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The re-use of scientific data has the potential to greatly increase communication, collaboration and synthesis within and among disciplines, and thus is fostered, supported and encouraged. Permission to use this dataset is granted to the Data User free of charge subject to the following terms:

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2 ) Redistribution. The data are provided for use by the Data User. The metadata and this license must accompany all copies made and be available to all users of this Data Set. The Data User will not redistribute the original Data Set beyond this collaboration sphere.
3 ) Citation. It is considered a matter of professional ethics to acknowledge the work of other scientists. Thus, the Data User will properly cite the Data Set in any publications or in the metadata of any derived data products that were produced using the Data Set. Citation should take the following general form: Creator, Year of Data Publication, Title of Dataset, Publisher, Dataset identifier. For example:

Shaver, G. 1989. Above ground biomass in acidic tussock tundra experimental site, 1989, Arctic LTER, Toolik, Alaska. Arctic LTER, Marine Biological Lab, Woods Hole, Ma 02543. 1989gsttbm http://ecosystems.mbl.edu/arc/terrest/biomass/index.shtml 

4 ) Acknowledgement. The Data User should acknowledge any institutional support or specific funding awards referenced in the metadata accompanying this dataset in any publications where the Data Set contributed significantly to its content. Acknowledgements should identify the supporting party, the party that received the support, and any identifying information such as grant numbers. For example:

Data sets were provided by the Arctic LTER. This material is based upon work supported by the National Science Foundation under Grants #DEB-981022, 9211775, 8702328; #OPP-9911278, 9911681, 9732281, 9615411, 9615563, 9615942, 9615949, 9400722, 9415411, 9318529; #BSR 9019055, 8806635, 8507493.

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Dataset URLs:METADATA: HTML, Rich Text, XML(EML compliant)
DATA: Comma Delimited, Excel file with Metadata and data, Dataset via LTER Data Poral
Dataset ID:2004-2009gsITEXfluxindices.04
Dataset Title:Vegetation indices calculated for ITEX flux plots in 2004-2009 at Toolik, Alaska; Abisko, Sweden; Svalbard, Norway; Zackenberg, Northeast Greenland; and Barrow, Alaska
Investigator 1: 
First Name:Gus
Last Name:Shaver
Organization:The Ecosystems Center, MBL
Address line 2:7 MBL St.
Address line 3:
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Associate Investigators:
Keywords:canopies, reflectance, spectra, vegetation indices, radiation, irradiance, normalized difference vegetation index, MODIS, Enhanced Vegetation Index, Enhanced Vegetation Index 2, Photochemical Reflectance Index, Water Band Index, chlorophyll, flux, ITEX
Abstract: A spectrophotometer was used to scan the canopy vegetation of ITEX flux plots. The resulting reflectance spectra were used to calculate several vegetation indices of interest (NDVI, EVI, EVI2, PRI, WBI, Chlorophyll Index). Average values of these vegetation indices for each ITEX flux plot are presented here.
For questions about the Metadata and data contact the Investigators.
For information about this web site contact:
Arctic LTER Information Manager
The Ecosystems Center
Marine Biological Lab
7 MBL St
Woods Hole, MA 02543
Phone (508) 289 7496
Email: arc_im@mbl.edu
Online URL: http://ecosystems.mbl.edu/ARC/
DATA FILE INFORMATION:
Data File URL http://metacat.lternet.edu/das/dataAccessServlet?docid=knb-lter-arc.10153&urlTail=terrest/tracegas/data/2004-2009gsITEXfluxindices.csv
Data File Name 2004-2009gsITEXfluxindices
Beginning Date 6/29/2004
End Date 8/17/2009
Number of Data Records 317
Other Files to Reference 2004-2009gsITEXfluxspectra.csv
Availability Status type 1
Quality Control Information Relectance values less than zero or greater than one were replaced with "NaN" before vegetation indices were calculated
Maintenance Description
Log of Changes: Updated Metadata sheet
Version 2: Updated to newer metadata with site sheet. CH March 2013.
Version 3: Corrected eml excel file name wrong extension. JimL 16May13
Version 4: Corrected Distrubution URL. It had xlsfiles in the path. Jim L 19Jun14
 
