AG真人百家乐官方网站

Skip to main content
NSF NEON, Operated by Battelle

Main navigation

  • AG真人百家乐官方网站 Us
    • Overview
      • Spatial and Temporal Design
      • History
    • Vision and Management
    • Advisory Groups
      • Science, Technology & Education Advisory Committee
      • Technical Working Groups (TWGs)
    • FAQ
    • Contact Us
      • Contact NEON Biorepository
      • Field Offices
    • User Accounts
    • Staff
    • Code of Conduct

    AG真人百家乐官方网站 Us

  • Data & Samples
    • Data Portal
      • Spatial Data & Maps
    • Data Themes
      • Biogeochemistry
      • Ecohydrology
      • Land Cover and Processes
      • Organisms, Populations, and Communities
    • Samples & Specimens
      • Discover and Use NEON Samples
        • Sample Types
        • Sample Repositories
        • Megapit and Distributed Initial Characterization Soil Archives
      • Sample Processing
      • Sample Quality
    • Collection Methods
      • Protocols & Standardized Methods
      • Airborne Remote Sensing
        • Flight Box Design
        • Flight Schedules and Coverage
        • Daily Flight Reports
          • AOP Flight Report Sign Up
        • Camera
        • Imaging Spectrometer
        • Lidar
      • Automated Instruments
        • Site Level Sampling Design
        • Sensor Collection Frequency
        • Instrumented Collection Types
          • Meteorology
          • Phenocams
          • Soil Sensors
          • Ground Water
          • Surface Water
      • Observational Sampling
        • Site Level Sampling Design
        • Sampling Schedules
        • Observation Types
          • Aquatic Organisms
            • Aquatic Microbes
            • Fish
            • Macroinvertebrates & Zooplankton
            • Periphyton, Phytoplankton, and Aquatic Plants
          • Terrestrial Organisms
            • Birds
            • Ground Beetles
            • Mosquitoes
            • Small Mammals
            • Soil Microbes
            • Terrestrial Plants
            • Ticks
          • Hydrology & Geomorphology
            • Discharge
            • Geomorphology
          • Biogeochemistry
          • DNA Sequences
          • Pathogens
          • Sediments
          • Soils
            • Soil Descriptions
        • Optimizing the Observational Sampling Designs
    • Data Notifications
    • Data Guidelines and Policies
      • Acknowledging and Citing NEON
      • Publishing Research Outputs
      • Usage Policies
    • Data Management
      • Data Availability
      • Data Formats and Conventions
      • Data Processing
      • Data Quality
      • Data Product Bundles
      • Data Product Revisions and Releases
        • Release 2021
        • Release 2022
        • Release 2023
        • Release 2024
        • Release-2025
      • NEON and Google
      • Externally Hosted Data

    Data & Samples

  • Field Sites
    • AG真人百家乐官方网站 Field Sites and Domains
    • Explore Field Sites

    Field Sites

  • Impact
    • Observatory Blog
    • Case Studies
    • Papers & Publications
    • Newsroom
      • NEON in the News
      • Newsletter Archive
      • Newsletter Sign Up

    Impact

  • Resources
    • Getting Started with NEON Data & Resources
    • Documents and Communication Resources
      • Papers & Publications
      • Outreach Materials
    • Code Hub
      • Code Resources Guidelines
      • Code Resources Submission
    • Learning Hub
      • Science Videos
      • Tutorials
      • Workshops & Courses
      • Teaching Modules
    • Research Support Services
      • Field Site Coordination
      • Letters of Support
      • Mobile Deployment Platforms
      • Permits and Permissions
      • AOP Flight Campaigns
      • Research Support FAQs
      • Research Support Projects
    • Funding Opportunities

    Resources

  • Get Involved
    • Advisory Groups
      • Science, Technology & Education Advisory Committee
      • Technical Working Groups
    • Upcoming Events
    • NEON Ambassador Program
      • Exploring NEON-Derived Data Products Workshop Series
    • Research and Collaborations
      • Environmental Data Science Innovation and Inclusion Lab
      • Collaboration with DOE BER User Facilities and Programs
      • EFI-NEON Ecological Forecasting Challenge
      • NEON Great Lakes User Group
      • NEON Science Summit
      • NCAR-NEON-Community Collaborations
        • NCAR-NEON Community Steering Committee
    • Community Engagement
      • How Community Feedback Impacts NEON Operations
    • Science Seminars and Data Skills Webinars
      • Past Years
    • Work Opportunities
      • Careers
      • Seasonal Fieldwork
      • Internships
        • Intern Alumni
    • Partners

