[R-sig-Geo] Extract Raster Data Values to Shapefile

Thu May 12 11:43:04 CEST 2022

Thanks for all the helpful input.
I have used terra::extract, and it worked.

I have included: touches = TRUE,na.rm = TRUE, to eliminate all NAs.

I was wondering what na.rm does here?
I know it from dplyr functions, but how can I imagine here how it works?

Zitat von Julien Rodriguez <julienrodriguez.ardaspm using gmail.com>:

> Thanks: it is true that handling missing values when extracting from a
> raster can sometimes be perilous.
>
> Same example with missing values and playing with terra::extract arguments
> to take the best decision about them.
>
> library(terra)
> library(sf)
>
> # Create a SpatRaster
> r <- rast(ncols=5, nrows=5, xmin=0, xmax=5, ymin=0, ymax=5)
> val <- 1:25
> # add randomly selected NAs
> set.seed(220512)
> val[sample(1:25,4)] <- NA
>
> values(r) <- val
>
> # Create a polygon object as sf
> p1 <- rbind(c(1, 1), c(3, 1), c(3, 3), c(1, 3), c(1, 1))
> p2 <- rbind(c(4, 0), c(4, 1), c(5, 1), c(5, 0), c(4, 0))
> p3 <- rbind(c(1.6, 1.6), c(3, 1.6), c(3, 3), c(1.6, 3), c(1.6, 1.6))
> myPol <- st_sf(code = c(1:3), geometry = st_sfc(list(st_polygon(list(p1)),
> st_polygon(list(p2)), st_polygon(list(p3)))))
>
> # Polygon object as SpatVector
> myPolAsSpatVect <- vect(st_geometry(myPol))
>
> plot(r)
> plot(myPolAsSpatVect, add = TRUE)
>
> # Here is your extraction, using fun argument, you can decide how to
> aggregate the values by district border
> terra::extract(r, myPolAsSpatVect, fun = mean)
> terra::extract(r, myPolAsSpatVect, fun = mean, na.rm = TRUE)
> # By default, the extraction will concern pixels whose center point is
> within the polygon
> terra::extract(r, myPolAsSpatVect, fun = mean, na.rm = TRUE, touches = TRUE)
> terra::extract(r, myPolAsSpatVect, fun = mean, na.rm = TRUE, exact = TRUE)
>
> # without aggregation
> terra::extract(r, myPolAsSpatVect)
> terra::extract(r, myPolAsSpatVect, exact = TRUE)
> terra::extract(r, myPolAsSpatVect, touches = TRUE)
>
> Regards
>
>
>
> Le jeu. 12 mai 2022 à 09:29, Jordan Chamberlin <jordan.chamberlin using gmail.com>
> a écrit :
>
>> One way to deal with NAs is simply to add an argument to terra::extract:
>> na.rm=TRUE
>>
>>
>>
>> On Wed, May 11, 2022 at 9:59 PM GilbertoCamara <
>> gilberto.camara.inpe using gmail.com> wrote:
>>
>>> Dear Julian,
>>>
>>> Your script works nicely if the raster data if well-behaved. In real
>>> life, raster data can have missing values, which have to be dealt with.
>>>
>>> Best
>>> Gilberto
>>> ============================
>>> Prof Dr Gilberto Camara
>>> Senior Researcher
>>> National Institute for Space Research (INPE), Brazil
>>>
>>> https://urldefense.com/v3/__https://gilbertocamara.org/__;!!HXCxUKc!xb3Skg9BEorRUu-1yoW_jHkQRP9y6tC81a3GXDuYrM-JEP1U_aBOybnpLw7uroqGQsB8yGdvdj8X4xbotnvel5LZQAkw$
>>> =============================
>>>
>>>
>>>
>>>
>>> > On 11 May 2022, at 14:52, Julien Rodriguez <
>>> julienrodriguez.ardaspm using gmail.com> wrote:
>>> >
>>> > Hi Luca and Zivan,
>>> >
>>> >
>>> > Maybe this toy example using terra and sf (probably the class of your
>>> > district borders object) may help.
>>> >
>>> > library(terra)
>>> > library(sf)
>>> >
>>> > # Create a SpatRaster
>>> > r <- rast(ncols=5, nrows=5, xmin=0, xmax=5, ymin=0, ymax=5)
>>> > values(r) <- 1:25
>>> >
>>> > # Create a polygon object as sf
>>> > p1 <- rbind(c(1, 1), c(3, 1), c(3, 3), c(1, 3), c(1, 1))
>>> > p2 <- rbind(c(4, 0), c(4, 1), c(5, 1), c(5, 0), c(4, 0))
>>> > myPol <- st_sf(code = c(1:2), geometry =
>>> st_sfc(list(st_polygon(list(p1)),
>>> > st_polygon(list(p2)))))
>>> >
>>> > # Polygon object as SpatVector
>>> > myPolAsSpatVect <- vect(st_geometry(myPol))
>>> >
>>> > plot(r)
>>> > plot(myPolAsSpatVect, add = TRUE)
>>> >
>>> > # Here is your extraction, using fun argument, you can decide how to
>>> > aggregate the values by district border
>>> > terra::extract(r, myPolAsSpatVect, fun = mean)
>>> >
>>> > Regards
>>> >
>>> > Julien
>>> >
>>> >
>>> >
>>> >
>>> > Le mer. 11 mai 2022 à 18:19, Zivan Karaman <zivan.karaman using gmail.com> a
>>> > écrit :
>>> >
>>> >> Hi Luca,
>>> >> You should perhaps have a look at the crop and mask function in the
>>> raster
>>> >> or terra package.
>>> >> Hope this helps!
>>> >> Zivan
>>> >>
>>> >> On Wed, May 11, 2022 at 6:09 PM <lucfrank using mail.uni-mannheim.de> wrote:
>>> >>
>>> >>> Hello Everyone,
>>> >>>
>>> >>> I have a shapefile with district borders and a raster data file
>>> (.tif).
>>> >>>
>>> >>> How can I extract the value from the raster data onto each district in
>>> >>> the shapefile?
>>> >>>
>>> >>> I have the exact thing I want with two shapefiles with the command:
>>> >>>
>>> >>> x <- st_join(x,y,join=st_overlaps,left=TRUE,largest=TRUE)
>>> >>>
>>> >>> This gives me the result I want. I tried to convert the .tif file to a
>>> >>> shapefile, but this didn't work for me with multiple different
>>> >>> solutions I found online.
>>> >>>
>>> >>> I would appreciate any ideas you might have.
>>> >>>
>>> >>> Luca
>>> >>>
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-- 
Luca Frank
Matrikelnr: 1698155
4.FS Politikwissenschaft