import packages

library(lidR)
## Loading required package: raster
## Loading required package: sp
library(stringr)
library(spatialEco)
## 
## Attaching package: 'spatialEco'
## The following object is masked from 'package:lidR':
## 
##     is.empty
## The following object is masked from 'package:raster':
## 
##     shift
library(SpaDES)
## loading reproducible     1.1.1
## loading quickPlot        0.1.6
## loading SpaDES.core      1.0.1
## loading SpaDES.tools     0.3.6
## loading SpaDES.addins    0.1.2
## Default paths for SpaDES directories set to:
##   cachePath:  
##   inputPath:  /Volumes/Temp/tmp/RtmpwAYmMa/SpaDES/inputs
##   modulePath: /Volumes/Temp/tmp/RtmpwAYmMa/SpaDES/modules
##   outputPath: /Volumes/Temp/tmp/RtmpwAYmMa/SpaDES/outputs
## These can be changed using 'setPaths()'. See '?setPaths'.

Read in .las file and use inverse distance weighting to make sure that the minum value is zero

las <- readLAS("/Users/lavran_pagano/Desktop/Brauerlas/245267.las")# imput your on path to your .lasfile
## Warning: There are 714 points flagged 'withheld'.
## Warning in showSRID(SRS_string, format = "PROJ", multiline = "NO"): Discarded datum NAD83_High_Accuracy_Reference_Network in CRS definition,
##  but +towgs84= values preserved
lasn <- lasnormalize(las, knnidw(),na.rm = TRUE) #inverse distance weighting
## Warning: There were 6 degenerated ground points. Some X Y Z coordinates were
## repeated. They were removed.
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Create a canopy height model.

chm <- grid_canopy(lasn, 0.25, pitfree(c(0,2,5,10,15), c(0,1), subcircle = 0.2))# Khosravipouret al. 2014
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Our lidar files were using feet as units so we need to convert all values to meters

CHM_m <- chm * 0.3048
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved

Making double sure that there are no points above 30 meters or below zero meters

CHM_m[CHM_m < 2] <- 0
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved

## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved
CHM_m[CHM_m > 30] <- 0
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved

## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved

Aply a Gaussian filter to remove spirious points

gf <- focalWeight(CHM_m, 2, "Gauss")
CHMrg <- focal(CHM_m, w=gf, na.rm=TRUE)
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved
## Warning in .rasterFromRasterFile(grdfile, band = band, objecttype, ...): size of
## values file does not match the number of cells (given the data type)

Write to a raster

writeRaster(CHMrg, filename = "Canopy_Height_Model", bylayer = TRUE, format = "GTiff", overwrite = TRUE)
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on GRS80 ellipsoid in CRS definition,
##  but +towgs84= values preserved