Vegetation indices calculated for ITEX harvest plots in 2004-2009 at Toolik, Alaska; Abisko, Sweden; Svalbard, Norway; Zackenberg, Northeast Greenland; and Barrow, Alaska

Abstract: 

A spectrophotometer was used to scan the canopy vegetation of ITEX harvest 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 harvest plot are presented here. These plots also had biomass harvests performed and were analyzed for leaf area and nitrogen content (see 2003-2009gsharvest.csv, 2003-2009gsharvestLAI-N.csv).

Project Keywords: 

Data set ID: 

10154

EML revision ID: 

8

Short name: 

2004-2009gsITEXharvestindices
People

Keywords: 

Arctic LTER keywords: 

Dates

Date Range: 

Thursday, July 15, 2004 to Friday, August 14, 2009

Publication Date: 

Wednesday, December 12, 2012

Methods: 

METHODS:
For each ITEX harvest plot, a spectrophotometer (Unispec SC, PP Systems, Amesbury, Massachusetts, USA) was used to scan the canopy vegetation and produce reflectance spectra. The end of the fibre optic was centered above the harvest frame and held at a height above the ground surface that resulted in a view of the vegetation approximately the size of the frame. For most plots, only one replicate scan was 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 instrument that produce 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.

Reflectance spectra were used to calculate the following vegetation indices for each replicate scan performed. Indices from replicate scans were then averaged to produce the values and standard deviations presented here.

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

Toolik, AK, USA 2004
18 - 20x20 cm quadrat harvests were collected around Toolik Lake (16 harvests) and the Imnavait Creek watershed (2 harvests). All Toolik Lake harvests were from fertilized plots at the Toolik Lake Long Term Ecological Research Sites.

Abisko, Sweden 2005
12 - 26cm diameter harvests were taken from within ITEX flux plots.

Zackenberg, Greenland 2006
30 - 26cm diameter harvests

Barrow, AK, USA 2009
23- 20 cm diameter harvests

Toolik, AK, USA 2009
54- 20 cm diameter harvests

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

OTHER DATA FILES TO REFERENCE:
2004-2009gsITEXfluxindices.csv (average vegetation indices calculated for all collection days)
2004-2009gsITEXfluxspectra.csv(full reflectance spectra for all ITEX flux plots)
2004-2009gsITEXharvestspectra.csv(full reflectance spectra for all ITEX harvest plots)
2003-2009gsharvest.csv(Data from biomass harvest of ITEX flux plots)
2003-2009gsharvestLAI-N.csv (LAI and N content of biomass harvest of ITEX harvest plots)

FORMAT OF DATA FILE: ASCII

See Methods

Sites sampled.

Download a comma delimited (csv) or Excel file (includes metadata and data sheets).

Use of the data requires acceptance of the data use policy --> Arctic LTER Data Use Policy

To cite this data set see the citation example on the LTER Network Data Portal page for this data set.

Variables Details

(Variables names are in the first line/row of the CSV file and Excel data sheet.)
YEAR
  • Label: YEAR
  • Definition: Year scan was made
  • Type: Date/time
  • Date format: YYYY
  • Missing values: None specified
DATE
  • Label: DATE
  • Definition: Date scan was made
  • Type: Date/time
  • Date format: dd-mmm-yyyy
  • Missing values: None specified
SITE
  • Label: SITE
  • Definition: Site where the plot is located
  • Type: Nominal
  • Missing values: None specified
GROUP
  • Label: GROUP
  • Definition: Group plot is associated with, subset of site
  • Type: Nominal
  • Missing values: None specified
PLOT
  • Label: PLOT
  • Definition: Plot identifier for area where scan was performed
  • Type: Nominal
  • Missing values: None specified
TREAT
  • Label: TREAT
  • Definition: Experimental treatment plot is undergoing
  • Type: Nominal
  • Missing values: None specified
VEGETATION
  • Label: VEGETATION
  • Definition: General description of canopy vegetation
  • Type: Nominal
  • Missing values: None specified
PLOT SIZE
  • Label: PLOT SIZE
  • Definition: Area of harvest plot
  • Type: Nominal
  • Missing values: None specified
Count of REP
  • Label: Count of REP
  • Definition: Number of replicate scans performed on the plot. Index values were calculated for each scan and then averaged.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
Average of NDVI (MODIS)
  • Label: Average of NDVI (MODIS)
  • Definition: Average value of calculated NDVI (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of NDVI (MODIS)
  • Label: StdDev of NDVI (MODIS)
  • Definition: Standard Deviation of averaged NDVI (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
Average of EVI (MODIS)
  • Label: Average of EVI (MODIS)
  • Definition: Average value of calculated EVI (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of EVI (MODIS)
  • Label: StdDev of EVI (MODIS)
  • Definition: Standard Deviation of averaged EVI (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
Average of EVI2 (MODIS)
  • Label: Average of EVI2 (MODIS)
  • Definition: Average value of calculated EVI2 (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of EVI2 (MODIS)
  • Label: StdDev of EVI2 (MODIS)
  • Definition: Standard Deviation of averaged EVI2 (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
Average of PRI (550 Reference)
  • Label: Average of PRI (550 Reference)
  • Definition: Average value of calculated PRI, 550 reference (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of PRI (550 Reference)
  • Label: StdDev of PRI (550 Reference)
  • Definition: Standard Deviation of averaged PRI, 550 reference (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
Average of PRI (570 Reference)
  • Label: Average of PRI (570 Reference)
  • Definition: Average value of calculated PRI, 570 reference (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of PRI (570 Reference)
  • Label: StdDev of PRI (570 Reference)
  • Definition: Standard Deviation of averaged PRI, 570 reference (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
Average of WBI
  • Label: Average of WBI
  • Definition: Average value of calculated WBI (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of WBI
  • Label: StdDev of WBI
  • Definition: Standard Deviation of average WBI (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
Average of CHL
  • Label: Average of CHL
  • Definition: Average value of calculated CHL (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured
StdDev of CHL
  • Label: StdDev of CHL
  • Definition: Standard Deviation of averaged CHL (see METHODS, CALCULATIONS)
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values:
    • #N/A = Missing or Not Measured