    Get Involved

  • My Account
  • Search

Search

Learning Hub

  • Science Videos
  • Tutorials
  • Workshops & Courses
  • Teaching Modules

Breadcrumb

  1. Resources
  2. Learning Hub
  3. Tutorials
  4. Raster 00: Intro to Raster Data in R

Tutorial

Raster 00: Intro to Raster Data in R

Authors: Leah A. Wasser, Megan A. Jones, Zack Brym, Kristina Riemer, Jason Williams, Jeff Hollister, Mike Smorul

Last Updated: Sep 4, 2024

In this tutorial, we will review the fundamental principles, packages and metadata/raster attributes that are needed to work with raster data in R. We discuss the three core metadata elements that we need to understand to work with rasters in R: CRS, extent and resolution. We also explore missing and bad data values as stored in a raster and how R handles these elements. Finally, we introduce the GeoTiff file format.

Learning Objectives

After completing this tutorial, you will be able to:

  • Understand what a raster dataset is and its fundamental attributes.
  • Know how to explore raster attributes in R.
  • Be able to import rasters into R using the terra package.
  • Be able to quickly plot a raster file in R.
  • Understand the difference between single- and multi-band rasters.

Things You鈥檒l Need To Complete This Tutorial

You will need the most current version of R and, preferably, RStudio loaded on your computer to complete this tutorial.

Install R Packages

  • terra: install.packages("terra")

  • More on Packages in R 鈥� Adapted from Software Carpentry.

Download Data

Data required for this tutorial will be downloaded using neonUtilities in the lesson.

The LiDAR and imagery data used in this lesson were collected over the National Ecological Observatory Network's Harvard Forest (HARV) field site.

The entire dataset can be accessed from the .


Set Working Directory: This lesson will explain how to set the working directory. You may wish to set your working directory to some other location, depending on how you prefer to organize your data.

An overview of setting the working directory in R can be found here.


  • Read more about the package in R.
  • NEON Data Skills tutorial: Raster Data in R - The Basics
  • NEON Data Skills tutorial: Image Raster Data in R - An Intro

AG真人百家乐官方网站 Raster Data

Raster or "gridded" data are stored as a grid of values which are rendered on a map as pixels. Each pixel value represents an area on the Earth's surface.

Satellite (raster) image with an inset map of a smaller extent. The inset map's structure is further shown as a grid of numeric values represented by colors on a the legend.
Source: National Ecological Observatory Network (NEON)

Raster Data in R

Let's first import a raster dataset into R and explore its metadata. To open rasters in R, we will use the terra package.

library(terra)



# set working directory, you can change this if desired

wd <- "~/data/" 

setwd(wd)

Download LiDAR Raster Data

We can use the neonUtilities function byTileAOP to download a single elevation tiles (DSM and DTM). You can run help(byTileAOP) to see more details on what the various inputs are. For this exercise, we'll specify the UTM Easting and Northing to be (732000, 4713500), which will download the tile with the lower left corner (732000,4713000). By default, the function will check the size total size of the download and ask you whether you wish to proceed (y/n). This file is ~8 MB, so make sure you have enough space on your local drive. You can set check.size=TRUE if you want to check the file size before downloading.

byTileAOP(dpID='DP3.30024.001', # lidar elevation

          site='HARV',

          year='2022',

          easting=732000,

          northing=4713500,

          check.size=FALSE, # set to TRUE or remove if you want to check the size before downloading

          savepath = wd)

This file will be downloaded into a nested subdirectory under the ~/data folder, inside a folder named DP3.30024.001 (the Data Product ID). The file should show up in this location: ~/data/DP3.30024.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/DiscreteLidar/DSMGtif/NEON_D01_HARV_DP3_732000_4713000_DSM.tif.

Open a Raster in R

We can use terra's rast("path-to-raster-here") function to open a raster in R.

Data Tip: VARIABLE NAMES! To improve code readability, file and object names should be used that make it clear what is in the file. The data for this tutorial were collected over from Harvard Forest (HARV), sowe'll use the naming convention of DATATYPE_HARV.

