# Manage, Analyse and Simulate Hyperspectral Data

## Documentation for package ‘hsdar’ version 1.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N P Q R S T U V W misc

hsdar-package | Manage, analyse and simulate hyperspectral data in R

## -- A --

addcp | Manually add fix point to continuum line
apply-method | Apply function for class DistMat3D
apply-method | Apply function for class Speclib
apply.DistMat3D | Apply function for class DistMat3D
apply.Speclib | Apply function for class Speclib
as.array-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
as.data.frame-method | Methods for * Nri-class
as.matrix-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
as.matrix-method | Methods for * Nri-class

## -- B --

bandnames | Handling names of bands
bandnames<- | Handling names of bands
bdri | Band depth ratio indices
blockSize-method | Functions for processing large hyperspectral raster files
Boruta-method | Methods for Function 'Boruta'
Boruta-methods | Methods for Function 'Boruta'
brick-method | Handle hyperspectral cubes using raster package (deprecated)
brick-method | Rasterbased methods for spectra

## -- C --

cancer_spectra | Hyperspectral samples
cellFromCol-method | Handling spectra
cellFromLine-method | Handling spectra
cellFromPolygon-method | Handling spectra
cellFromRow-method | Handling spectra
cellFromRowCol-method | Handling spectra
cellFromRowColCombine-method | Handling spectra
cellFromXY-method | Handling spectra
checkhull | Check continuum line
Clman | * Clman class
Clman-class | * Clman class
colFromX-method | Handling spectra
cor.test-method | Test for association/correlation between nri values and vector of samples
cor.test.nri | Test for association/correlation between nri values and vector of samples
createDataPartition-method | Methods for Function 'createDataPartition'
createDataPartition-methods | Methods for Function 'createDataPartition'
createFolds-method | Methods for Function 'createFolds' and 'createMultiFolds'
createFolds-methods | Methods for Function 'createFolds' and 'createMultiFolds'
createMultiFolds-method | Methods for Function 'createFolds' and 'createMultiFolds'
createMultiFolds-methods | Methods for Function 'createFolds' and 'createMultiFolds'
createResample-method | Methods for Function 'createResample'
createResample-methods | Methods for Function 'createResample'
cubePlot | cubePlot
cut_specfeat | Cut absorption features

## -- D --

deletecp | Delete fix point
derivative.speclib | Derivation
dim-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
dim-method | Dimensions of Speclib
dim-method | Methods for * Nri-class
dim.speclib | Dimensions of Speclib
dist.speclib | Distance between spectra
distMat3D | Methods to create, manipulate and query objects of class 'DistMat3D'.
DistMat3D-class | * DistMat3D class
distMat3D-method | Methods to create, manipulate and query objects of class 'DistMat3D'.

## -- E --

extract-method | Rasterbased methods for spectra

## -- F --

featurePlot-method | Methods for Function 'featurePlot'
featurePlot-methods | Methods for Function 'featurePlot'
feature_properties | Calculation of properties of features
fourCellsFromXY-method | Handling spectra
fwhm | Handling wavelength and fwhm
fwhm-method | Handling wavelength and fwhm
fwhm<- | Handling wavelength and fwhm
fwhm<--method | Handling wavelength and fwhm

## -- G --

gafs-method | Methods for Function 'gafs'
gafs-methods | Methods for Function 'gafs'
get.gaussian.response | Gaussian response function
get.sensor.characteristics | Sensor characteristics
getcp | Get fix points
getFiniteNri | Methods for * Nri-class
getNRI | Return nri-values
getValuesBlock,HyperSpecRaster | Handle hyperspectral cubes using raster package (deprecated)
getValuesBlock-method | Handle hyperspectral cubes using raster package (deprecated)
getValuesBlock-method | Functions for processing large hyperspectral raster files
get_Boruta | Methods for Function 'Boruta'
get_gafs | Methods for Function 'gafs'
get_landsat4_response | Spectral resampling
get_landsat5_response | Spectral resampling
get_landsat7_response | Spectral resampling
get_landsat8_response | Spectral resampling
get_quickbird_response | Spectral resampling
get_reflectance | Get reflectance values
get_rfe | Methods for Function 'rfe'
get_safs | Methods for Function 'safs'
get_sbf | Methods for Function 'sbf'
get_sentinel2_response | Spectral resampling
get_wv2_4_response | Spectral resampling
get_wv2_8_response | Spectral resampling
glm.nri | (Generalised) Linear models from normalised ratio indices

## -- H --

hsdar | Manage, analyse and simulate hyperspectral data in R
hsdardocs | Load additional documents
hsdar_parallel | hsdar_parallel
HyperSpecRaster | Handle hyperspectral cubes using raster package (deprecated)
HyperSpecRaster-class | HyperSpecRaster* class (deprecated)
HyperSpecRaster-method | Handle hyperspectral cubes using raster package (deprecated)

