Cut points falling in a polygon out of the point cloud

Question

Using lidR 3.1.3, is it possible to classify points inside polygons shapefile for a LASCatalog, something like the previous lasclassify() function. I'm looking for a equivalent of this PDAL method.
ctg <- lidR::readLAScatalog(path_to_folder)
shapefile = rgdal::readOGR(shapefile_file)
opt_output_files(ctg) <- paste0(path_to_folder, "/{ORIGINALFILENAME}_classified")

# Need to classify here
output<- classify_within_polygons(ctg, shapefile)

JRR · Accepted Answer

With a loaded point-cloud (LAS) you can use merge_spatial(). Lets load some data first:
library(lidR)
library(sf)

LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
shp <- system.file("extdata", "lake_polygons_UTM17.shp", package = "lidR")
las <- readLAS(LASfile)
poly <- st_read(shp, quiet = TRUE)
plot(las@header)
plot(poly, add = TRUE)

We can now use merge_spatial() to know if points are in or out the polygon(s). Then we can use this information to clip or classify.
las <- merge_spatial(las, poly, "inpoly")
las$Classification[las$inpoly == TRUE] <- LASWATER
las$Classification[las$inpoly == FALSE & las$Classification != LASGROUND] <- LASLOWVEGETATION
plot(las, color = "Classification")

veg = filter_poi(las, inpoly == FALSE)
plot(veg)

However it is not possible (yet) to directly classify the point-cloud from a LAScatalog. You must build your own tools based on this answer and catalog_apply()

Cut points falling in a polygon out of the point cloud

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