I am having a problem when over() doesn't give a value but keep giving meNA for every field in the outcome data.frame. The aim is to have the counts of tardigrade occurrences in each biogeoregion. Here is my data set and its compositions.
#extention=europe area
> tardigrade <- <- gbif("Eutardigrada",ext=e, sp=T, removeZeros=T, download=T)
> tardigrade_sp <- as(tardigrade, "SpatialPoints")
tardigrade_sp
class : SpatialPoints
features : 2033
extent : -8.250667, 32.14889, 34.66667, 66.28333 (xmin, xmax, ymin, ymax)
crs : +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs
> biogeo # can be find at https://www.eea.europa.eu/data-and-maps/data/biogeographical-regions-europe-3
class : SpatialPolygonsDataFrame
features : 12
extent : 943611, 8500000, 6e+05, 7800000 (xmin, xmax, ymin, ymax)
crs : +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs
variables : 4
names : short_name, pre_2012, code, name
min values : alpine, ALP, Alpine, Alpine Bio-geographical Region
max values : steppic, STE, Steppic, outside Europe
> over (biogeo, tardigrade_sp)
1 2 3 4 5 6 7 8 9 10 11 12
NA NA NA NA NA NA NA NA NA NA NA NA
Can anyone tell me what did I do wrong and what should I do? Thank you in advance
library(dismo) # I add to find this one!
library(sp)
library(sf)
tardigrade <- dismo::gbif("Eutardigrada", sp = T, removeZeros = T, download = T)
tardigrade_sp <- as(tardigrade, "SpatialPoints")
tardigrade_sp
I get more point I assume you used a particular extent with ext = e that I could not reproduce.
here I didn't get a CRS. In your post it looked like 3035 but my return looked more like 4326 so after testing it I stayed with 4326 (I assume this was your problem)
# sp::proj4string(tardigrade_sp) <- sp::CRS("+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs")
sp::proj4string(tardigrade_sp) <- sp::CRS("+init=epsg:4326")
# I will go with in sf object
tardi_sf <- sf::st_as_sf(tardigrade_sp)
tardi_3035 <- sf::st_transform(tardi_sf, 3035) # it seems to me that you want this CRS
tardi_3035_sp <- as(tardi_3035, "Spatial") # going back to sp
biogeo <- sf::st_read("BiogeoRegions2016_shapefile/BiogeoRegions2016.shp")
# CRS 3035 ETRS89_LAEA_Europe
biogeo_3035 <- sf::st_transform(biogeo, 3035) # formating of CRS was weird
# so I dide a transform just to be exactly the same
biogeo_sp <- as(biogeo, "Spatial")
# a quick plot, I used a subset because this shape is quite heavy
plot(biogeo$geometry[biogeo$code == "Continental"])
plot(tardi_3035 , add = TRUE)
# this seems to works now !
sp::over(tardi_3035_sp, biogeo_sp, fn = NULL)
you shoud read about sf and probably check https://geocompr.robinlovelace.net/