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

```
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), ...)
```

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

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

`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 | - |

```
# 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)
# }
```

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