# Load raster into R

dsm_harv_file <- paste0(wd, "DP3.30024.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/DiscreteLidar/DSMGtif/NEON_D01_HARV_DP3_732000_4713000_DSM.tif")

DSM_HARV <- rast(dsm_harv_file)



# View raster structure

DSM_HARV 

## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 732000, 733000, 4713000, 4714000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 18N (EPSG:32618) 
## source      : NEON_D01_HARV_DP3_732000_4713000_DSM.tif 
## name        : NEON_D01_HARV_DP3_732000_4713000_DSM 
## min value   :                               317.91 
## max value   :                               433.94

# plot raster 

plot(DSM_HARV, main="Digital Surface Model - HARV")

Digital surface model showing the elevation of NEON's site Harvard Forest

Types of Data Stored in Raster Format

Raster data can be continuous or categorical. Continuous rasters can have a range of quantitative values. Some examples of continuous rasters include:

  1. Precipitation maps.
  2. Maps of tree height derived from LiDAR data.
  3. Elevation values for a region.

The raster we loaded and plotted earlier was a digital surface model, or a map of the elevation for Harvard Forest derived from the NEON AOP LiDAR sensor. Elevation is represented as a continuous numeric variable in this map. The legend shows the continuous range of values in the data from around 300 to 420 meters.

Some rasters contain categorical data where each pixel represents a discrete class such as a landcover type (e.g., "forest" or "grassland") rather than a continuous value such as elevation or temperature. Some examples of classified maps include:

  1. Landcover/land-use maps.
  2. Tree height maps classified as short, medium, tall trees.
  3. Elevation maps classified as low, medium and high elevation.

Categorical Landcover Map for the United States

Map of the United States showing land cover as categorical data. Each color is a different land cover category. Source:

Categorical Elevation Map of the NEON Harvard Forest Site

The legend of this map shows the colors representing each discrete class.

# add a color map with 5 colors

col=terrain.colors(3)

# add breaks to the colormap (4 breaks = 3 segments)

brk <- c(250,350, 380,500)



# Expand right side of clipping rect to make room for the legend

par(xpd = FALSE,mar=c(5.1, 4.1, 4.1, 4.5))

# DEM with a custom legend

plot(DSM_HARV, 
	col=col, 
	breaks=brk, 
	main="Classified Elevation Map - HARV",
	legend = FALSE
	)



# turn xpd back on to force the legend to fit next to the plot.

par(xpd = TRUE)

# add a legend - but make it appear outside of the plot

legend( 733100, 4713700,
        legend = c("High Elevation", "Middle","Low Elevation"), 
        fill = rev(col))

Classified elevation map of NEON's site Harvard Forest

What is a GeoTIFF??

Raster data can come in many different formats. In this tutorial, we will use the geotiff format which has the extension .tif. A .tif file stores metadata or attributes about the file as embedded tif tags. For instance, your camera might store a tag that describes the make and model of the camera or the date the photo was taken when it saves a .tif. A GeoTIFF is a standard .tif image format with additional spatial (georeferencing) information embedded in the file as tags. These tags can include the following raster metadata:

  1. A Coordinate Reference System (CRS)
  2. Spatial Extent (extent)
  3. Values that represent missing data (NoDataValue)
  4. The resolution of the data

In this tutorial we will discuss all of these metadata tags.

More about the .tif format:

Coordinate Reference System

The Coordinate Reference System or CRS tells R where the raster is located in geographic space. It also tells R what method should be used to "flatten" or project the raster in geographic space.

Four different map projections (Mercator, UTM Zone 11N, U.S. National Atlas Equal Area, and WGS84) of the continental United States demonstrating that each projection produces a map with a different shape and proportions.
Maps of the United States in different projections. Notice the differences in shape associated with each different projection. These differences are a direct result of the calculations used to "flatten" the data onto a 2-dimensional map. Source: M. Corey, opennews.org

What Makes Spatial Data Line Up On A Map?

There are many great resources that describe coordinate reference systems and projections in greater detail (read more, below). For the purposes of this activity, it is important to understand that data from the same location but saved in different projections will not line up in any GIS or other program. Thus, it's important when working with spatial data in a program like R to identify the coordinate reference system applied to the data and retain it throughout data processing and analysis.

Read More:

How Map Projections Can Fool the Eye

Check out this short video, from , highlighting how map projections can make continents seems proportionally larger or smaller than they actually are!

View Raster Coordinate Reference System (CRS) in R

We can view the CRS string associated with our R object using thecrs() method. We can assign this string to an R object, too.

# view crs description

crs(DSM_HARV,describe=TRUE)

##                    name authority  code
## 1 WGS 84 / UTM zone 18N      EPSG 32618
##                                                                                                                                                                                                                                                          area
## 1 Between 78掳W and 72掳W, northern hemisphere between equator and 84掳N, onshore and offshore. Bahamas. Canada - Nunavut; Ontario; Quebec. Colombia. Cuba. Ecuador. Greenland. Haiti. Jamaica. Panama. Turks and Caicos Islands. United States (USA). Venezuela
##            extent
## 1 -78, -72, 84, 0

# assign crs to an object (class) to use for reprojection and other tasks

harvCRS <- crs(DSM_HARV)

The CRS of our DSM_HARV object tells us that our data are in the UTM projection, in zone 18N.

