vegindex: vegindex

In hsdar: Manage, Analyse and Simulate Hyperspectral Data

vegindex

Description

Function calculates a variety of hyperspectral vegetation indices

Usage

vegindex(x, index, returnHCR = "auto", L = 0.5, 
         weighted = TRUE, ...)

Arguments

x	Object of class Speclib
index	Character string. Name or definition of index or vector with names/definitions of indices to calculate. See Details section for further information.
returnHCR	If TRUE, the result will be of class HyperSpecRaster, otherwise it is a data frame. If "auto", the class is automatically determined by passed Speclib.
L	Factor for SAVI index. Unused for other indices.
weighted	Logical indicating if reflectance values should be interpolated to fit wavelength position. If FALSE the reflectance values of nearest neighbour to passed position are returned. See get_reflectance for further explanation.
...	Further arguments passed to derivative functions. Only used for indices requiring derivations.

Details

Index must be a charater vector containing pre-defined indices (selected by their name) or self defined indices or any combination of pre- and self-defined indices.

Pre-defined indices

The following indices are available:

Name	Formula	Reference*
Boochs	D_{703}	Boochs et al. (1990)
Boochs2	D_{720}	Boochs et al. (1990)
CAI	0.5*(R_{2000}+R_{2200})-R_{2100}	Nagler et al. (2003)
CARI	a = (R_{700}-R_{550}) / 150	Kim et al. (1994)
	b = R_{550}-(a*550)
	R_{700}*abs(a*670+R_{670}+b)/R_{670}*
	(a^2+1)^{0.5}
Carter	R_{695}/R_{420}	Carter (1994)
Carter2	R_{695}/R_{760}	Carter (1994)
Carter3	R_{605}/R_{760}	Carter (1994)
Carter4	R_{710}/R_{760}	Carter (1994)
Carter5	R_{695}/R_{670}	Carter (1994)
Carter6	R_{550}	Carter (1994)
CI	R_{675}*R_{690}/R_{683}^2	Zarco-Tejada et al.
		(2003)
CI2	R_{760}/R_{700}-1	Gitelson et al. (2003)
ClAInt	\int_{600 nm}^{735 nm} R	Oppelt and Mauser
		(2004)
CRI1	1/R_{515}-1/R_{550}	Gitelson et al. (2003)
CRI2	1/R_{515}-1/R_{770}	Gitelson et al. (2003)
CRI3	1/R_{515}-1/R_{550}*R_{770}	Gitelson et al. (2003)
CRI4	1/R_{515}-1/R_{700}*R_{770}	Gitelson et al. (2003)
D1	D_{730}/D_{706}	Zarco-Tejada et al.
		(2003)
D2	D_{705}/D_{722}	Zarco-Tejada et al.
		(2003)
Datt	(R_{850}-R_{710})/(R_{850}-R_{680})	Datt (1999b)
Datt2	R_{850}/R_{710}	Datt (1999b)
Datt3	D_{754}/D_{704}	Datt (1999b)
Datt4	R_{672}/(R_{550}*R_{708})	Datt (1998)
Datt5	R_{672}/R_{550}	Datt (1998)
Datt6	(R_{860})/(R_{550}*R_{708})	Datt (1998)
Datt7	(R_{860} - R_{2218})/(R_{860} - R_{1928})	Datt (1999a)
Datt8	(R_{860} - R_{1788})/(R_{860} - R_{1928})	Datt (1999a)
DD	(R_{749}-R_{720})-(R_{701}-R_{672})	le Maire et al. (2004)
DDn	2*(R_{710}-R_{660}-R_{760})	le Maire et al. (2008)
DPI	(D_{688}*D_{710})/D_{697}^2	Zarco-Tejada et al.
		(2003)
DWSI1	R_{800}/R_{1660}	Apan et al. (2004)
DWSI2	R_{1660}/R_{550}	Apan et al. (2004)
DWSI3	R_{1660}/R_{680}	Apan et al. (2004)
DWSI4	R_{550}/R_{680}	Apan et al. (2004)
DWSI5	(R_{800} + R_{550})/(R_{1660} + R_{680})	Apan et al. (2004)
EGFN	(\max(D_{650:750})-\max(D_{500:550}))/	Penuelas et al.
	(\max(D_{650:750})+\max(D_{500:550}))	(1994)
EGFR	\max(D_{650:750})/\max(D_{500:550})	Penuelas et al. (1994)
EVI	2.5*((R_{800}-R_{670})/	Huete et al. (1997)
	(R_{800}-(6*R_{670})-(7.5*R_{475})+1))
GDVI	(R_{800}^n-R_{680}^n) / (R_{800}^n+R_{680}^n)**	Wu (2014)
GI	R_{554}/R_{677}	Smith et al. (1995)
Gitelson	1/R_{700}	Gitelson et al. (1999)
Gitelson2	(R_{750}-R_{800}/R_{695}-R_{740})-1	Gitelson et al. (2003)
GMI1	R_{750}/R_{550}	Gitelson et al. (2003)
GMI2	R_{750}/R_{700}	Gitelson et al. (2003)
Green NDVI	(R_{800}-R_{550})/(R_{800}+R_{550})	Gitelson et al. (1996)
LWVI_1	(R_{1094}-R_{983}) / (R_{1094}+R_{983})	Galvao et al. (2005)
LWVI_2	(R_{1094}-R_{1205}) / (R_{1094}+R_{1205})	Galvao et al. (2005)
Maccioni	(R_{780}-R_{710})/(R_{780}-R_{680})	Maccioni et al. (2001)
MCARI	((R_{700}-R_{670})-0.2*(R_{700}-R_{550}))*	Daughtry et al. (2000)
	(R_{700}/R_{670})
MCARI/OSAVI		Daughtry et al. (2000)
MCARI2	((R_{750}-R_{705})-0.2*(R_{750}-R_{550}))*	Wu et al. (2008)
	(R_{750}/R_{705})
MCARI2/OSAVI2		Wu et al. (2008)