RESEARCH LOCATION:                  
Location Name Toolik Imnavait Creek Abisko Stepps Abisko Paddus Abisko Latnjajare Adventdalen Svalbard, Norway Zackenberg Greenland Barrow Alaska  
Geographic Description Toolik Lake (68 degrees 38N, 149 degrees 34W) Imnavait Creek (68 degrees 37N, 149 degrees 18W) Alaska, U.S. Stepps (68 degrees 18N, 18 degrees 51E) near Abisko, Sweden. Paddus (68 degrees 19N, 18 degrees 51E) near Abisko, Sweden. Latnjajaure (68 degrees 21N, 18 degrees 30E) near Abisko, Sweden. Adventdalen (78 degrees 13N, 15 degrees 38E) Svalbard, Norway. Zackenberg research area zone 1a (7428 N, 2034 W), Northeast Greenland. Barrow ( 71 18' N, 156 36' W) Alaska, USA.  
Location Bounding Box                  
West Bounding Coordinate                  
East Bounding Coordinate                  
North Bounding Coordinate                  
South Bounding Coordinate                  
OR if single point location                  
Latitude 68.62405 68.6167 68.3 68.3167 68.35 78.2166666666667 74.4666666666667 71.31  
Longitude -149.61058 -149.31 18.85 18.85 18.5 15.6333333333333 -19.4333333333333 -156.6  
Elevation                  
Link to Google Map View on Google Map View on Google Map View on Google Map View on Google Map View on Google Map View on Google Map View on Google Map View on Google Map  
                   
 
TAXONOMIC COVERAGE:
Organisms studied
 
Methods:METHODS:
For each ITEX flux plot, a spectrophotometer (Unispec SC, PP Systems, Amesbury, Massachusetts, USA) was used to scan the canopy vegetation and produce reflectance spectra. Scans with the spectrophotometer have a circular field of view with a diameter of approximately 20cm and were performed in a regular grid across the plot. For most plots, 9 replicate scans were performed.

The Unispec SC instrument generates reflectance spectra by measuring incoming irradiance and radiance reflected by the canopy vegetation. A foreoptic cable (UNI-684) extending from the machine is equipped with a ferrule over which a 100mm hypotube (UNI-688) is placed. This produces a field of view that extends at an angle of 20 degrees from the end of the hypotube. The hypotube is held vertically over the target vegetation during a data scan. The foreoptic cable is connected to a miniature photodiode array detector in the intrument that produces a signals ranging from zero to 65,000 A/D counts for 256 wavebands. These wavebands represent 3.3 nm wide portions of the visible and near infrared spectrum from 310 to 1100 nm. A scan is performed over a period of milliseconds with the exact integration time determined by the user based on current light conditions.

At the time of data collection, a reference scan is performed by positioning the foreoptic cable over a white standard (UNI-420). This reference scan represents the incoming irradiance due to the highly reflective nature of the white standard. A dark scan is also performed by covering the foreoptic with a dark cloth. The raw signal from the dark scan is used by the machine to correct for background noise. Canopy reflectance is calculated for each waveband as follows using the program Multispec (available at http://specnet.info/specnet_toolkit.htm).:

Reflectance= (Icanopy / Ireference)

Icanopy= signal from foreoptic during data scan (radiance reflected from target vegetation)
Ireference = signal from the foreoptic during reflectance scan (incoming irradiance)

In most cases, data was processed and immediately interpolated from 3.3nm wavebands to single nanometer intervals in the Multispec program. For some of the data presented here, the reflectance spectra was originally produced for only for 3.3nm wavebands. This data was later linearly interpolated to produce spectra with 1 nm intervals to allow for compilation into this database.

Vegetation indices were calculated for a ll replicate reflectance spectra and were then averaged per plot to produces the values (and standard deviations) presented here.

Reflectance values equal to or greater than one were replaced with "NaN" before vegetation indices were calculated. Reflectance values equal to or less than one were also replaced with "NaN" before vegetation indices were calculated.

VEGETATION INDEX CALCULATIONS:

For MODIS indices, Spectral bands are defined as follows:

NIR=avg(841nm-876nm)

RED=avg(620nm-670nm)

Blue=avg(459nm-479nm)

Normalized Difference Vegetation Index

NDVI (MODIS) = (NIR-Red)/(NIR+Red)
Enhanced Vegetation Index

EVI (MODIS) =2.5*(NIR-Red)/(NIR+6*Red-7.5*Blue+1)
Enhanced Vegetation Index 2

EVI2 (MODIS) =2.5*((NIR-Red)/(NIR+2.4*Red+1))
Photochemical Reflective Index

PRI (550 Reference) =(550nm-531nm)/(550nm+531nm)
Photochemical Reflective Index

PRI (570 Ref) = (570nm -531nm)/(570nm+531nm)
Water Band Index

WBI= 900nm/970nm
Chlorophyll Index

CHL=(750nm-705nm)/(750nm+705nm)


RESEARCH LOCATIONS:
Imnavait Creek, Alaska 2004: Measurements were made on 15 plots along a topographic sequence of the west facing slope of Imnavait Creek catchment. A light response curve was measured on each plot once in late June/early July and once in August.