The UTM zones across the continental United States. Source: Chrismurf, wikimedia.org.

The CRS in this case is in a char format. This means that the projection information is strung together as a series of text elements.

We'll focus on the first few components of the CRS, as described above.

  • name: The projection of the dataset. Our data are in WGS84 (World Geodetic System 1984) / UTM (Universal Transverse Mercator) zone 18N. WGS84 is the datum. The UTM projection divides up the world into zones, this element tells you which zone the data are in. Harvard Forest is in Zone 18.
  • authority: EPSG (European Petroleum Survey Group) - organization that maintains a geodetic parameter database with standard codes
  • code: The EPSG code. For more details, see .

Extent

The spatial extent is the geographic area that the raster data covers.

Image of three different spatial extent types: Points extent, lines extent, and polygons extent. Points extent shows three points along the edge of a square object. Lines extent shows a line drawn with three points along the edge of a square object. Polygons extent shows a polygon drawn with three points inside of a square object.
Image Source: National Ecological Observatory Network (NEON)

The spatial extent of an R spatial object represents the geographic "edge" or location that is the furthest north, south, east and west. In other words, extent represents the overall geographic coverage of the spatial object.

You can see the spatial extent using terra::ext:

ext(DSM_HARV)

## SpatExtent : 732000, 733000, 4713000, 4714000 (xmin, xmax, ymin, ymax)

Resolution

A raster has horizontal (x and y) resolution. This resolution represents the area on the ground that each pixel covers. The units for our data are in meters. Given our data resolution is 1 x 1, this means that each pixel represents a 1 x 1 meter area on the ground.

Four images of a raster over the same extent, but at four different resolutions from 8 meters to 1 meter. At 8 meters, the image is really blurry. At 1m, the image is really clear. At 4 and 2 meters, the image is somewhere in the middle.
Source: National Ecological Observatory Network (NEON)

The best way to view resolution units is to look at the coordinate reference system string crs(rast,proj=TRUE). Notice our data contains: +units=m.

crs(DSM_HARV,proj=TRUE)

## [1] "+proj=utm +zone=18 +datum=WGS84 +units=m +no_defs"

Display Raster Min and Max Values

It can be useful to know the minimum or maximum values of a raster dataset. In this case, given we are working with elevation data, these values represent the min/max elevation range at our site.

Raster statistics are often calculated and embedded in a Geotiff for us. However if they weren't already calculated, we can calculate them using the min() or max() functions.

# view the min and max values

min(DSM_HARV)

## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 732000, 733000, 4713000, 4714000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 18N (EPSG:32618) 
## source(s)   : memory
## varname     : NEON_D01_HARV_DP3_732000_4713000_DSM 
## name        :    min 
## min value   : 317.91 
## max value   : 433.94

We can see that the elevation at our site ranges from 317.91 m to 433.94 m.

NoData Values in Rasters

Raster data often has a NoDataValue associated with it. This is a value assigned to pixels where data are missing or no data were collected.

By default the shape of a raster is always square or rectangular. So if we have a dataset that has a shape that isn't square or rectangular, some pixels at the edge of the raster will have NoDataValues. This often happens when the data were collected by an airplane which only flew over some part of a defined region.

Let's take a look at some of the RGB Camera data over HARV, this time downloading a tile at the edge of the flight box.

byTileAOP(dpID='DP3.30010.001',

          site='HARV',

          year='2022',

          easting=737500,

          northing=4701500,

          check.size=FALSE, # set to TRUE or remove if you want to check the size before downloading

          savepath = wd)

This file will be downloaded into a nested subdirectory under the ~/data folder, inside a folder named DP3.30010.001 (the Camera Data Product ID). The file should show up in this location: ~/data/DP3.30010.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/Camera/Mosaic/2022_HARV_7_737000_4701000_image.tif.

In the image below, the pixels that are black have NoDataValues. The camera did not collect data in these areas.

# Use rast function to read in all bands

RGB_HARV <- 
  rast(paste0(wd,"DP3.30010.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/Camera/Mosaic/2022_HARV_7_737000_4701000_image.tif"))



# Create an RGB image from the raster

par(col.axis="white",col.lab="white",tck=0)

plotRGB(RGB_HARV, r = 1, g = 2, b = 3, axes=TRUE)

Colorized raster image with NoDataValues around the edge rendered in black

In the next image, the black edges have been assigned NoDataValue. R doesn't render pixels that contain a specified NoDataValue. R assigns missing data with the NoDataValue as NA.

