RStoolbox (version 0.1.10)

spectralIndices: Spectral Indices

Description

Calculate a suite of multispectral indices such as NDVI, SAVI etc. in an efficient way.

Usage

spectralIndices(img, blue = NULL, green = NULL, red = NULL, nir = NULL,
  swir1 = NULL, swir2 = NULL, swir3 = NULL, scaleFactor = 1,
  skipRefCheck = FALSE, indices = NULL, index = NULL, maskLayer = NULL,
  maskValue = 1, coefs = list(L = 0.5, G = 2.5, L_evi = 1, C1 = 6, C2 = 7.5,
  s = 1, swir2ccc = NULL, swir2coc = NULL), ...)

Arguments

img

Raster* object. Typically remote sensing imagery, which is to be classified.

blue

Character or integer. Blue band.

green

Character or integer. Green band.

red

Character or integer. Red band.

nir

Character or integer. Near-infrared band (700-1100nm).

swir1

[temporarily deprecated]

swir2

Character or integer. Short-wave-infrared band (1400-1800nm).

swir3

Character or integer. Short-wave-infrared band (2000-2500nm).

scaleFactor

Numeric. Scale factor for the conversion of scaled reflectances to [0,1] value range (applied as reflectance/scaleFactor) Neccesary for calculating EVI/EVI2 with scaled reflectance values.

skipRefCheck

Logical. When EVI/EVI2 is to be calculated there is a rough heuristic check, whether the data are inside [0,1]+/-0.5 (after applying a potential scaleFactor). If there are invalid reflectances, e.g. clouds with reflectance > 1 this check will result in a false positive and skip EVI calculation. Use this argument to skip this check in such cases *iff* you are sure the data and scaleFactor are valid.

indices

Character. One or more spectral indices to calculate (see Details). By default (NULL) all implemented indices given the spectral bands which are provided will be calculated.

index

Character. Alias for indices.

maskLayer

RasterLayer containing a mask, e.g. clouds, for which pixels are set to NA. Alternatively a layername or -number can be provided if the mask is part of img.

maskValue

Integer. Pixel value in maskLayer which should be masked in output, i.e. will be set to NA in all calculated indices.

coefs

List of coefficients (see Details).

...

further arguments such as filename etc. passed to writeRaster

Value

RasterBrick or a RasterLayer if length(indices) == 1

Details

spectralIndices calculates all indices in one go in C++, which is more efficient than calculating each index separately (for large rasters). By default all indices which can be calculated given the specified indices will be calculated. If you don't want all indices, use the indices argument to specify exactly which indices are to be calculated. See the table bellow for index names and required bands.

Index values outside the valid value ranges (if such a range exists) will be set to NA. For example a pixel with NDVI > 1 will be set to NA.

