[R-sig-Geo] Reclassification of raster

[Ben Tupper]

Hi John,

I'm happy to help, but I have copied the r-sig-geo list as the community (and you and I) benefit from using the list.

I'm not very clear on what you mean by 'I loose the negative values'. Also, I don't see the connection between the raster you show and the quantile values computed.  If you asked for the 0% quantile you should get the lowest available value - (since all pixels are at or above this value).  According to the raster info you show that should be -0.893809, but instead your 0% quantile is shown to be 40.00199   Perhaps you have unwittingly mixed up the rasters you are using.

Here is what I get using a small reproducible example (thanks, reprex! https://github.com/tidyverse/reprex <https://github.com/tidyverse/reprex>)  You can see that all of the -1 values are classified to class #1.

library(raster)
#> Loading required package: sp

# make a dummy matrix that ranges from -1 to 6 
nx = 10
ny = 5
m <- matrix(sample(-1:6, nx*ny, replace = TRUE), nrow = nx, ncol = ny)

# and make a raster
r <- raster(m)
r
#> class       : RasterLayer 
#> dimensions  : 10, 5, 50  (nrow, ncol, ncell)
#> resolution  : 0.2, 0.1  (x, y)
#> extent      : 0, 1, 0, 1  (xmin, xmax, ymin, ymax)
#> coord. ref. : NA 
#> data source : in memory
#> names       : layer 
#> values      : -1, 6  (min, max)


# compute the quantiles
pp <- quantile(r, c(0, 0.15, 0.85))
pp
#>  0% 15% 85% 
#>  -1   0   5

# classify the pixels according to the quantile each pixel belongs to
ix <- findInterval(getValues(r), pp)

# make a classified version of r (class 0, 1 or 3)
classified_r <- setValues(r, ix) 
classified_r
#> class       : RasterLayer 
#> dimensions  : 10, 5, 50  (nrow, ncol, ncell)
#> resolution  : 0.2, 0.1  (x, y)
#> extent      : 0, 1, 0, 1  (xmin, xmax, ymin, ymax)
#> coord. ref. : NA 
#> data source : in memory
#> names       : layer 
#> values      : 1, 3  (min, max)

# show how they pair up
df <- data.frame(value = getValues(r), class = getValues(classified_r))
df
#>    value class
#> 1      0     2
#> 2      0     2
#> 3      5     2
#> 4      6     3
#> 5      5     2
#> 6      4     2
#> 7      1     2
#> 8      5     2
#> 9     -1     1
#> 10     2     2
#> 11     0     2
#> 12     1     2
#> 13     3     2
#> 14     3     2
#> 15     6     3
#> 16    -1     1
#> 17     2     2
#> 18     6     3
#> 19     1     2
#> 20     0     2
#> 21     1     2
#> 22     5     2
#> 23     4     2
#> 24     2     2
#> 25     1     2
#> 26     0     2
#> 27     4     2
#> 28     6     3
#> 29     3     2
#> 30     0     2
#> 31     6     3
#> 32     6     3
#> 33     0     2
#> 34     2     2
#> 35     2     2
#> 36     6     3
#> 37     5     2
#> 38     6     3
#> 39     1     2
#> 40     5     2
#> 41     4     2
#> 42     4     2
#> 43     3     2
#> 44     4     2
#> 45     0     2
#> 46     4     2
#> 47     0     2
#> 48     1     2
#> 49     1     2
#> 50    -1     1


Cheers,
Ben


> On Dec 8, 2017, at 7:36 AM, John Wasige <johnwasige at gmail.com> wrote:
> 
> Hi Ben,
> 
> We had an email exchange on r-sig-geo at r-project.org <mailto:r-sig-geo at r-project.org> in June this year on raster classification where you made some suggestions. See the link below
> 
>  <http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html>
> 
>  <http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html>
> http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html <http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html>
> 
>  <http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html>
> However, when I run the reclassification, I loose the negative values. Any suggestion on how I can have all data classified & not loose pixels?
> Thanks for your help
> 
> pp <- quantile(r, c(0, 0.15, 0.85)) 
> # pp 
> #       0%      15%      85% 
> # 40.00199 47.64569 82.50751 
> ix <- findInterval(getValues(r), pp) 
> classified_r <- setValues(r, ix) 
> 
> ########
> 
> My raster looks;
> 
> class       : RasterLayer 
> dimensions  : 6557, 4281, 28070517  (nrow, ncol, ncell)
> resolution  : 0.0002335903, 0.0001525088  (x, y)
> extent      : 0, 1, 0, 1  (xmin, xmax, ymin, ymax)
> coord. ref. : NA 
> data source : J:\LPD_data\gpp.tif 
> names       : gpp 
> values      : -0.893809, 5.855252  (min, max)
> 
> 
>  <http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html>
> 
>  <http://r-sig-geo.2731867.n2.nabble.com/Thresholds-amp-reclassify-raster-td7591266.html>
> 

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

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