# reassign cells with 0,0,0 to NA

func <- function(x) {
  x[rowSums(x == 0) == 3, ] <- NA
  x}



newRGBImage <- app(RGB_HARV, func)

## 

|---------|---------|---------|---------|

par(col.axis="white",col.lab="white",tck=0)

# Create an RGB image from the raster stack

plotRGB(newRGBImage, r = 1, g = 2, b = 3, axis=TRUE)

## Warning in plot.window(...): "axis" is not a graphical parameter

## Warning in plot.xy(xy, type, ...): "axis" is not a graphical parameter

## Warning in title(...): "axis" is not a graphical parameter

Colorized raster image with NoDataValues around the edge removed

NoData Value Standard

The assigned NoDataValue varies across disciplines; -9999 is a common value used in both the remote sensing field and the atmospheric fields. It is also the standard used by the National Ecological Observatory Network (NEON).

If we are lucky, our GeoTIFF file has a tag that tells us what is the NoDataValue. If we are less lucky, we can find that information in the raster's metadata. If a NoDataValue was stored in the GeoTIFF tag, when R opens up the raster, it will assign each instance of the value to NA. Values of NA will be ignored by R as demonstrated above.

Bad Data Values in Rasters

Bad data values are different from NoDataValues. Bad data values are values that fall outside of the applicable range of a dataset.

Examples of Bad Data Values:

  • The normalized difference vegetation index (NDVI), which is a measure of greenness, has a valid range of -1 to 1. Any value outside of that range would be considered a "bad" value.
  • Reflectance data in an image should range from 0-1 (or 0-10,000 depending upon how the data are scaled). Thus a value greater than 1 or greater than 10,000 is likely caused by an error in either data collection or processing. These erroneous values can occur, for example, in water vapor absorption bands, which contain invalid data, and are meant to be disregarded.

Find Bad Data Values

Sometimes a raster's metadata will tell us the range of expected values for a raster. Values outside of this range are suspect and we need to consider than when we analyze the data. Sometimes, we need to use some common sense and scientific insight as we examine the data - just as we would for field data to identify questionable values.

Create A Histogram of Raster Values

We can explore the distribution of values contained within our raster using the hist() function which produces a histogram. Histograms are often useful in identifying outliers and bad data values in our raster data.

# view histogram of data

hist(DSM_HARV,
     main="Distribution of Digital Surface Model Values\n NEON Harvard Forest (HARV)",
     xlab="DSM Elevation Value (m)",
     ylab="Frequency",
     col="lightblue")

Histogram showing the distribution of digital surface model values

The distribution of elevation values for our Digital Surface Model (DSM) looks reasonable. It is likely there are no bad data values in this particular raster.

Raster Bands

The Digital Surface Model object (DSM_HARV) that we've been working with is a single band raster. This means that there is only one dataset stored in the raster: surface elevation in meters for one time period.

Left: 3D image of a raster with only one band. Right: 3D image showing four separate layers of a multi band raster.
Source: National Ecological Observatory Network (NEON).

A raster dataset can contain one or more bands. We can use the rast()function to import all bands from a single OR multi-band raster. We can view the number of bands in a raster using thenlyr()` function.

# view number of bands in the Lidar DSM raster

nlyr(DSM_HARV)

## [1] 1

# view number of bands in the RGB Camera raster

nlyr(RGB_HARV)

## [1] 3

As we see from the RGB camera raster, raster data can also be multi-band, meaning one raster file contains data for more than one variable or time period for each cell. By default the terra::rast() function imports all bands of a multi-band raster. You can set lyrs = 1 if you only want to read in the first layer, for example.

Jump to the fourth tutorial in this series for a tutorial on multi-band rasters: Work with Multi-band Rasters: Images in R.

View Raster File Attributes

Remember that a GeoTIFF contains a set of embedded tags that contain metadata about the raster. So far, we've explored raster metadata after importing it in R. However, we can use the describe("path-to-raster-here") function to view raster information (such as metadata) before we open a file in R. Use help(describe) to see other options for exploring the file contents.

