[R] boxplot of raster and shapefile
Ben Tupper
btupper @end|ng |rom b|ge|ow@org
Wed Aug 28 15:16:26 CEST 2024
Hi,
> e <- extract(r,v)
Error in (function (classes, fdef, mtable) :
kann keine vererbte Methode finden für Funktion ‘extract’ für Signatur
‘"RasterLayer", "SpatVector"’
The error message is telling you that extract(r, v) hasn't been configured
for the combination extract(RasterLayer, SpatVector). If you bring up the
help for terra::extract you can see the various datatypes that extract()
has been configured for. In the help document
<https://search.r-project.org/CRAN/refmans/terra/html/extract.html>the
various "signatures" for r and v are detailed.
So, if you read your raster data with terra::rast() rather than
raster::raster() your r variable will be of type 'SpatRaster' then your
signatures will be extract(SpatRaster, SpatVector) which should work.
CHeers,
Ben
On Wed, Aug 28, 2024 at 3:35 AM SIBYLLE STÖCKLI via R-help <
r-help using r-project.org> wrote:
> Dear Ivan
>
>
>
> In the meantime I have found a much easier function. As before the code
> does not work with my own dataset, probably because of my multipolygonal
> shape file. There is a warning, that z coordinate are ignored. I provided
> the output of my shapefile. I changed from read_sf to vect() as I have read
> that this would work better.
>
>
>
> Probably this warming message drives the error when running e <-
> extract(r,v): “ cannot find an inherited method for function ‘extract’ for
> signature ‘’RasterLayer‘, “SpatVector”’
>
>
>
> Working example
>
>
>
> # load libraries
>
> library(terra)
>
> library(ggplot2)
>
>
>
> # Load shp and raster from example files of terra
>
> (v <- vect(system.file("ex/lux.shp", package="terra")))
>
> (r <- rast(system.file("ex/elev.tif", package="terra")))
>
> plot(r); plot(v, add = TRUE); text(v, labels = "NAME_2", col=c("white"))
>
> # extract, include names from vector attributes
>
> e <- extract(r,v)
>
> e$NAME_2 <- v$NAME_2[e$ID]
>
> str(e)
>
> # plot
>
> ggplot(e, aes(x = NAME_2, y = elevation)) +
>
> geom_boxplot() +
>
> theme_minimal() +
>
> theme(axis.text.x = element_text(angle = 45))
>
>
>
>
>
> Personal example not working
>
>
>
> # Load shp file
>
> > v <- vect("C:/Users/…._BiogeoRegion.shp")
>
> Warning message:
>
> [vect] Z coordinates ignored
>
> > str(v)
>
> S4 class 'SpatVector' [package "terra"]
>
> > names(v)
>
> [1] "RegionNumm" "RegionName" "Unterregio" "Unterreg_1" "ObjNummer"
> "Version" "Shape_Leng" "Shape_Area" "DERegionNa" "FRRegionNa"
> "ITRegionNa"
>
> [12] "DEBioBedeu" "FRBioBedeu" "ITBioBedeu"
>
>
>
> > v
>
> class : SpatVector
>
> geometry : polygons
>
> dimensions : 12, 14 (geometries, attributes)
>
> extent : 2485410, 2833842, 1075268, 1295934 (xmin, xmax, ymin, ymax)
>
> source : N2020_Revision_BiogeoRegion.shp
>
> coord. ref. : CH1903+ / LV95 (EPSG:2056)
>
> names : RegionNumm RegionName Unterregio Unterreg_1 ObjNummer
> Version Shape_Leng Shape_Area DERegionNa FRRegionNa (and 4 more)
>
> type : <int> <chr> <int> <chr> <chr>
> <chr> <num> <num> <chr> <chr>
>
> values : 1 R1 11 U11 1
> 2020/05/08 7.251e+05 4.171e+09 Jura Jura
>
> 2 R2 21 U21 2
> 2020/05/08 3.344e+05 1.112e+09 Mittelland Plateau
>
> 2 R2 22 U22 3
> 2020/05/08 5.397e+05 1.068e+09 Mittelland Plateau
>
>
>
>
>
> # lodad raster files
>
> #first import all files in a single folder as a list
>
> rastlist_pres <- list.files(path ="C:/Users/….presence", pattern='.tif$',
> all.files= T, full.names= T)
>
> rastlist_RCP85P2 <- list.files(path ="C:/Users/…._bee_RCP85P2",
> pattern='.tif$', all.files= T, full.names= T)
>
> #import all raster files in folder using lapply
>
> allrasters_pres <- lapply(rastlist_pres, raster)
>
> allrasters_RCP85P2 <- lapply(rastlist_RCP85P2, raster)
>
> r <- allrasters_pres[[1]]
>
>
>
>
>
> > r
>
> class : RasterLayer
>
> dimensions : 9200, 14400, 132480000 (nrow, ncol, ncell)
>
> resolution : 25, 25 (x, y)
>
> extent : 2480000, 2840000, 1070000, 1300000 (xmin, xmax, ymin, ymax)
>
> crs : +proj=somerc +lat_0=46.9524055555556 +lon_0=7.43958333333333
> +k_0=1 +x_0=2600000 +y_0=1200000 +ellps=bessel +units=m +no_defs
>
> source : Andrena.barbilabris_glo_ensemble.tif
>
> names : Andrena.barbilabris_glo_ensemble
>
> values : 0, 53 (min, max)
>
>
>
> > str(r)
>
> Formal class 'RasterLayer' [package "raster"] with 13 slots
