

I'm a bit unsure about whether the itervals are closed which way.

It's up to the raster developers to answer.

Roger

--
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no

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