# view metadata attributes before opening the file

describe(path.expand(dsm_harv_file),meta=TRUE)

##  [1] "AREA_OR_POINT=Area"                                                                                                                                                                                                                                                                                   
##  [2] "TIFFTAG_ARTIST=Created by the National Ecological Observatory Network (NEON)"                                                                                                                                                                                                                         
##  [3] "TIFFTAG_COPYRIGHT=The National Ecological Observatory Network is a project sponsored by the National Science Foundation and managed under cooperative agreement by Battelle. This material is based in part upon work supported by the National Science Foundation under Grant No. DBI-0752017."      
##  [4] "TIFFTAG_DATETIME=Flown on 2022080312, 2022080412, 2022081213, 2022081413"                                                                                                                                                                                                                             
##  [5] "TIFFTAG_IMAGEDESCRIPTION=Elevation LiDAR - NEON.DP3.30024 acquired at HARV by RIEGL LASER MEASUREMENT SYSTEMS Q780 2220855 as part of 2022-P3C1"                                                                                                                                                      
##  [6] "TIFFTAG_MAXSAMPLEVALUE=434"                                                                                                                                                                                                                                                                           
##  [7] "TIFFTAG_MINSAMPLEVALUE=318"                                                                                                                                                                                                                                                                           
##  [8] "TIFFTAG_RESOLUTIONUNIT=2 (pixels/inch)"                                                                                                                                                                                                                                                               
##  [9] "TIFFTAG_SOFTWARE=Tif file created with a Matlab script (write_gtiff.m) written by Tristan Goulden ([email protected]) with data processed from the following scripts: create_tiles_from_mosaic.m, combine_dtm_dsm_gtif.m, lastools_workflow.csh which implemented LAStools version 210418."
## [10] "TIFFTAG_XRESOLUTION=1"                                                                                                                                                                                                                                                                                
## [11] "TIFFTAG_YRESOLUTION=1"

Specifying options=c("stats") will show some summary statistics:

# view summary statistics before opening the file

describe(path.expand(dsm_harv_file),options=c("stats"))

