How do I change extent of shapefile into lat lon of NetCDF file?

Question

I have loaded a shapefile and NetCDF into R, and I want to extract data based on the extent of the shapefile. I have done the following, but when I want to extract it I get NA's as the extent differs between the file:

library(rgdal)
library(sf)
library(raster)
library(ncdf4)

shp = readOGR("shapefile.shp")
net = brick("netCDF.nc")
extent(net)
extent(shp)

crs(shp)
crs(net)

net.mask = mask(net.brick, shp)
net.df = as.data.frame(net.mask[[1]], xy = TRUE)
head(temp.df)

> shp
class       : SpatialPolygonsDataFrame 
features    : 1 
extent      : -2939454, -1610437, 3261153, 4333895  (xmin, xmax, ymin, ymax)
crs         : +proj=longlat +datum=WGS84 +no_defs 
variables   : 8
names       : NA_L2CODE,              NA_L2NAME, NA_L1CODE, NA_L1NAME,                    NA_L2KEY, NA_L1KEY,    Shape_Leng,   Shape_Area 
value       :       3.1, ALASKA BOREAL INTERIOR,         3,     TAIGA, 3.1  ALASKA BOREAL INTERIOR, 3  TAIGA, 11989512.2816, 423471100811 

> crs(shp)
CRS arguments: +proj=longlat +datum=WGS84 +no_defs 
> crs(net)
CRS arguments: +proj=longlat +datum=WGS84 +no_defs 

> extent(net)
class      : Extent 
xmin       : -180.125 
xmax       : -51.875 
ymin       : 40.875 
ymax       : 90.125 

> extent(shp)
class      : Extent 
xmin       : -2939454 
xmax       : -1610437 
ymin       : 3261153 
ymax       : 4333895 

How can I change the extent of the shapefile so it gets latitude and longitude rather than X and Y coordinates?

EDIT:

Answer 1

Maybe this will help:

library(sf)
eco_l2 <- st_read("na_cec_eco_l2/NA_CEC_Eco_Level2.shp")
Reading layer `NA_CEC_Eco_Level2' from data source `/home/micha/work/tmp/na_cec_eco_l2/NA_CEC_Eco_Level2.shp' using driver `ESRI Shapefile'
Simple feature collection with 2261 features and 8 fields
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: -4334052 ymin: -3313739 xmax: 3324076 ymax: 4267265
Projected CRS: Sphere_ARC_INFO_Lambert_Azimuthal_Equal_Area

# Clearly NOT WGS84. Here's the correct projection of the original shapefile:

st_crs(eco_l2)
Coordinate Reference System:
  User input: Sphere_ARC_INFO_Lambert_Azimuthal_Equal_Area 
  wkt:
PROJCRS["Sphere_ARC_INFO_Lambert_Azimuthal_Equal_Area",
    BASEGEOGCRS["GCS_Sphere_ARC_INFO",
        DATUM["D_Sphere_ARC_INFO",
            ELLIPSOID["Sphere_ARC_INFO",6370997,0,
                LENGTHUNIT["metre",1,
                    ID["EPSG",9001]]]],
        PRIMEM["Greenwich",0,
            ANGLEUNIT["Degree",0.0174532925199433]]],
    CONVERSION["unnamed",
        METHOD["Lambert Azimuthal Equal Area (Spherical)",
            ID["EPSG",1027]],
        PARAMETER["Latitude of natural origin",45,
            ANGLEUNIT["Degree",0.0174532925199433],
            ID["EPSG",8801]],
        PARAMETER["Longitude of natural origin",-100,
            ANGLEUNIT["Degree",0.0174532925199433],
            ID["EPSG",8802]],
        PARAMETER["False easting",0,
            LENGTHUNIT["metre",1],
            ID["EPSG",8806]],
        PARAMETER["False northing",0,
            LENGTHUNIT["metre",1],
            ID["EPSG",8807]]],
    CS[Cartesian,2],
        AXIS["(E)",east,
            ORDER[1],
            LENGTHUNIT["metre",1,
                ID["EPSG",9001]]],
        AXIS["(N)",north,
            ORDER[2],
            LENGTHUNIT["metre",1,
                ID["EPSG",9001]]]]

# Now just reproject to the projection of the netcdf raster
eco_l2_wgs84 <- st_transform(eco_l2, "EPSG:4326")

Now you should be able to do your extract.