Toolik Lake, Alaska 2004. Measurements were made on a total of 20 flux plots in treatment (N +P) and control blocks of the LTER fertilization experiment at Toolik Lake, including the moist acidic tussock, non-acidic tussock, non acidic non-tussock, inlet wet sedge and heath sites. Light curves were measured on each plot once in late June/early July and once in August.

Abisko, Sweden 2004. Measurements were made on 11 plots at the "Stepps" site, each measured once in July and once in August. Measurements were also made on 13 plots at Paddus and 12 plots at Latnjajaure.

Abisko, Sweden 2005. 15 plots were located at the "Stepps" site, measurements were made on 3 occasions through June/ early July and once in mid August.

Svalbard 2005. Measurements were made on 40 plots at various sites in Adventdalen.

Zackenberg 2006. Data were collected on 35 1 x 1m plots and 25 0.3 x 0.3m plots across a range of vegetation types. 13 of the 0.3 x 0.3m plots were located within 1m x 1m plots (identified by plot name with suffix "b1, b2 or b3"), the remainder were independent of the 1 x 1m plots (B14-25).

Toolik, Alaska 2009: Data were collected 9 plots, three in each vegetation type. Vegetation types included moist acidic tundra (MAT), dry heath (HTH) and wet sedge (WSG). Each plot was measured at approximately 2 weeks intervals from mid-June to mid-August 2009.

Barrow, Alaska 2009: Data was collected on 13 plots along a moisture gradient of wet coastal tundra.

FOR MORE INFORMATION CONTACT: Gus Shaver, The Ecosystems Center, Woods Hole, MA, 02543, USA


OTHER DATA FILES TO REFERENCE:
2004-2009gsITEXfluxspectra.csv(full reflectance spectra for ITEX flux plots)
2004-2009gsITEXharvestspectra.csv (full reflectance spectra for all ITEX harvest plots)
2004-2009gsITEXharvestindices.csv(average vegetation indices calculated for all ITEX harvest plots)
2003-2009gsfluxleafN.csv (ITEX flux plot leaf N content)
2003-2009gscurveparameters.csv (ITEX flux plot light response curves fit parameters)
2003-2009gsflux.csv (ITEX flux plot light response curves)
2003-2009gsGPSandveg.csv (ITEX flux plot GPS coordinates and vegetation classifications)
2004-2009gscoverft.csv (ITEX flux plot percent cover by functional type)
2004-2009gscoversp.csv (ITEX flux plot percent cover by plant species)

FORMAT OF DATA FILE: ASCII

Data Table

Variable Name Variable Description Data Type Units DateTime Format Code Information Missing Value Code
YEAR Year scan was made datetime   YYYY    
DATE Date scan was made datetime   DD-MMM-YYYY    
SITE Site where the plot is located text        
GROUP Group plot is associated with, subgroup of site text        
PLOT Unique plot identifier for area where scan was performed text        
TREAT Experimental treatment plot is undergoing text        
PHASE Measurement series (round of measurements within each year) text        
PLOT SIZE Total area of plot encompassed by replicate scans in meters text        
Count of SCAN # Number of scans performed on the plot. Index values were calculated for each scan and then averaged. number dimensionless      
Average of NDVI (MODIS) Average value of calculated NDVI (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of NDVI (MODIS) Standard Deviation of averaged NDVI (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
Average of EVI (MODIS) Average value of calculated EVI (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of EVI (MODIS) Standard Deviation of averaged EVI (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
Average of EVI2 (MODIS) Average value of calculated EVI2 (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of EVI2 (MODIS) Standard Deviation of averaged EVI2 (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
Average of PRI (550 Reference) Average value of calculated PRI, 550 reference (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of PRI (550 Reference) Standard Deviation of averaged PRI, 550 reference (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
Average of PRI (570 Reference) Average value of calculated PRI, 570 reference (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of PRI (570 Reference) Standard Deviation of averaged PRI, 570 reference (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
Average of WBI Average value of calculated WBI (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of WBI Standard Deviation of average WBI (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
Average of CHL Average value of calculated CHL Index (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured
StdDev of CHL Standard Deviation of averaged CHL Index (see METHODS, CALCULATIONS) number dimensionless     #N/A=Missing or Not Measured

Please contact arc_im@mbl.edu with questions, comments, or for technical assistance regarding this web site.