Download and Explore NEON Data

This tutorial covers downloading NEON data, using the Data Portal and the neonUtilities R package, as well as basic instruction in beginning to explore and work with the downloaded data, including guidance in navigating data documentation.

NEON data

There are 3 basic categories of NEON data:

1. Remote sensing (AOP) - Data collected by the airborne observation platform, e.g. LIDAR, surface reflectance
2. Observational (OS) - Data collected by a human in the field, or in an analytical laboratory, e.g. beetle identification, foliar isotopes
3. Instrumentation (IS) - Data collected by an automated, streaming sensor, e.g. net radiation, soil carbon dioxide. This category also includes the eddy covariance (EC) data, which are processed and structured in a unique way, distinct from other instrumentation data (see Tutorial for EC data for details).

This lesson covers all three types of data. The download procedures are similar for all types, but data navigation differs significantly by type.

install.packages("devtools")
install.packages("neonUtilities")
install.packages("raster")
devtools::install_github("NEONScience/NEON-geolocation/geoNEON")
install.packages("BiocManager")
BiocManager::install("rhdf5")

Getting started: Download data from the Portal and load packages

Go to the NEON Data Portal and download some data! Almost any IS or OS data product can be used for this section of the tutorial, but we will proceed assuming you've downloaded Photosynthetically Active Radiation (PAR) (DP1.00024.001) data. For optimal results, download three months of data from two sites. The downloaded file should be a zip file named NEON_par.zip. For this tutorial, we will be using PAR data from the Wind Reiver Experimental Forest (WREF) in Washington state.

Now switch over to R and load all the packages installed above.

# load packages
library(neonUtilities)
library(geoNEON)
library(raster)
library(rhdf5)

# Set global option to NOT convert all character variables to factors
options(stringsAsFactors=F)

Stack the downloaded data files: stackByTable()

The stackByTable() function will unzip and join the files in the downloaded zip file.

# Modify the file path to match the path to your zip file
stackByTable("~/Downloads/NEON_par.zip")

In the same directory as the zipped file, you should now have an unzipped folder of the same name. When you open this you will see a new folder called stackedFiles, which should contain five files: PARPAR_30min.csv, PARPAR_1min.csv, sensor_positions.csv, variables.csv, and readme.txt.

We'll look at these files in more detail below.

Download files and load directly to R: loadByProduct()

In the section above, we downloaded a .zip file from the data portal to our downloads folder, then used the stackByTable() function to transform those data into a usable format. However, there is a faster way to load data directly into the R Global Environment using loadByProduct().

The most popular function in neonUtilities is loadByProduct(). This function downloads data from the NEON API, merges the site-by-month files, and loads the resulting data tables into the R environment, assigning each data type to the appropriate R class. This is a popular choice because it ensures you're always working with the latest data, and it ends with ready-to-use tables in R. However, if you use it in a workflow you run repeatedly, keep in mind it will re-download the data every time.

loadByProduct() works on most observational (OS) and sensor (IS) data, but not on surface-atmosphere exchange (SAE) data, remote sensing (AOP) data, and some of the data tables in the microbial data products. For functions that download AOP data, see the byFileAOP() and byTileAOP() sections in this tutorial. For functions that work with SAE data, see the NEON eddy flux data tutorial.

The inputs to loadByProduct() control which data to download and how to manage the processing:

• dpID: the data product ID, e.g. DP1.00002.001
• site: defaults to "all", meaning all sites with available data; can be a vector of 4-letter NEON site codes, e.g. c("HARV","CPER","ABBY").
• startdate and enddate: defaults to NA, meaning all dates with available data; or a date in the form YYYY-MM, e.g. 2017-06. Since NEON data are provided in month packages, finer scale querying is not available. Both start and end date are inclusive.
• package: either basic or expanded data package. Expanded data packages generally include additional information about data quality, such as chemical standards and quality flags. Not every data product has an expanded package; if the expanded package is requested but there isn't one, the basic package will be downloaded.
• avg: defaults to "all", to download all data; or the number of minutes in the averaging interval. See example below; only applicable to IS data.
• savepath: the file path you want to download to; defaults to the working directory.
• check.size: T or F: should the function pause before downloading data and warn you about the size of your download? Defaults to T; if you are using this function within a script or batch process you will want to set it to F.
• nCores: Number of cores to use for parallel processing. Defaults to 1, i.e. no parallelization.
• forceParallel: If the data volume to be processed does not meet minimum requirements to run in parallel, this overrides.

The dpID is the data product identifier of the data you want to download. The DPID can be found on the Explore Data Products page. It will be in the form DP#.#####.###

Here, we'll download woody vegetation structure data from Wind River Experimental Forest (WREF).

veg_str <- loadByProduct(dpID="DP1.10098.001", site="WREF", 
              package="expanded", check.size=T)

The object returned by loadByProduct() is a named list of data frames. To work with each of them, select them from the list using the $ operator.

names(veg_str)
View(veg_str$vst_perplotperyear)

If you prefer to extract each table from the list and work with it as an independent object, you can use the list2env() function:

list2env(veg_str, .GlobalEnv)

If you want to be able to close R and come back to these data without re-downloading, you'll want to save the tables locally. We recommend also saving the variables file, both so you'll have it to refer to, and so you can use it with readTableNEON() (see below).

write.csv(vst_apparentindividual, 
          "~/Downloads/vst_apparentindividual.csv", 
          row.names=F)
write.csv(variables_10098, 
          "~/Downloads/variables_10098.csv", 
          row.names=F)

But, if you want to save files locally and load them into R (or another platform) each time you run a script, instead of downloading from the API every time, you may prefer to use zipsByProduct() and stackByTable() instead of loadByProduct(), as we did in the first section above. Details can be found in our neonUtilities tutorial.