##  [1] "Driver: GTiff/GeoTIFF"                                                                                                                                                                                                                                                                                  
##  [2] "Files: C:/Users/bhass/Documents/data/DP3.30024.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/DiscreteLidar/DSMGtif/NEON_D01_HARV_DP3_732000_4713000_DSM.tif"                                                                                                                                   
##  [3] "       C:/Users/bhass/Documents/data/DP3.30024.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/DiscreteLidar/DSMGtif/NEON_D01_HARV_DP3_732000_4713000_DSM.tif.aux.xml"                                                                                                                           
##  [4] "Size is 1000, 1000"                                                                                                                                                                                                                                                                                     
##  [5] "Coordinate System is:"                                                                                                                                                                                                                                                                                  
##  [6] "PROJCRS[\"WGS 84 / UTM zone 18N\","                                                                                                                                                                                                                                                                     
##  [7] "    BASEGEOGCRS[\"WGS 84\","                                                                                                                                                                                                                                                                            
##  [8] "        ENSEMBLE[\"World Geodetic System 1984 ensemble\","                                                                                                                                                                                                                                              
##  [9] "            MEMBER[\"World Geodetic System 1984 (Transit)\"],"                                                                                                                                                                                                                                          
## [10] "            MEMBER[\"World Geodetic System 1984 (G730)\"],"                                                                                                                                                                                                                                             
## [11] "            MEMBER[\"World Geodetic System 1984 (G873)\"],"                                                                                                                                                                                                                                             
## [12] "            MEMBER[\"World Geodetic System 1984 (G1150)\"],"                                                                                                                                                                                                                                            
## [13] "            MEMBER[\"World Geodetic System 1984 (G1674)\"],"                                                                                                                                                                                                                                            
## [14] "            MEMBER[\"World Geodetic System 1984 (G1762)\"],"                                                                                                                                                                                                                                            
## [15] "            MEMBER[\"World Geodetic System 1984 (G2139)\"],"                                                                                                                                                                                                                                            
## [16] "            ELLIPSOID[\"WGS 84\",6378137,298.257223563,"                                                                                                                                                                                                                                                
## [17] "                LENGTHUNIT[\"metre\",1]],"                                                                                                                                                                                                                                                              
## [18] "            ENSEMBLEACCURACY[2.0]],"                                                                                                                                                                                                                                                                    
## [19] "        PRIMEM[\"Greenwich\",0,"                                                                                                                                                                                                                                                                        
## [20] "            ANGLEUNIT[\"degree\",0.0174532925199433]],"                                                                                                                                                                                                                                                 
## [21] "        ID[\"EPSG\",4326]],"                                                                                                                                                                                                                                                                            
## [22] "    CONVERSION[\"UTM zone 18N\","                                                                                                                                                                                                                                                                       
## [23] "        METHOD[\"Transverse Mercator\","                                                                                                                                                                                                                                                                
## [24] "            ID[\"EPSG\",9807]],"                                                                                                                                                                                                                                                                        
## [25] "        PARAMETER[\"Latitude of natural origin\",0,"                                                                                                                                                                                                                                                    
## [26] "            ANGLEUNIT[\"degree\",0.0174532925199433],"                                                                                                                                                                                                                                                  
## [27] "            ID[\"EPSG\",8801]],"                                                                                                                                                                                                                                                                        
## [28] "        PARAMETER[\"Longitude of natural origin\",-75,"                                                                                                                                                                                                                                                 
## [29] "            ANGLEUNIT[\"degree\",0.0174532925199433],"                                                                                                                                                                                                                                                  
## [30] "            ID[\"EPSG\",8802]],"                                                                                                                                                                                                                                                                        
## [31] "        PARAMETER[\"Scale factor at natural origin\",0.9996,"                                                                                                                                                                                                                                           
## [32] "            SCALEUNIT[\"unity\",1],"                                                                                                                                                                                                                                                                    
## [33] "            ID[\"EPSG\",8805]],"                                                                                                                                                                                                                                                                        
## [34] "        PARAMETER[\"False easting\",500000,"                                                                                                                                                                                                                                                            
## [35] "            LENGTHUNIT[\"metre\",1],"                                                                                                                                                                                                                                                                   
## [36] "            ID[\"EPSG\",8806]],"                                                                                                                                                                                                                                                                        
## [37] "        PARAMETER[\"False northing\",0,"                                                                                                                                                                                                                                                                
## [38] "            LENGTHUNIT[\"metre\",1],"                                                                                                                                                                                                                                                                   
## [39] "            ID[\"EPSG\",8807]]],"                                                                                                                                                                                                                                                                       
## [40] "    CS[Cartesian,2],"                                                                                                                                                                                                                                                                                   
## [41] "        AXIS[\"(E)\",east,"                                                                                                                                                                                                                                                                             
## [42] "            ORDER[1],"                                                                                                                                                                                                                                                                                  
## [43] "            LENGTHUNIT[\"metre\",1]],"                                                                                                                                                                                                                                                                  
## [44] "        AXIS[\"(N)\",north,"                                                                                                                                                                                                                                                                            
## [45] "            ORDER[2],"                                                                                                                                                                                                                                                                                  
## [46] "            LENGTHUNIT[\"metre\",1]],"                                                                                                                                                                                                                                                                  
## [47] "    USAGE["                                                                                                                                                                                                                                                                                             
## [48] "        SCOPE[\"Navigation and medium accuracy spatial referencing.\"],"                                                                                                                                                                                                                                
## [49] "        AREA[\"Between 78掳W and 72掳W, northern hemisphere between equator and 84掳N, onshore and offshore. Bahamas. Canada - Nunavut; Ontario; Quebec. Colombia. Cuba. Ecuador. Greenland. Haiti. Jamaica. Panama. Turks and Caicos Islands. United States (USA). Venezuela.\"],"                        
## [50] "        BBOX[0,-78,84,-72]],"                                                                                                                                                                                                                                                                           
## [51] "    ID[\"EPSG\",32618]]"                                                                                                                                                                                                                                                                                
## [52] "Data axis to CRS axis mapping: 1,2"                                                                                                                                                                                                                                                                     
## [53] "Origin = (732000.000000000000000,4714000.000000000000000)"                                                                                                                                                                                                                                              
## [54] "Pixel Size = (1.000000000000000,-1.000000000000000)"                                                                                                                                                                                                                                                    
## [55] "Metadata:"                                                                                                                                                                                                                                                                                              
## [56] "  AREA_OR_POINT=Area"                                                                                                                                                                                                                                                                                   
## [57] "  TIFFTAG_ARTIST=Created by the National Ecological Observatory Network (NEON)"                                                                                                                                                                                                                         
## [58] "  TIFFTAG_COPYRIGHT=The National Ecological Observatory Network is a project sponsored by the National Science Foundation and managed under cooperative agreement by Battelle. This material is based in part upon work supported by the National Science Foundation under Grant No. DBI-0752017."      
## [59] "  TIFFTAG_DATETIME=Flown on 2022080312, 2022080412, 2022081213, 2022081413"                                                                                                                                                                                                                             
## [60] "  TIFFTAG_IMAGEDESCRIPTION=Elevation LiDAR - NEON.DP3.30024 acquired at HARV by RIEGL LASER MEASUREMENT SYSTEMS Q780 2220855 as part of 2022-P3C1"                                                                                                                                                      
## [61] "  TIFFTAG_MAXSAMPLEVALUE=434"                                                                                                                                                                                                                                                                           
## [62] "  TIFFTAG_MINSAMPLEVALUE=318"                                                                                                                                                                                                                                                                           
## [63] "  TIFFTAG_RESOLUTIONUNIT=2 (pixels/inch)"                                                                                                                                                                                                                                                               
## [64] "  TIFFTAG_SOFTWARE=Tif file created with a Matlab script (write_gtiff.m) written by Tristan Goulden ([email protected]) with data processed from the following scripts: create_tiles_from_mosaic.m, combine_dtm_dsm_gtif.m, lastools_workflow.csh which implemented LAStools version 210418."
## [65] "  TIFFTAG_XRESOLUTION=1"                                                                                                                                                                                                                                                                                
## [66] "  TIFFTAG_YRESOLUTION=1"                                                                                                                                                                                                                                                                                
## [67] "Image Structure Metadata:"                                                                                                                                                                                                                                                                              
## [68] "  INTERLEAVE=BAND"                                                                                                                                                                                                                                                                                      
## [69] "Corner Coordinates:"                                                                                                                                                                                                                                                                                    
## [70] "Upper Left  (  732000.000, 4714000.000) ( 72d10'28.52\"W, 42d32'36.84\"N)"                                                                                                                                                                                                                              
## [71] "Lower Left  (  732000.000, 4713000.000) ( 72d10'29.98\"W, 42d32' 4.46\"N)"                                                                                                                                                                                                                              
## [72] "Upper Right (  733000.000, 4714000.000) ( 72d 9'44.73\"W, 42d32'35.75\"N)"                                                                                                                                                                                                                              
## [73] "Lower Right (  733000.000, 4713000.000) ( 72d 9'46.20\"W, 42d32' 3.37\"N)"                                                                                                                                                                                                                              
## [74] "Center      (  732500.000, 4713500.000) ( 72d10' 7.36\"W, 42d32'20.11\"N)"                                                                                                                                                                                                                              
## [75] "Band 1 Block=1000x1 Type=Float32, ColorInterp=Gray"                                                                                                                                                                                                                                                     
## [76] "  Min=317.910 Max=433.940 "                                                                                                                                                                                                                                                                             
## [77] "  Minimum=317.910, Maximum=433.940, Mean=358.584, StdDev=17.156"                                                                                                                                                                                                                                        
## [78] "  NoData Value=-9999"                                                                                                                                                                                                                                                                                   
## [79] "  Metadata:"                                                                                                                                                                                                                                                                                            
## [80] "    STATISTICS_MAXIMUM=433.94000244141"                                                                                                                                                                                                                                                                 
## [81] "    STATISTICS_MEAN=358.58371301653"                                                                                                                                                                                                                                                                    
## [82] "    STATISTICS_MINIMUM=317.91000366211"                                                                                                                                                                                                                                                                 
## [83] "    STATISTICS_STDDEV=17.156044149253"                                                                                                                                                                                                                                                                  
## [84] "    STATISTICS_VALID_PERCENT=100"

