lidar2

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

setwd("~/Desktop/Hopkins/forested landscapes")

library(lidR)
#Collection of tools for processing and analyzing LIDAR data
library(RCSF)
#Helps separate ground from non-ground points
library(terra)

## terra 1.8.70

## 
## Attaching package: 'terra'

## The following object is masked from 'package:lidR':
## 
##     watershed

#Does spatial data analysis with raster and vector data
library(viridis)

## Loading required package: viridisLite

#Works on colouring
## Loading required package: viridisLite
library(raster) #Manipulates raster data or data organized in grids of pixels

## Loading required package: sp

## 
## Attaching package: 'sp'

## The following object is masked from 'package:lidR':
## 
##     wkt

## 
## Attaching package: 'raster'

## The following objects are masked from 'package:lidR':
## 
##     projection, projection<-

las=readLAS('fernow1.laz')

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## Warning: There are 1962235 points flagged 'withheld'.

## Warning: There are 1962235 points flagged 'synthetic'.

## Warning: Invalid data: 16 points with a return number equal to 0 found.

## Warning: Invalid data: 128 points with a number of returns equal to 0 found.

## Warning: Invalid data: 112 points with a 'return number' greater than the
## 'number of returns'.

las

## class        : LAS (v1.4 format 7)
## memory       : 1.5 Gb 
## extent       : -8869615, -8867360, 4730582, 4731954 (xmin, xmax, ymin, ymax)
## coord. ref.  : WGS 84 / Pseudo-Mercator 
## area         : 3.1 km²
## points       : 16.59 million points
## type         : airborne
## density      : 5.35 points/m²
## density      : 2.83 pulses/m²

chm <- rasterize_canopy(las, res = 1, algorithm = pitfree())

## Delaunay rasterization[==================================----------------] 69% (1 threads)Delaunay rasterization[===================================---------------] 70% (1 threads)Delaunay rasterization[===================================---------------] 71% (1 threads)Delaunay rasterization[====================================--------------] 72% (1 threads)Delaunay rasterization[====================================--------------] 73% (1 threads)Delaunay rasterization[=====================================-------------] 74% (1 threads)Delaunay rasterization[=====================================-------------] 75% (1 threads)Delaunay rasterization[======================================------------] 76% (1 threads)Delaunay rasterization[======================================------------] 77% (1 threads)Delaunay rasterization[=======================================-----------] 78% (1 threads)Delaunay rasterization[=======================================-----------] 79% (1 threads)Delaunay rasterization[========================================----------] 80% (1 threads)Delaunay rasterization[========================================----------] 81% (1 threads)Delaunay rasterization[=========================================---------] 82% (1 threads)Delaunay rasterization[=========================================---------] 83% (1 threads)Delaunay rasterization[==========================================--------] 84% (1 threads)Delaunay rasterization[==========================================--------] 85% (1 threads)Delaunay rasterization[===========================================-------] 86% (1 threads)Delaunay rasterization[===========================================-------] 87% (1 threads)Delaunay rasterization[============================================------] 88% (1 threads)Delaunay rasterization[============================================------] 89% (1 threads)Delaunay rasterization[=============================================-----] 90% (1 threads)Delaunay rasterization[=============================================-----] 91% (1 threads)Delaunay rasterization[==============================================----] 92% (1 threads)Delaunay rasterization[==============================================----] 93% (1 threads)Delaunay rasterization[===============================================---] 94% (1 threads)Delaunay rasterization[===============================================---] 95% (1 threads)Delaunay rasterization[================================================--] 96% (1 threads)Delaunay rasterization[================================================--] 97% (1 threads)Delaunay rasterization[=================================================-] 98% (1 threads)Delaunay rasterization[=================================================-] 99% (1 threads)Delaunay rasterization[==================================================] 100% (1 threads)

plot(chm, main = "Canopy Height Model")

ws_values <- c(3, 6, 9, 12, 15)
# Sequence of window sizes
th_values <- c(0.1, 0.2, 0.3, 0.4, 0.5)
# Sequence of height thresholds

las_classified <- classify_ground(las, algorithm = pmf(ws = ws_values, th = th_values))

