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The National Ecological Observation Network Daily Isotopic Composition of Environmental Exchanges (NEON-DICEE) Dataset


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Created: Sep 01, 2021 at 12:56 p.m.
Last updated: Feb 03, 2024 at 5:10 p.m.
DOI: 10.4211/hs.e74edc35d45441579d51286ea01b519f
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Sharing Status: Published
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Abstract

The National Ecological Observatory Network (NEON) provides open-access measurements of stable isotope ratios in atmospheric water vapor (δ2H, δ18O) and carbon dioxide (δ13C) at different tower heights, as well as aggregated biweekly precipitation samples (δ2H, δ18O) across the United States. These measurements were used to create the NEON Daily Isotopic Composition of Environmental Exchanges (NEON-DICEE) dataset estimating precipitation (P; δ2H, δ18O), evapotranspiration (ET; δ2H, δ18O), and net ecosystem exchange (NEE; δ13C) isotope ratios. Statistically downscaled precipitation datasets were generated to be consistent with the estimated covariance between isotope ratios and precipitation amounts at daily time scales. Isotope ratios in ET and NEE fluxes were estimated using a mixing-model approach with calibrated NEON tower measurements. NEON-DICEE is publicly available on HydroShare and can be reproduced or modified to fit user specific applications or include additional NEON data records as they become available. The NEON-DICEE dataset can facilitate understanding of terrestrial ecosystem processes through their incorporation into environmental investigations that require daily δ2H, δ18O, and δ13C flux data.

Subject Keywords

Coverage

Spatial

Coordinate System/Geographic Projection:
WGS 84 EPSG:4326
Coordinate Units:
Decimal degrees
North Latitude
71.2889°
East Longitude
-49.6813°
South Latitude
14.5688°
West Longitude
-172.3766°

Temporal

Start Date:
End Date:

Content

README.txt

ReadMe for NEON DICEE Dataset
Date Edited: 04/11/2022 

Associated data paper: [add reference here]

Abstract

This directory contains datasets of and scripts to reproduce the National Ecological Observation Network Daily Isotopic Composition of Environmental Exchanges (NEON-DICEE). 


Description of script folder 

Folder name: 'DICEE Code'
Description: Scripts 'Iso_Precip.R', and 'Estimate_daily_p_flux_iso.py' were used for modeling daily isotopic composition of precipitation found in folder 'P Files'. 

	Name: 'Iso_Precip.R'
	Description: R Script (version 4.1.3) to download raw NEON Isotopes in Precipitation ratios and Precipiation amounts (mm).
		input:
		- dpID addresses for Isotopes in Precipitation (dpID="DP1.00038.001", both d18O and d2H) and Precipitation (dpID="DP1.00006.001")
			- See url's here: https://data.neonscience.org/data-products/DP1.00006.001 and https://data.neonscience.org/data-products/DP1.00038.001 
		- 'siteNamexxx' (Iso or Precip) station ID for the two seperate name lists for Isotopes in Precipitation and Precipiation data. All Isotopes in Precipitation data has Precipiation data.
		- 'Path_xxx' (Iso or Precip) where the user wants the files saved to
		process:
		- Loops through each siteName ID list to download raw NEON data
		- Merges raw data into one csv file per siteName ID
		output:
		- Output csv files coordinate with each siteName ID to organize the raw data

	Name: 'Estimate_daily_flux_iso.py'
	Description: Python Script (version 3.8) to calculate the daily downscaling of Isotopes in Precipitation (d2H and d18O)
		dependencies: 
		- 'precip_iso_downscaling_scripts.py'
		input:
		- downscaling method from 'precip_iso_downscaling_scripts.py' to produce estimates of d2H and d18O isotopes in precipitation
		- 'site_list' for all sites with both Istopes in Precipitation and Precipitation data
		process:
		- runs 100 ensembles of downscaling method for a defined period of interest (whole record of data used)
		- takes the mean and standard deviation (std) of 100 ensembles for d2H and d18O downscaled files
		output:
		- four csv files (two mean and two std for d2H and d18) plus one metadata file of quality flags (see flags at bottom of this document)

Description: Scripts 'mixing_model_d2H.R', 'mixing_model_d18O.R', 'mixing_model_d13C.R', and 'et_nee_flux.py' were used to estimate daily flux of d2H, d18O, and d13C found in folders 'ET Files' and 'NEE Files', respectively.

	Name: 'mixing_model_xxx.R' (where 'xxx' is the stable isotope)
	Description: R-script (version 4.1.3) to calculate the flux for the given stable isotope
		input:
		- 'inpath' where the calibrated hdf5 files for each of the NEON sites are stored.
		- 'radfile' file with downwelling radiance to determine which time-window a datapoint belongs to (daytime or nighttime).
		- 'outpath' where the flux data will be stored
		- 'which_part' variable for the stable isotope (either 'H2', 'O18', or 'C13')
		process:
		- reads in calibrated stable isotope file and applies the Miller-Tans regression to estimate the slope and uncertainty for each time-window.
		output:
		- three csv files with flux and uncertainty for each of the time-windows.

