# load packages
require(raster)
require(rgdal)

# Step 1: read in raster from .tif file
r <- raster("C:/.../raster.tif")
# Q: how do you do this with a .sid file?

# read in shapefile used for clip
shp <- readOGR(dsn="C:/.../folder", layer="shapefile")

# Step 2: clip raster to shapefile
r.clip <- crop(r, shp)

# Step 3: save clipped raster as tiff
writeRaster(r.clip, "C:/.../raster_clip.tif", format="GTiff")

library(rgdal)
r <- readGDAL("C:/.../raster.sid")

library(gdalUtils)
gdal_setInstallation(search_path =...) # choose GDAL version with this function
r <- gdal_translate(src_dataset = "C:/.../raster.sid",
           dst_dataset = "raster.tif",
           output_Raster = TRUE) # create R raster object