## Morphological filter: 5% (1 threads)Morphological filter: 6% (1 threads)Morphological filter: 7% (1 threads)Morphological filter: 8% (1 threads)Morphological filter: 9% (1 threads)Morphological filter: 10% (1 threads)Morphological filter: 11% (1 threads)Morphological filter: 12% (1 threads)Morphological filter: 13% (1 threads)Morphological filter: 14% (1 threads)Morphological filter: 15% (1 threads)Morphological filter: 16% (1 threads)Morphological filter: 17% (1 threads)Morphological filter: 18% (1 threads)Morphological filter: 19% (1 threads)Morphological filter: 20% (1 threads)Morphological filter: 21% (1 threads)Morphological filter: 22% (1 threads)Morphological filter: 23% (1 threads)Morphological filter: 24% (1 threads)Morphological filter: 25% (1 threads)Morphological filter: 26% (1 threads)Morphological filter: 27% (1 threads)Morphological filter: 28% (1 threads)Morphological filter: 29% (1 threads)Morphological filter: 30% (1 threads)Morphological filter: 31% (1 threads)Morphological filter: 32% (1 threads)Morphological filter: 33% (1 threads)Morphological filter: 34% (1 threads)Morphological filter: 35% (1 threads)Morphological filter: 36% (1 threads)Morphological filter: 37% (1 threads)Morphological filter: 38% (1 threads)Morphological filter: 39% (1 threads)Morphological filter: 40% (1 threads)Morphological filter: 41% (1 threads)Morphological filter: 42% (1 threads)Morphological filter: 43% (1 threads)Morphological filter: 44% (1 threads)Morphological filter: 45% (1 threads)Morphological filter: 46% (1 threads)Morphological filter: 47% (1 threads)Morphological filter: 48% (1 threads)Morphological filter: 49% (1 threads)Morphological filter: 50% (1 threads)Morphological filter: 51% (1 threads)Morphological filter: 52% (1 threads)Morphological filter: 53% (1 threads)Morphological filter: 54% (1 threads)Morphological filter: 55% (1 threads)Morphological filter: 56% (1 threads)Morphological filter: 57% (1 threads)Morphological filter: 58% (1 threads)Morphological filter: 59% (1 threads)Morphological filter: 60% (1 threads)Morphological filter: 61% (1 threads)Morphological filter: 62% (1 threads)Morphological filter: 63% (1 threads)Morphological filter: 64% (1 threads)Morphological filter: 65% (1 threads)Morphological filter: 66% (1 threads)Morphological filter: 67% (1 threads)Morphological filter: 68% (1 threads)Morphological filter: 69% (1 threads)Morphological filter: 70% (1 threads)Morphological filter: 71% (1 threads)Morphological filter: 72% (1 threads)Morphological filter: 73% (1 threads)Morphological filter: 74% (1 threads)Morphological filter: 75% (1 threads)Morphological filter: 76% (1 threads)Morphological filter: 77% (1 threads)Morphological filter: 78% (1 threads)Morphological filter: 79% (1 threads)Morphological filter: 80% (1 threads)Morphological filter: 81% (1 threads)Morphological filter: 82% (1 threads)Morphological filter: 83% (1 threads)Morphological filter: 84% (1 threads)Morphological filter: 85% (1 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## Original dataset already contains 4520551 ground points. These points were reclassified as 'unclassified' before performing a new ground classification.