	Name: 'et_nee_flux.py'
	Description: Python script (version 3.8) to create three files: data file, error estimate, and metadata with quality flags of the flux of the given stable isotope.
		input:
		- 'C13_iso_file',' H2_iso_file', and 'O18_iso_file' paths and names of the csv files generated in 'mixing_model_xxx.R' (where 'xxx' is the stable isotope).
		- 'Outpath' where the output will be stored.
		process:
		- reads in flux files and reshapes is to a matrix with dates for rows and sites for columns
		- extracts the error estimate to determine the uncertainty of the flux
		- assigns quality flags based on the criteria described in section on 'ET Files'
			- criteria for the quality flags can be altered within the script
		output:
		- per isotope, nine csv files will be generated (for the three time-windows there will be three files each: data, error, and metadata)		
	


Description of dataset folders

Folder name: 'ET Files'
Description: Contains 18 csv files for daily d2H and d18O flux for three time-windows: 1) alltime (this dataset uses all data points), 2) daytime (this dataset only uses data points where downwelling radiation >= 10 Wm-2), and 3) nighttime (this dataset only uses data points where downwelling radiation < 10 Wm-2).
	For each time-window we have three associated files; 1) the data file, 2) the estimated absolute error in ‰, and 3) the metadata file with the quality flags. 
	
	- data file ('daily_et_flux_xxx_yyy.csv', where 'xxx' is the stable isotope and 'yyy' is the time-window):
	Contains isotopic composition of the daily flux in ‰. Each row in these files represents one calendar date, indicated in the first column. The columns are labeled with the NEON site abbreviation codes. A value of -9999 indicates that no calibrated isotope ratios were available. 

	- error file ('daily_et_flux_xxx_yyy_error.csv', where 'xxx' is the stable isotope and 'yyy' is the time-window):
	Contains standard error of the Miller-Tans regression slope as the uncertainty of the composition of daily flux in ‰.

	- metadata file ('daily_et_flux_xxx_yyy_metadata.csv', where 'xxx' is the stable isotope and 'yyy' is the time-window):
	Contains quality flags for each of the daily flux data points. Interpretation of quality flags:
	
		1	no calibrated isotope ratios were available, and a value of -9999 was used in the data file
		2	low number (n ≤ 5) of calibrated isotope values used to generate the daily flux values
		3	Miller-Tans model r-squared (R2) was below 0.9
		4	inferred isotope value was beyond the 1.5 times IQR of the 25th percentile (Q1 - 1.5 IQR) and 75th percentile (Q3 + 1.5 IQR) of the observation data
		0	good quality, passed criteria described above
		

Folder name: 'NEE Files'
Description: Contains nine csv files in same fashion as folder 'ET Files' but for d13C daily flux to estimate the net ecosystem exchange.


Folder name: 'P Files'
Description: Contains five csv files and one folder for daily precipitation isotopic composition for d2H and d18O.
		
	- data file ('daily_p_xxx_mean.csv' and 'daily_p_xxx_std.csv', where 'xxx' is the stable isotope):
	Contains mean and standard deviation of the modeled time series of isotopic composition corresponding to observed precipitation in ‰. Each row in these files represents one calendar date and the columns are labeled with the NEON site abbreviation codes. Days with no precipitation contain values of -9999.

	- metadata file ('daily_p_metadata.csv')
	Contains quality flags for the data files. Interpretation of quality flags:

		0 	observed precipitation was larger than trace event (≥ 0.25 mm)
		1	no precipitation data on that day
		2	observed precipitation was less than trace event (< 0.25 mm)

	- P_Ensemble folder
	Contains 200 csv files of the the individual runs of the model. 100 runs for d2H and d18O each. These runs are used to create the mean and standard deviation files. 

Related Resources

The content of this resource is derived from NEON (National Ecological Observatory Network). Bundled data products - eddy covariance (DP4.00200.001). https://data.neonscience.org (2021)
The content of this resource is derived from NEON (National Ecological Observatory Network). Precipitation (DP1.00006.001). https://data.neonscience.org (2021)
The content of this resource is derived from NEON (National Ecological Observatory Network). Stable isotopes in precipitation (DP1.00038.001). https://data.neonscience.org (2021)

Credits

Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
E.R. Jackman Alumni and Friends, College of Agricultural Sciences , Oregon State University Beginning Undergraduate Researcher Support Program
United States National Science Foundation MSB-ENSA: Leveraging NEON to Build a Predictive Cross-scale Theory of Ecosystem Transpiration DEB-1802885, DEB-1802880, NSF-1954660

How to Cite

Finkenbiner, C., B. Li, L. Spencer, Z. Butler, M. Haagsma, R. Fiorella, S. Allen, C. Still, D. Noone, W. Anderegg, G. Bowen, S. P. Good (2022). The National Ecological Observation Network Daily Isotopic Composition of Environmental Exchanges (NEON-DICEE) Dataset, HydroShare, https://doi.org/10.4211/hs.e74edc35d45441579d51286ea01b519f

This resource is shared under the Creative Commons Attribution CC BY.

http://creativecommons.org/licenses/by/4.0/
CC-BY

Comments

Catherine Finkenbiner 2 years, 10 months ago

This resource has an associated data descriptor that is currently under review in Scientific Data (https://www.nature.com/sdata/).

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