NEON Domain and Site Shapefiles and Maps

This tutorial explores NEON domain- and site-level spatial data, using shapefiles and tabular data provided by the NEON project. The intent of this tutorial is to provide guidance in navigating the data and files provided by NEON, and in creating maps of the domain and site locations. We hope these data and methods will assist users in generating images and figures for publications or presentations related to NEON.

Setup R Environment

We'll need several R packages in this tutorial. Install the packages, if not already installed, and load the libraries for each.

# run once to get the package, and re-run if you need to get updates
install.packages("sp")  # work with spatial data
install.packages("rgdal")  # work with spatial data



# run every time you start a script
library(sp)
library(rgdal)

options(stringsAsFactors=F)

# set working directory to ensure R can find the file we wish to import and where
# we want to save our files. 

wd <- "~/data/" # This will depend on your local environment
setwd(wd)

NEON spatial data files

NEON spatial data are available in a number of different files depending on which spatial data you are interested in. This section covers a variety of spatial data files that can be directly downloaded from the NEONScience.org website instead of being delivered with a downloaded data product.

The goal of this section is to create a map of the entire Observatory that includes the NEON domain boundaries and differentiates between aquatic and terrestrial field sites.

Site locations & domain boundaries

Most NEON spatial data files that are not part of the data downloads are available on the Spatial Data and Maps page as both shapefiles and kmz files.

In addition, latitude, longitude, elevation, and some other basic metadata for each site are available for download from the Field Sites page on the NEON website (linked above the image). In this summary of each field site, the geographic coordinates for each site correspond to the tower location for terrestrial sites and the center of the permitted reach for aquatic sites.

To continue, please download these files from the NEON website:

• NEON Domain Polygons: A polygon shapefile defining NEON's domain boundaries. Like all NEON data the Coordinate Reference system is Geographic WGS 84. Available on the Spatial Data and Maps page.
• Field Site csv: generic locations data for each NEON field site. Available on the Field Sites page.

The Field Site location data is also available as a shapefile and KMZ on the Spatial Data and Maps page. We use the file from the site list to demonstrate alternative ways to work with spatial data.

Map NEON domains

Using the domain shapefile and the field sites list, let's make a map of NEON site locations.

We'll read in the spatial data using the rgdal and sp packages and plot it using base R. First, read in the domain shapefile.

Be sure to move the downloaded and unzipped data files into the working directory you set earlier!

# upload data
neonDomains <- readOGR(paste0(wd,"NEONDomains_0"), layer="NEON_Domains")

The data come as a Large SpatialPolygonsDataFrame. Base R has methods for working with this data type, and will recognize it automatically with the generic plot() function. Let's first plot the domains without the sites.

plot(neonDomains)

The data are currently in a Lat-Long projection. The map will look a little more familiar if we convert it to a Mercator projection. There are many, many map projections possible, and Mercator is distorted in very well-documented ways! Here, we'll use it as a demonstration, but you may want to use a different projection in your own work.

The spTransform() and CRS() functions in the sp package can be used to convert the projection:

neonMercator <- spTransform(neonDomains,
                            CRS("+proj=merc"))
plot(neonMercator)

Map NEON field sites

Now that we have a map of all the NEON domains, let's plot the NEON field site locations on it. To do this, we need to load and explore the field sites data.

