R help - Aug 2024 - boxplot of raster and shapefile

Dear community

This example code works

library(raster)
library(sp)
library(rgdal)
library(ggplot2)

# Create some sample raster data
raster_file <- raster(ncol=36, nrow=18)
raster_file[] <- 1:ncell(raster_file)
plot(raster_file)

#Create some sample polygons
cds1 <- rbind(c(-180,-20), c(-160,5), c(-60, 0), c(-160,-60), c(-180,-20))
cds2 <- rbind(c(80,0), c(100,60), c(120,0), c(120,-55), c(80,0))
shape_file <- SpatialPolygons(list(Polygons(list(Polygon(cds1)), 1), 
                              Polygons(list(Polygon(cds2)), 2)))
plot(shape_file)


# 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)

# Create the boxplot
bp<-ggplot(data, aes(x = factor(polygon), y = value)) +
  geom_boxplot() +
  labs(x = "Polygon", y = "Raster Values") +
  theme_minimal()
bp



For my own dataset I encountered problems in reading in the polygons. 
The error message comes in the boxplot function

Here may shape file
> # load shape file including all layers and print layers
> shape_file<-shapefile("C:/Users/.....BiogeoRegion.shp")
Warning message:
[vect] Z coordinates ignored 
> names(shape_file)
 [1] "RegionNumm" "RegionName" "Unterregio"
"Unterreg_1" "ObjNummer"
"Version"    "Shape_Leng" "Shape_Area"
"DERegionNa" "FRRegionNa"
[11] "ITRegionNa" "DEBioBedeu" "FRBioBedeu"
"ITBioBedeu"
> str(shape_file)
Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5
slots
  ..@ data       :'data.frame':	12 obs. of  14 variables:
  .. ..$ RegionNumm: int [1:12] 1 2 2 2 2 3 3 4 5 5 ...
  .. ..$ RegionName: chr [1:12] "R1" "R2" "R2"
"R2" ...
  .. ..$ Unterregio: int [1:12] 11 21 22 23 24 31 32 41 51 52 ...
  .. ..$ Unterreg_1: chr [1:12] "U11" "U21" "U22"
"U23" ...
  .. ..$ ObjNummer : chr [1:12] "1" "2" "3"
"4" ...
  .. ..$ Version   : chr [1:12] "2020/05/08" "2020/05/08"
"2020/05/08"
"2020/05/08" ...
  .. ..$ Shape_Leng: num [1:12] 725117 334364 539746 576810 555541 ...
  .. ..$ Shape_Area: num [1:12] 4.17e+09 1.11e+09 1.07e+09 4.64e+09 4.47e+09
...
  .. ..$ DERegionNa: chr [1:12] "Jura" "Mittelland"
"Mittelland"
"Mittelland" ...
  .. ..$ FRRegionNa: chr [1:12] "Jura" "Plateau"
"Plateau" "Plateau" ...
  .. ..$ ITRegionNa: chr [1:12] "Giura" "Altipiano"
"Altipiano" "Altipiano"
...
  .. ..$ DEBioBedeu: chr [1:12] "Jura und Randen"
"Genferseegebiet"
"Hochrheingebiet" "Westliches Mittelland" ...
  .. ..$ FRBioBedeu: chr [1:12] "Jura et Randen" "Bassin
l?manique" "Bassin
rh?nan" "Plateau occidental" ...
  .. ..$ ITBioBedeu: chr [1:12] "Giura e Randen" "Regione del
Lemano"
"Regione dell?Alto Reno" "Altipiano occidentale" ...
  ..@ polygons   :List of 12

> # select a specific raster file from a list
> raster_file<-allrasters_pres[[1]]
> names(raster_file)
[1] "Andrena.barbilabris_glo_ensemble"
> 
> # 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()`). 
>

? Mon, 26 Aug 2024 14:33:02 +0200
SIBYLLE ST?CKLI via R-help <r-help at r-project.org> ?????:
> > # 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