mND705	(R_{750}-R_{705})/(R_{750}+R_{705}-2*R_{445})	Sims and Gamon (2002)
mNDVI	(R_{800}-R_{680})/(R_{800}+R_{680}-2*R_{445})	Sims and Gamon (2002)
MPRI	(R_{515}-R_{530})/(R_{515}+R_{530})	Hernandez-Clemente et al.
		(2011)
mREIP	Red-edge inflection point using Gaussain fit	Miller et al. (1990)
MSAVI	0.5*(2*R_{800}+1-	Qi et al. (1994)
	((2*R_{800}+1)^2-8*(R_{800}-R_{670}))^{0.5})
MSI	R_{1600}/ R_{817}	Hunt and Rock (1989)
mSR	(R_{800}-R_{445})/(R_{680}-R_{445})	Sims and Gamon (2002)
mSR2	(R_{750}/R_{705})-1/(R_{750}/R_{705}+1)^{0.5}	Chen (1996)
mSR705	(R_{750}-R_{445})/(R_{705}-R_{445})	Sims and Gamon (2002)
MTCI	(R_{754}-R_{709})/(R_{709}-R_{681})	Dash and Curran (2004)
MTVI	1.2*(1.2*(R_{800}-R_{550})-	Haboudane et al.
	2.5* (R_{670}-R_{550}))	(2004)
NDLI	(log(1/R_{1754}) - log(1/R_{1680}))/	Serrano et al. (2002)
	(log(1/R_{1754}) + log(1/R_{1680}))
NDNI	(log(1/R_{1510}) - log(1/R_{1680}))/	Serrano et al. (2002)
	(log(1/R_{1510}) + log(1/R_{1680}))
NDVI	(R_{800}-R_{680}) / (R_{800}+R_{680})	Tucker (1979)
NDVI2	(R_{750}-R_{705})/(R_{750}+R_{705})	Gitelson and Merzlyak
		(1994)
NDVI3	(R_{682}-R_{553})/(R_{682}+R_{553})	Gandia et al. (2004)
NDWI	(R_{860}-R_{1240}) / (R_{860}+R_{1240})	Gao (1996)
NPCI	(R_{680}-R_{430})/(R_{680}+R_{430})	Penuelas et al. (1994)
OSAVI	(1+0.16)*(R_{800}-R_{670})/	Rondeaux et al.
	(R_{800}+R_{670}+0.16)	(1996)
OSAVI2	(1+0.16)*(R_{750}-R_{705})/	Wu et al. (2008)
	(R_{750}+R_{705}+0.16)
PARS	R_{746}/R_{513}	Chappelle et al. (1992)
PRI	(R_{531}-R_{570})/(R_{531}+R_{570})	Gamon et al. (1992)
PRI_norm	PRI*(-1)/(RDVI*R_{700}/R_{670})	Zarco-Tejada et al.
		(2013)
PRI*CI2	PRI*CI2	Garrity et al. (2011)
PSRI	(R_{678}-R_{500}/R_{750}	Merzlyak et al. (1999)
PSSR	R_{800}/R_{635}	Blackburn (1998)
PSND	(R_{800}-R_{470})/(R_{800}-R_{470})	Blackburn (1998)
PWI	R_{900}/R_{970}	Penuelas et al. (1997)
RDVI	(R_{800}-R_{670})/√{R_{800}+R_{670}}	Roujean and Breon (1995)
REP_LE	Red-edge position through linear extrapolation.	Cho and Skidmore (2006)
REP_Li	R_{re}=(R_{670}+R_{780})/2	Guyot and Baret (1988)
	700 + 40*((R_{re} -R_{700})/(R_{740}-R_{700}))
SAVI	(1+L)*(R_{800}-R_{670})/(R_{800}+R_{670}+L)	Huete (1988)
SIPI	(R_{800}-R_{445})/(R_{800}-R_{680})	Penuelas et al. (1995),
		Penuelas et al. (1995a)
SPVI	0.4*3.7*(R_{800}-R_{670})-1.2*	Vincini et al. (2006)
	((R_{530}-R_{670})^2)^{0.5}
SR	R_{800}/R_{680}	Jordan (1969)
SR1	R_{750}/R_{700}	Gitelson and Merzlyak
		(1997)
SR2	R_{752}/R_{690}	Gitelson and Merzlyak
		(1997)
SR3	R_{750}/R_{550}	Gitelson and Merzlyak
		(1997)
SR4	R_{700}/R_{670}	McMurtrey et al. (1994)
SR5	R_{675}/R_{700}	Chappelle et al. (1992)
SR6	R_{750}/R_{710}	Zarco-Tejada and Miller
		(1999)
SR7	R_{440}/R_{690}	Lichtenthaler et al. (1996)
SR8	R_{515}/R_{550}	Hernandez-Clemente et al.
		(2012)
SRPI	R_{430}/R_{680}	Penuelas et al. (1995)
SRWI	R_{850}/R_{1240}	Zarco-Tejada et al.
		(2003)
Sum_Dr1	∑_{i=626}^{795} D1_i	Elvidge and Chen (1995)
Sum_Dr2	∑_{i=680}^{780} D1_i	Filella and Penuelas
		(1994)
SWIR FI	R_{2133}^2/(R_{2225} \cdot R_{2209}^3	Levin et al. (2007)
SWIR LI	3.87 \cdot (R_{2210} - R_{2090}) -	Lobell et al. (2001)
	27.51 \cdot (R_{2280} - R_{2090}) - 0.2
SWIR SI	-41.59 \cdot (R_{2210} - R_{2090}) +	Lobell et al. (2001)
	1.24 \cdot (R_{2280} - R_{2090}) + 0.64
SWIR VI	37.72 \cdot (R_{2210} - R_{2090}) +	Lobell et al. (2001)
	26.27 \cdot (R_{2280} - R_{2090}) + 0.57
TCARI	3*((R_{700}-R_{670})-0.2*R_{700}-R_{550})*	Haboudane et al. (2002)
	(R_{700}/R_{670}))
TCARI/OSAVI	TCARI/OSAVI	Haboudane et al. (2002)
TCARI2	3*((R_{750}-R_{705})-0.2*(R_{750}-R_{550})*	Wu et al. (2008)
	(R_{750}/R_{705}))
TCARI2/OSAVI2	TCARI2/OSAVI2	Wu et al. (2008)
TGI	-0.5 (190 (R_{670} - R_{550} ) - 120 (R_{670} - R_{480} ))	Hunt et al. (2013)
TVI	0.5*(120*(R_{750}-R_{550})-	Broge and Leblanc
	200*(R_{670}-R_{550}))	(2000)
Vogelmann	R_{740}/R_{720}	Vogelmann et al. (1993)
Vogelmann2	(R_{734}-R_{747})/(R_{715}+R_{726})	Vogelmann et al. (1993)
Vogelmann3	D_{715}/D_{705}	Vogelmann et al. (1993)
Vogelmann4	(R_{734}-R_{747})/(R_{715}+R_{720})	Vogelmann et al. (1993)