Index	Description	Source	Bands	Formula
CTVI	Corrected Transformed Vegetation Index	Perry1984	red, nir	\((NDVI + 0.5)/sqrt(abs(NDVI + 0.5))\)
DVI	Difference Vegetation Index	Richardson1977	red, nir	\(s * nir - red\)
EVI	Enhanced Vegetation Index	Huete1999	red, nir, blue	\(G * ((nir - red)/(nir + C1 * red - C2 * blue + L_evi))\)
EVI2	Two-band Enhanced Vegetation Index	Jiang 2008	red, nir	\(G * (nir - red)/(nir + 2.4 * red + 1)\)
GEMI	Global Environmental Monitoring Index	Pinty1992	red, nir	\((((nir^2 - red^2) * 2 + (nir * 1.5) + (red * 0.5))/(nir + red + 0.5)) * (1 - ((((nir^2 - red^2) * 2 + (nir * 1.5) + (red * 0.5))/(nir + red + 0.5)) * 0.25)) - ((red - 0.125)/(1 - red))\)
GNDVI	Green Normalised Difference Vegetation Index	Gitelson1998	green, nir	\((nir - green)/(nir + green)\)
MNDWI	Modified Normalised Difference Water Index	Xu2006	green, swir2	\((green - swir2)/(green + swir2)\)
MSAVI	Modified Soil Adjusted Vegetation Index	Qi1994	red, nir	\(nir + 0.5 - (0.5 * sqrt((2 * nir + 1)^2 - 8 * (nir - (2 * red))))\)
MSAVI2	Modified Soil Adjusted Vegetation Index 2	Qi1994	red, nir	\((2 * (nir + 1) - sqrt((2 * nir + 1)^2 - 8 * (nir - red)))/2\)
NBRI	Normalised Burn Ratio Index	Garcia1991	nir, swir3	\((nir - swir3)/(nir + swir3)\)
NDVI	Normalised Difference Vegetation Index	Rouse1974	red, nir	\((nir - red)/(nir + red)\)
NDVIC	Corrected Normalised Difference Vegetation Index	Nemani1993	red, nir, swir2	\((nir - red)/(nir + red) * (1 - ((swir2 - swir2ccc)/(swir2coc - swir2ccc)))\)
NDWI	Normalised Difference Water Index	McFeeters1996	green, nir	\((green - nir)/(green + nir)\)
NDWI2	Normalised Difference Water Index	Gao1996	nir, swir2	\((nir - swir2)/(nir + swir2)\)
NRVI	Normalised Ratio Vegetation Index	Baret1991	red, nir	\((red/nir - 1)/(red/nir + 1)\)
RVI	Ratio Vegetation Index		red, nir	\(red/nir\)
SATVI	Soil Adjusted Total Vegetation Index	Marsett2006	red, swir2, swir3	\((swir2 - red)/(swir2 + red + L) * (1 + L) - (swir3/2)\)
SAVI	Soil Adjusted Vegetation Index	Huete1988	red, nir	\((nir - red) * (1 + L)/(nir + red + L)\)
SLAVI	Specific Leaf Area Vegetation Index	Lymburger2000	red, nir, swir2	\(nir/(red + swir2)\)
SR	Simple Ratio Vegetation Index	Birth1968	red, nir	\(nir/red\)
TVI	Transformed Vegetation Index	Deering1975	red, nir	\(sqrt((nir - red)/(nir + red) + 0.5)\)
TTVI	Thiam's Transformed Vegetation Index	Thiam1997	red, nir	\(sqrt(abs((nir - red)/(nir + red) + 0.5))\)

Some indices require additional parameters, such as the slope of the soil line which are specified via a list to the coefs argument. Although the defaults are sensible values, values like the soil brightnes factor L for SAVI should be adapted depending on the characteristics of the scene. The coefficients are:

Coefficient	Description	Affected Indices
s	slope of the soil line	DVI, WDVI
L_evi, C1, C2, G	various	EVI
L	soil brightness factor	SAVI, SATVI
swir2ccc	minimum swir2 value (completely closed forest canopy)	NDVIC
swir2coc	maximum swir2 value (completely open canopy)	NDVIC

The wavelength band names are defined following Schowengertd 2007, p10. The last column shows exemplarily which Landsat 5 TM bands correspond to which wavelength range definition.

Band	Description	Wavl_min	Wavl_max	Landsat5_Band
vis	visible	400	700	1,2,3
nir	near infra-red	700	1100	4
swir1	short-wave infra-red	1100	1351	-
swir2	short-wave infra-red	1400	1800	5
swir3	short-wave infra-red	2000	2500	7
mir1	mid-wave infra-red	3000	4000	-
mir2	mid-wave infra-red	45000	5000	-
tir1	thermal infra-red	8000	9500	-

Examples

# NOT RUN {
library(ggplot2)
library(raster)
data(lsat)

## Calculate NDVI
ndvi <- spectralIndices(lsat, red = "B3_dn", nir = "B4_dn", indices = "NDVI")
ndvi
ggR(ndvi, geom_raster = TRUE) +
        scale_fill_gradientn(colours = c("black", "white")) 

## Calculate all possible indices, given the provided bands 
## Convert DNs to reflectance (required to calculate EVI and EVI2)
mtlFile  <- system.file("external/landsat/LT52240631988227CUB02_MTL.txt", package="RStoolbox")
lsat_ref <- radCor(lsat, mtlFile, method = "apref")

SI <- spectralIndices(lsat_ref, red = "B3_tre", nir = "B4_tre")
plot(SI)
# }