clipLevel2AMGeometry(level2AM, polygon_spdf, split_by)

# Specifying the path to GEDI level2A data (zip file)
outdir = tempdir()
level2A_fp_zip <- system.file("extdata",
                  "GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip",
                  package="rGEDI")

# Unzipping GEDI level2A data
level2Apath <- unzip(level2A_fp_zip,exdir = outdir)

# Reading GEDI level2A data (h5 file)
level2a<-readLevel2A(level2Apath=level2Apath)

# Extracting GEDI Elevation and Height Metrics
level2AM = getLevel2AM(level2a)

# Specifying the path to shapefile
polygon_filepath <- system.file("extdata", "stands_cerrado.shp", package="rGEDI")

# Reading shapefile as SpatialPolygonsDataFrame object
library(raster)
polygon_spdf<-shapefile(polygon_filepath)

# Clipping GEDI data by Geometry
level2AM_clip = clipLevel2AMGeometry(level2AM, polygon_spdf, split_by="id")

hasLeaflet = require(leaflet)

if (hasLeaflet) {
leaflet() %>%
 addCircleMarkers(level2AM_clip$lat_lowestmode,
                  level2AM_clip$lon_lowestmode,
                  radius = 1,
                  opacity = 1,
                  color = "red")  %>%
 addScaleBar(options = list(imperial = FALSE)) %>%
 addPolygons(data=polygon_spdf,weight=1,col = 'white',
             opacity = 1, fillOpacity = 0) %>%
 addProviderTiles(providers$Esri.WorldImagery)
}

close(level2a)