Creating_Canopy_Height

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

Creating_Canopy_Height_Models

Lavran Pagano

3/16/2021

import packages

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

Create a canopy height model.

Our lidar files were using feet as units so we need to convert all values to meters

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

Aply a Gaussian filter to remove spirious points

Write to a raster