## Morphological filter: 7% (1 threads)Morphological filter: 100% (1 threads)
## Original dataset already contains 5554383 ground points. These points were reclassified as 'unclassified' before performing a new ground classification.

dtm <- rasterize_terrain(las_classified, res = 1, algorithm = knnidw())

## Inverse distance weighting: [============--------------------------------------] 25% (1 threads)Inverse distance weighting: [=============-------------------------------------] 26% (1 threads)Inverse distance weighting: [=============-------------------------------------] 27% (1 threads)Inverse distance weighting: [==============------------------------------------] 28% (1 threads)Inverse distance weighting: [==============------------------------------------] 29% (1 threads)Inverse distance weighting: [===============-----------------------------------] 30% (1 threads)Inverse distance weighting: [===============-----------------------------------] 31% (1 threads)Inverse distance weighting: [================----------------------------------] 32% (1 threads)Inverse distance weighting: [================----------------------------------] 33% (1 threads)Inverse distance weighting: [=================---------------------------------] 34% (1 threads)Inverse distance weighting: [=================---------------------------------] 35% (1 threads)Inverse distance weighting: [==================--------------------------------] 36% (1 threads)Inverse distance weighting: [==================--------------------------------] 37% (1 threads)Inverse distance weighting: [===================-------------------------------] 38% (1 threads)Inverse distance weighting: [===================-------------------------------] 39% (1 threads)Inverse distance weighting: [====================------------------------------] 40% (1 threads)Inverse distance weighting: [====================------------------------------] 41% (1 threads)Inverse distance weighting: [=====================-----------------------------] 42% (1 threads)Inverse distance weighting: [=====================-----------------------------] 43% (1 threads)Inverse distance weighting: [======================----------------------------] 44% (1 threads)Inverse distance weighting: [======================----------------------------] 45% (1 threads)Inverse distance weighting: [=======================---------------------------] 46% (1 threads)Inverse distance weighting: [=======================---------------------------] 47% (1 threads)Inverse distance weighting: [========================--------------------------] 48% (1 threads)Inverse distance weighting: [========================--------------------------] 49% (1 threads)Inverse distance weighting: [=========================-------------------------] 50% (1 threads)Inverse distance weighting: [=========================-------------------------] 51% (1 threads)Inverse distance weighting: [==========================------------------------] 52% (1 threads)Inverse distance weighting: [==========================------------------------] 53% (1 threads)Inverse distance weighting: [===========================-----------------------] 54% (1 threads)Inverse distance weighting: [===========================-----------------------] 55% (1 threads)Inverse distance weighting: [============================----------------------] 56% (1 threads)Inverse distance weighting: [============================----------------------] 57% (1 threads)Inverse distance weighting: [=============================---------------------] 58% (1 threads)Inverse distance weighting: [=============================---------------------] 59% (1 threads)Inverse distance weighting: [==============================--------------------] 60% (1 threads)Inverse distance weighting: [==============================--------------------] 61% (1 threads)Inverse distance weighting: [===============================-------------------] 62% (1 threads)Inverse distance weighting: [===============================-------------------] 63% (1 threads)Inverse distance weighting: [================================------------------] 64% (1 threads)Inverse distance weighting: [================================------------------] 65% (1 threads)Inverse distance weighting: [=================================-----------------] 66% (1 threads)Inverse distance weighting: [=================================-----------------] 67% (1 threads)Inverse distance weighting: [==================================----------------] 68% (1 threads)Inverse distance weighting: [==================================----------------] 69% (1 threads)Inverse distance weighting: [===================================---------------] 70% (1 threads)Inverse distance weighting: [===================================---------------] 71% (1 threads)Inverse distance weighting: [====================================--------------] 72% (1 threads)Inverse distance weighting: [====================================--------------] 73% (1 threads)Inverse distance weighting: [=====================================-------------] 74% (1 threads)Inverse distance weighting: [=====================================-------------] 75% (1 threads)Inverse distance weighting: [======================================------------] 76% (1 threads)Inverse distance weighting: [======================================------------] 77% (1 threads)Inverse distance weighting: [=======================================-----------] 78% (1 threads)Inverse distance weighting: [=======================================-----------] 79% (1 threads)Inverse distance weighting: [========================================----------] 80% (1 threads)Inverse distance weighting: [========================================----------] 81% (1 threads)Inverse distance weighting: [=========================================---------] 82% (1 threads)Inverse distance weighting: [=========================================---------] 83% (1 threads)Inverse distance weighting: [==========================================--------] 84% (1 threads)Inverse distance weighting: [==========================================--------] 85% (1 threads)Inverse distance weighting: [===========================================-------] 86% (1 threads)Inverse distance weighting: [===========================================-------] 87% (1 threads)Inverse distance weighting: [============================================------] 88% (1 threads)Inverse distance weighting: [============================================------] 89% (1 threads)Inverse distance weighting: [=============================================-----] 90% (1 threads)Inverse distance weighting: [=============================================-----] 91% (1 threads)Inverse distance weighting: [==============================================----] 92% (1 threads)Inverse distance weighting: [==============================================----] 93% (1 threads)Inverse distance weighting: [===============================================---] 94% (1 threads)Inverse distance weighting: [===============================================---] 95% (1 threads)Inverse distance weighting: [================================================--] 96% (1 threads)Inverse distance weighting: [================================================--] 97% (1 threads)Inverse distance weighting: [=================================================-] 98% (1 threads)Inverse distance weighting: [=================================================-] 99% (1 threads)Inverse distance weighting: [==================================================] 100% (1 threads)