>
> ..@ file :Formal class '.RasterFile' [package "raster"] with 13 slots
>
> .. .. ..@ name : chr "C:\\Users\\.......\\Andren"| __truncated__
>
> .. .. ..@ datanotation: chr "INT2U"
>
> .. .. ..@ byteorder : chr "little"
>
> .. .. ..@ nodatavalue : num -Inf
>
> .. .. ..@ NAchanged : logi FALSE
>
> .. .. ..@ nbands : int 1
>
> .. .. ..@ bandorder : chr "BIL"
>
> .. .. ..@ offset : int 0
>
> .. .. ..@ toptobottom : logi TRUE
>
> .. .. ..@ blockrows : Named int 1
>
> .. .. .. ..- attr(*, "names")= chr "rows"
>
> .. .. ..@ blockcols : Named int 14400
>
> .. .. .. ..- attr(*, "names")= chr "cols"
>
> .. .. ..@ driver : chr "gdal"
>
> .. .. ..@ open : logi FALSE
>
> ..@ data :Formal class '.SingleLayerData' [package "raster"] with 13
> slots
>
> .. .. ..@ values : logi(0)
>
> .. .. ..@ offset : num 0
>
> .. .. ..@ gain : num 1
>
> .. .. ..@ inmemory : logi FALSE
>
> .. .. ..@ fromdisk : logi TRUE
>
> .. .. ..@ isfactor : logi FALSE
>
> .. .. ..@ attributes: list()
>
> .. .. ..@ haveminmax: logi TRUE
>
> .. .. ..@ min : num 0
>
> .. .. ..@ max : num 53
>
> .. .. ..@ band : int 1
>
> .. .. ..@ unit : chr ""
>
> .. .. ..@ names : chr "Andrena.barbilabris_glo_ensemble"
>
> ..@ legend :Formal class '.RasterLegend' [package "raster"] with 5 slots
>
> .. .. ..@ type : chr(0)
>
> .. .. ..@ values : logi(0)
>
> .. .. ..@ color : logi(0)
>
> .. .. ..@ names : logi(0)
>
> .. .. ..@ colortable: logi(0)
>
> ..@ title : chr(0)
>
> ..@ extent :Formal class 'Extent' [package "raster"] with 4 slots
>
> .. .. ..@ xmin: num 2480000
>
> .. .. ..@ xmax: num 2840000
>
> .. .. ..@ ymin: num 1070000
>
> .. .. ..@ ymax: num 1300000
>
> ..@ rotated : logi FALSE
>
> ..@ rotation:Formal class '.Rotation' [package "raster"] with 2 slots
>
> .. .. ..@ geotrans: num(0)
>
> .. .. ..@ transfun:function ()
>
> ..@ ncols : int 14400
>
> ..@ nrows : int 9200
>
> ..@ crs :Formal class 'CRS' [package "sp"] with 1 slot
>
> .. .. ..@ projargs: chr "+proj=somerc +lat_0=46.9524055555556
> +lon_0=7.43958333333333 +k_0=1 +x_0=2600000 +y_0=1200000 +ellps=bessel
> +units=m +no_defs"
>
> .. .. ..$ comment: chr "PROJCRS[\"unknown\",\n
> BASEGEOGCRS[\"unknown\",\n DATUM[\"Unknown based on Bessel 1841
> ellipsoid\",\n"| __truncated__
>
> ..@ srs : chr "+proj=somerc +lat_0=46.9524055555556
> +lon_0=7.43958333333333 +k_0=1 +x_0=2600000 +y_0=1200000 +ellps=bessel
> +units=m +no_defs"
>
> ..@ history : list()
>
> ..@ z : list()
>
>
>
>
>
> > e <- extract(r,v)
>
> Error in (function (classes, fdef, mtable) :
>
> kann keine vererbte Methode finden für Funktion ‘extract’ für Signatur
> ‘"RasterLayer", "SpatVector"’
>
>
>
>
>
> Kind regards
>
> Sibylle
>
>
>
> -----Original Message-----
> From: Ivan Krylov <ikrylov using disroot.org>
> Sent: Tuesday, August 27, 2024 6:55 PM
> To: SIBYLLE STÖCKLI via R-help <r-help using r-project.org>
> Cc: sibylle.stoeckli using gmx.ch
> Subject: Re: [R] boxplot of raster and shapefile
>
>
>
> В Mon, 26 Aug 2024 14:33:02 +0200
>
> SIBYLLE STÖCKLI via R-help < <mailto:r-help using r-project.org>
> r-help using r-project.org> пишет:
>
>
>
> > > # Extract raster values within the shapefile extracted_values <-
>
> > > extract(raster_file, shape_file)
>
>
>
> > > # Assuming the shapefile has multiple polygons and you want to #
>
> > > create a boxplot for each data_list <-
>
> > > lapply(1:length(extracted_values), function(i) {
>
> > + data.frame(value = extracted_values[[i]], polygon = i)
>
> > + })
>
> > > data <- do.call(rbind, data_list)
>
>
>
> > > names(data)
>
> > [1] "value" "polygon"
>
> > > # Create the boxplot
>
> > > bp<-ggplot(data, aes(x = factor(polygon), y = value)) +
>
> > + geom_boxplot() +
>
> > + labs(x = "Polygon", y = "Raster Values") +
>
> > + theme_minimal()
>
> > > bp
>
> > Error in UseMethod("depth") :
>
> > no applicable method for 'depth' applied to an object of class
>
> > "NULL"
>
> > In addition: Warning message:
>
> > Removed 452451 rows containing non-finite outside the scale range
>
> > (`stat_boxplot()`).
>
>
>
> Thank you for providing a runnable example! Could you please also show
>
> the output of str(extracted_values) and str(data)?
>
>
>
> --
>
> Best regards,
>
> Ivan
>
>
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>
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