It can be useful to use describe to explore your file before reading it into R.

Challenge: Explore Raster Metadata

Without using the terra function to read the file into R, determine the following information about the DTM file. This was downloaded at the same time as the DSM file, and as long as you didn't move the data, it should be located here: ~/data/DP3.30024.001/neon-aop-products/2022/FullSite/D01/2022_HARV_7/L3/DiscreteLidar/DTMGtif/NEON_D01_HARV_DP3_732000_4713000_DTM.tif.

  1. Does this file has the same CRS as DSM_HARV?
  2. What is the NoDataValue?
  3. What is resolution of the raster data?
  4. Is the file a multi- or single-band raster?
  5. On what dates was this site flown?

Get Lesson Code

00-Raster-Structure.R

Questions?

If you have questions or comments on this content, please contact us.

Contact Us
NSF NEON, Operated by Battelle

Follow Us:

Join Our Newsletter

Get updates on events, opportunities, and how NEON is being used today.

Subscribe Now

Footer

  • AG真人百家乐官方网站 Us
  • Newsroom
  • Contact Us
  • Terms & Conditions
  • Careers
  • Code of Conduct

Copyright © Battelle, 2025

The National Ecological Observatory Network is a major facility fully funded by the U.S. National Science Foundation.

Any opinions, findings and conclusions or recommendations expressed in this material do not necessarily reflect the views of the U.S. National Science Foundation.