# read in the data
neonSites <- read.delim(paste0(wd,"field-sites.csv"), sep=",", header=T)

# view data structure for each variable
str(neonSites)

## 'data.frame':	81 obs. of  26 variables:
##  $ Site.Name                 : chr  "Little Rock Lake" "West St Louis Creek" "Pu'u Maka'ala Natural Area Reserve" "Flint River" ...
##  $ Site.ID                   : chr  "LIRO" "WLOU" "PUUM" "FLNT" ...
##  $ Domain.Name               : chr  "Great Lakes" "Southern Rockies & Colorado Plateau" "Pacific Tropical" "Southeast" ...
##  $ Domain.Number             : chr  "D05" "D13" "D20" "D03" ...
##  $ State                     : chr  "WI" "CO" "HI" "GA" ...
##  $ Nearest.Town              : logi  NA NA NA NA NA NA ...
##  $ Latitude                  : num  46 39.9 19.6 31.2 38.9 ...
##  $ Longitude                 : num  -89.7 -105.9 -155.3 -84.4 -96.4 ...
##  $ Site.Type                 : chr  "Relocatable Aquatic" "Relocatable Aquatic" "Core Terrestrial" "Relocatable Aquatic" ...
##  $ Site.Subtype              : chr  "Lake" "Wadeable Stream" "" "Non-wadeable River" ...
##  $ Site.Host                 : chr  "Wisconsin Department of Natural Resources" "U.S. Forest Service" "Hawaii State Forest Reserve System Department of Land and Natural Resources, Division of Forestry and Wildlife" "Private Owner" ...
##  $ Overview                  : chr  "LIRO is a seepage lake located in Wisconsin and is representative of the Great Lakes ecosystems.\nTotal data pr"| __truncated__ "Total data products planned for this site: 79\n" "NEON's PUUM field site is located in the Pu'u Maka'ala Natural Area Reserve (NAR) on the eastern side of Hawaii"| __truncated__ "Total data products planned for this site: 75\n" ...
##  $ Site.Access               : chr  "Yes" "Yes" "TBD" "No" ...
##  $ Mean.Annual.Temperature   : chr  "4.4C/39.92F" "-0.3C/31.46F" "13C/55.4F" "19.5C/67.1F" ...
##  $ Mean.Annual.Precipitation : chr  "793 mm" "758 mm" "2685 mm" "1307 mm" ...
##  $ Dominant.NLCD.Classes     : chr  "Deciduous Forest, Mixed Forest" "Evergreen Forest" "Evergreen Forest" "Mixed Forest" ...
##  $ Elevation                 : chr  "502 m" "3103 m" "1685 m" "45 m" ...
##  $ Site.Characteristics      : chr  "" "Watershed Size\n5.19 km2\nUSGS HUC: h14010001\nGeology\nSchist, migmatite, and biotitic gneiss.  Paleoproterozoic.\n" "Geology: \nPahoehoe and aa of the Kau Basalt, deposited between 200-750 years ago.\nUSGS HUC: h20010000\nWind D"| __truncated__ "Watershed Size\n29,100 km2\nUSGS HUC: h03130008\nGeology\nUndifferentiated clay, mud, and beach sand. Pleistoce"| __truncated__ ...
##  $ Data.Collection.Types     : chr  "Airborne Remote Sensing Surveys\nRemote sensing surveys of this site collect lidar, spectrometer and high resol"| __truncated__ "Airborne Remote Sensing Surveys\nRemote sensing surveys of this site collect lidar, spectrometer and high resol"| __truncated__ "Airborne Remote Sensing Surveys\nRemote sensing surveys of this field site collect lidar, spectrometer and high"| __truncated__ "Airborne Remote Sensing Surveys\nRemote sensing surveys of this site collect lidar, spectrometer and high resol"| __truncated__ ...
##  $ Adjacent.Research.Networks: chr  "" "" "" "Jones Ecological Research Center\n" ...
##  $ Field.Office              : chr  "Domain 05\n7647 Notre Dame LaneLand O Lakes, WI 54540\nTelephone: 906.842.2119\nContact us\n" "Domain 10/13\n1685 38th Street, Suite 100Boulder, CO 80301\n​Telephone: 720.836.2439\nContact us\n" "Domain 20\n60 Nowelo StreetHilo, Hawaii  96720\nContact us\n" "Domain 03\n4579 NW 6th Street, Unit B-2Gainesville, FL 32609\nTelephone: 352.505.2019\nContact us\n" ...
##  $ Gallery                   : chr  "LIRO D05 Bathymetry Map, LIRO D05 Habitat Map" "WLOU-D13-Stream-Morpology-Map" "PUUM plot establishment, Field ecologists venture out to do field sampling at PUUM Hawaii" "FLNT D03 Bathymetry Map, FLNT D03 Habitat Map" ...
##  $ Thumbnail                 : chr  "" "" "" "" ...
##  $ Overview.Image            : chr  "" "" "" "" ...
##  $ Google.Maps.Embed.Code    : logi  NA NA NA NA NA NA ...
##  $ Related.Content           : logi  NA NA NA NA NA NA ...

Here there is a lot of associated data about the field sites that may be of interest, such as site descriptions and dominant vegetation types. For mapping purposes, we can see that there are both Latitude and Longitude data, so we can plot this data onto our previous map.

plot(neonDomains)
points(neonSites$Latitude~neonSites$Longitude,
       pch=20)

Now we can see all the sites across the Observatory. Note that we've switched back to the Lat-Long projection, which makes it simple to plot the site locations onto the map using their latitude and longitude. To plot them on the Mercator projection, we would need to convert the site latitude and longitude values into a SpatialPoints object, and then perform the same conversion. See sp package documentation if you are interested in doing this.

NEON has both aquatic and terrestrial sites, with important differences between the two. Looking back at the variables in this data set, we can see that Site.Type designates the aquatic and terrestrial sites.

Let's differentiate the site types by adding color to our plot, with terrestrial sites in green and aquatic sites in blue.

# create empty variable
siteCol <- character(nrow(neonSites))

# populate new variable with colors, according to Site.Type
siteCol[grep("Aquatic", neonSites$Site.Type)] <- "blue"
siteCol[grep("Terrestrial", neonSites$Site.Type)] <- "green"

# add color to points on map
plot(neonDomains)
points(neonSites$Latitude~neonSites$Longitude,
       pch=20, col=siteCol)

Now we can see where NEON sites are located within the domains. Note that a significant number of terrestrial and aquatic sites are co-located; in those cases both sites are plotted here, but one color may be superimposed over the other.

Map locations at a specific site

Also available on the Spatial Data and Maps page are shapefiles containing location data at the within-site level.

If you are interested in maps of NEON sampling locations and regions, explore the downloads available for Terrestrial Observation Sampling Locations, Flight Boundaries, and Aquatic Sites Watersheds. These downloads contain shapefiles of these locations, and the terrestrial sampling file also contains spatial data in tabular form.

If you are interested in learning how to work with sampling location data that are provided along with downloads of NEON sensor and observational data, see the Geolocation Data tutorial.