* For references please type: hsdardocs("References.pdf").
** For GDVI n must be defined appending an underscore and the intended exponent to the index name. E.g., for n = 2, the correct index name would be "GDVI_2". Note that GDVI-indices with n = 2, 3, 4 will be derived if all available indices are calculated.

Self-defining indices

Self-defined indices may be passed using the following syntax:

• Rxxx: Reflectance at wavelength 'xxx'. Note that R must be upper case.

• Dxxx: First derivation of reflectance values at wavelength 'xxx'. Note that D must be upper case.

• Sxxx: Second derivation of reflectance values at wavelength 'xxx'. Note that S must be upper case.

Using this syntax, complex indices can be easily defined. Note that the entire definition of the index must be passed as one character string. Consequently, the NDVI would be written as
"(R800-R680)/(R800+R680)".

Value

A vector containing indices values. If index is a vector with length > 1, a data frame with ncol = length(index) and nrow = number of spectra in x is returned.

If function is called without any arguments, return value will be a vector containing all available indices in alphabetical order.

Author(s)

Hanna Meyer and Lukas Lehnert

References

See hsdardocs("References.pdf")

See Also

soilindex, derivative.speclib, rededge, get_reflectance

Examples

## Example calculating NDVI
data(spectral_data)
ndvi <- vegindex(spectral_data, "NDVI")


## Example calculating all available indices
## Get available indices
avl <- vegindex()
vi <- vegindex(spectral_data, avl)

## Self-defined indices
## NDVI
vi <- vegindex(spectral_data, "(R800-R680)/(R800+R680)")
## NDNI
vi <- vegindex(spectral_data, 
               "(log(1/R1510) - log(1/R1680))/(log(1/R1510) + log(1/R1680))")
## D1
vi <- vegindex(spectral_data, "D730/D706")
## Example using second derivative spectra
vi <- vegindex(spectral_data, "(S930-S710)/(S930+S710)")

hsdar documentation built on March 18, 2022, 6:35 p.m.