#res=1 establishes grid
#size in the point cloud units or 1 x 1 meters.
## Inverse distance weighting: [==============------------------------------------] 28% (1 threads) 100% (1 threads)

plot(dtm, main = "Digital Terrain Model")

#lets do this a second time!!

las2=readLAS('fernow2.laz')

## Warning: There are 319403 points flagged 'withheld'.

## Warning: Invalid data: 1 points with a return number equal to 0 found.

## Warning: Invalid data: 8 points with a number of returns equal to 0 found.

## Warning: Invalid data: 7 points with a 'return number' greater than the 'number
## of returns'.

las2

## class        : LAS (v1.4 format 7)
## memory       : 200.7 Mb 
## extent       : -8869409, -8868618, 4730048, 4730507 (xmin, xmax, ymin, ymax)
## coord. ref.  : WGS 84 / Pseudo-Mercator 
## area         : 365588 m²
## points       : 2.29 million points
## type         : airborne
## density      : 6.26 points/m²
## density      : 3.44 pulses/m²

chm2 <- rasterize_canopy(las2, res = 1, algorithm = pitfree())
plot(chm2, main = "Canopy Height Model 2")

ws_values <- c(3, 6, 9, 12, 15)
# Sequence of window sizes
th_values <- c(0.1, 0.2, 0.3, 0.4, 0.5)
# Sequence of height thresholds

las_classified2 <- classify_ground(las2, algorithm = pmf(ws = ws_values, th = th_values))

## Morphological filter: 30% (1 threads)Morphological filter: 31% (1 threads)Morphological filter: 32% (1 threads)Morphological filter: 33% (1 threads)Morphological filter: 34% (1 threads)Morphological filter: 35% (1 threads)Morphological filter: 36% (1 threads)Morphological filter: 37% (1 threads)Morphological filter: 38% (1 threads)Morphological filter: 39% (1 threads)Morphological filter: 40% (1 threads)Morphological filter: 41% (1 threads)Morphological filter: 42% (1 threads)Morphological filter: 43% (1 threads)Morphological filter: 44% (1 threads)Morphological filter: 45% (1 threads)Morphological filter: 46% (1 threads)Morphological filter: 47% (1 threads)Morphological filter: 48% (1 threads)Morphological filter: 49% (1 threads)Morphological filter: 50% (1 threads)Morphological filter: 51% (1 threads)Morphological filter: 52% (1 threads)Morphological filter: 53% (1 threads)Morphological filter: 54% (1 threads)Morphological filter: 55% (1 threads)Morphological filter: 56% (1 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## Original dataset already contains 544502 ground points. These points were reclassified as 'unclassified' before performing a new ground classification.

dtm2 <- rasterize_terrain(las_classified2, res = 1, algorithm = knnidw())

plot(dtm2, main = "Digital Terrain Model 2")