Download remote sensing data: byFileAOP() and byTileAOP()

Remote sensing data files are very large, so downloading them can take a long time. byFileAOP() and byTileAOP() enable easier programmatic downloads, but be aware it can take a very long time to download large amounts of data.

Input options for the AOP functions are:

• dpID: the data product ID, e.g. DP1.00002.001
• site: the 4-letter code of a single site, e.g. HARV
• year: the 4-digit year to download
• savepath: the file path you want to download to; defaults to the working directory
• check.size: T or F: should the function pause before downloading data and warn you about the size of your download? Defaults to T; if you are using this function within a script or batch process you will want to set it to F.
• easting: byTileAOP() only. Vector of easting UTM coordinates whose corresponding tiles you want to download
• northing: byTileAOP() only. Vector of northing UTM coordinates whose corresponding tiles you want to download
• buffer: byTileAOP() only. Size in meters of buffer to include around coordinates when deciding which tiles to download

Here, we'll download one tile of Ecosystem structure (Canopy Height Model) (DP3.30015.001) from WREF in 2017.

byTileAOP("DP3.30015.001", site="WREF", year="2017", check.size = T,
          easting=580000, northing=5075000, savepath="~/Downloads")

In the directory indicated in savepath, you should now have a folder named DP3.30015.001 with several nested subfolders, leading to a tif file of a canopy height model tile. We'll look at this in more detail below.

Navigate data downloads: IS

Let's take a look at the PAR data we downloaded earlier. We'll read in the 30-minute file using the function readTableNEON(), which uses the variables.csv file to assign data types to each column of data:

par30 <- readTableNEON(
  dataFile="~/Downloads/NEON_par/stackedFiles/PARPAR_30min.csv", 
  varFile="~/Downloads/NEON_par/stackedFiles/variables_00024.csv")
View(par30)

The first four columns are added by stackByTable() when it merges files across sites, months, and tower heights. The final column, publicationDate, is the date-time stamp indicating when the data were published. This can be used as an indicator for whether data have been updated since the last time you downloaded them.

The remaining columns are described by the variables file:

parvar <- read.csv("~/Downloads/NEON_par/stackedFiles/variables_00024.csv")
View(parvar)

The variables file shows you the definition and units for each column of data.

Now that we know what we're looking at, let's plot PAR from the top tower level:

plot(PARMean~startDateTime, 
     data=par30[which(par30$verticalPosition=="080"),],
     type="l")

Looks good! The sun comes up and goes down every day, and some days are cloudy. If you want to dig in a little deeper, try plotting PAR from lower tower levels on the same axes to see light attenuation through the canopy.

Navigate data downloads: OS

Let's take a look at the vegetation structure data. OS data products are simple in that the data generally tabular, and data volumes are lower than the other NEON data types, but they are complex in that almost all consist of multiple tables containing information collected at different times in different ways. Complexity in working with OS data involves bringing those data together.

As with the IS data, the variables file can tell you more about the data. OS data also come with a validation file, which contains information about the validation and controlled data entry that were applied to the data:

View(variables_10098)

View(validation_10098)

OS data products each come with a Data Product User Guide, which can be downloaded with the data or accessed from the document library on the Data Portal. Here, we'll use information that can be found in the User Guide about how to (1) calculate stem locations for each tree and (2) how to join the mapping and individual data.

First, use the geoNEON package to calculate stem locations:

names(vst_mappingandtagging) #this object was created using list2env() above
vegmap <- geoNEON::getLocTOS(vst_mappingandtagging, "vst_mappingandtagging")
names(vegmap)

And now merge the mapping data with the individual measurements. individualID is the linking variable, the others are included to avoid having duplicate columns.

veg <- merge(vst_apparentindividual, vegmap, by=c("individualID","namedLocation",
                                  "domainID","siteID","plotID"))

Using the merged data, now we can map the stems in plot 85 (plot chosen at random). Note that the coordinates are in meters but stem diameters are in cm. Furthermore, the symbols() function wants the radii, not the diameters, of the circles, so we divide by 2 to convert diameters to radii after unit conversion.

symbols(veg$adjEasting[which(veg$plotID=="WREF_085")], 
        veg$adjNorthing[which(veg$plotID=="WREF_085")], 
        circles=veg$stemDiameter[which(veg$plotID=="WREF_085")]/100/2, 
        xlab="Easting", ylab="Northing", inches=F)

Navigate data downloads: AOP

To work with AOP data, the best bet is the raster package. It has functionality for most analyses you might want to do.

We'll use it to read in the tile we downloaded:

chm <- raster("~/Downloads/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D16_WREF_DP3_580000_5075000_CHM.tif")

The raster package includes plotting functions:

plot(chm, col=topo.colors(6))