I'm extracting mean values from a raster with polygon shapefile. The CRS of both raster and vector are same, but then also extract function returns NA values.
library(rgdal)
library(raster)
options(stringsAsFactors = FALSE)
Shapefile <- readOGR("Fishnet_geolocated.shp",layer="Fishnet_geolocated")
plot(Shapefile)
CHM_Napi<-raster("Napi_CRS.tif")
crs(Shapefile)
crs(CHM_Napi)
Napi_extract <- raster::extract(CHM_Napi, # the raster that you wish to extract values from
Shapefile, # a point, or polygon spatial object
fun = mean, # extract the MEAN value from each plot
sp = TRUE) # create spatial object
class(Napi_extract)
summary(Napi_extract$Napi_CRS)
After running this code I get a result-
> Shapefile <- readOGR("Fishnet_geolocated.shp",layer="Fishnet_geolocated")
OGR data source with driver: ESRI Shapefile
Source: ""
with 63 features
It has 5 fields
Integer64 fields read as strings: id
> plot(Shapefile)
> CHM_Napi<-raster("Napi_CRS.tif")
> crs(Shapefile)
CRS arguments:
+proj=utm +zone=36 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84
+towgs84=0,0,0
> crs(CHM_Napi)
CRS arguments:
+proj=utm +zone=36 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84
+towgs84=0,0,0
> class(Napi_extract)
[1] "SpatialPolygonsDataFrame"
attr(,"package")
[1] "sp"
> summary(Napi_extract$Napi_CRS)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
NA NA NA NaN NA NA 63
Is there something which I'm missing in the extract function, should I reproject the raster and shapefile. P.S. In QGIS both the vector and raster layer overlap, but not in R. Any useful tips are appreciated.
There are probably NA values in the raster. Use na.rm=TRUE like this
Napi_extract <- raster::extract(CHM_Napi, Shapefile, fun = mean, na.rm =TRUE, sp = TRUE)