## -- I --

idSpeclib | Handling IDs of spectra
idSpeclib<- | Handling IDs of spectra
initialize-method | Methods to create, manipulate and query objects of class 'Clman'.
initialize-method | Handling supplementary information (SI) of spectra
initialize-method | Methods to create objects of class Speclib
interpolate.mask | Mask spectra
is.speclib | Methods to create objects of class Speclib

## -- L --

Landsat_4_response | Spectral resampling
Landsat_5_response | Spectral resampling
Landsat_7_response | Spectral resampling
Landsat_8_response | Spectral resampling
legendSpeclib | Plot speclib
list.available.sensors | Sensor characteristics
lm.nri | (Generalised) Linear models from normalised ratio indices

## -- M --

makehull | Re-calculate hull
mark_nri_best_performance | Best performing model(s) with NRI
mask | Mask spectra
mask-method | Mask spectra
mask<- | Mask spectra
mask<--method | Mask spectra
maskSpeclib | Mask spectra
meanfilter | Apply mean filter
merge-method | Merge speclibs

## -- N --

names-method | Handling supplementary information (SI) of spectra
nbands | Dimensions of Speclib
ncol-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
ncol-method | Handling supplementary information (SI) of spectra
ncol-method | Methods to create objects of class Speclib
noiseFiltering | Smooth spectra
nri | Normalised ratio index
Nri-class | * Nri class
nri_best_performance | Best performing model(s) with NRI
nrow-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
nrow-method | Handling supplementary information (SI) of spectra
nrow-method | Methods to create objects of class Speclib
nspectra | Dimensions of Speclib
n_features | Function to isolate absorption features
n_features-method | Function to isolate absorption features

## -- P --

plot-method | Methods to create, manipulate and query objects of class 'Clman'.
plot-method | Plot function for (g)lm.nri and cor.test.nri
plot-method | Plot Specfeat
plot-method | Plot speclib
plot.Nri | Plot function for (g)lm.nri and cor.test.nri
plot.Specfeat | Plot Specfeat
plot.Speclib | Plot speclib
plotRGB-method | Rasterbased methods for spectra
postprocessASD | Read ASD binary file
predictHyperspec | Prediction based on train-object and Speclib
predictHyperspec-method | Prediction based on train-object and Speclib
preProcess-class | Methods for Function 'preProcess'
preProcess-method | Methods for Function 'preProcess'
preProcess-methods | Methods for Function 'preProcess'
print-method | Methods for * Nri-class
print-method | Methods to create objects of class Speclib
print-method | Handling spectra
print.getNRI | Return nri-values
PROSAIL | Simulate canopy spectrum
PROSPECT | Simulate plant spectrum
PROSPECTinvert | Simulate plant spectrum

## -- Q --

Quickbird_response | Spectral resampling

## -- R --

RapidEye_response | Spectral resampling
Raster-methods | Rasterbased methods for spectra
rastermeta | Create list containing rastermeta-information
read.ASD | Read ASD binary file
readAll-method | Handling spectra
read_header | Get reflectance values
rededge | Red edge parameter
response_functions | Spectral resampling
rfe-method | Methods for Function 'rfe'
rfe-methods | Methods for Function 'rfe'
rowFromY-method | Handling spectra

## -- S --

safs-method | Methods for Function 'safs'
safs-methods | Methods for Function 'safs'
sam | Distance between spectra
sam_distance | Distance between spectra
sbf-method | Methods for Function 'sbf'
sbf-methods | Methods for Function 'sbf'
Sentinel2A_response | Spectral resampling
Sentinel2B_response | Spectral resampling
setPredictor | Set predictor variable(s)
setPredictor-method | Set predictor variable(s)
setPredictor-methods | Set predictor variable(s)
setResponse | Set response variable
setResponse-method | Set response variable
setResponse-methods | Set response variable
show-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
show-method | HyperSpecRaster* class (deprecated)
show-method | Methods for Function 'preProcess'
show-method | Methods for * Nri-class
show-method | Methods to create objects of class Speclib
show-method | Handling spectra
showCaretParameters | Show caret related parameters
showCaretParameters-method | Show caret related parameters
SI | Handling supplementary information (SI) of spectra
SI-method | Handling supplementary information (SI) of spectra
SI.speclib | Handling supplementary information (SI) of spectra
SI<- | Handling supplementary information (SI) of spectra
SI<--method | Handling supplementary information (SI) of spectra
smgm | SMGM
smoothSpeclib | Smooth spectra
soilindex | soilindex
specfeat | Function to isolate absorption features
Specfeat-class | * Specfeat class
speclib | Methods to create objects of class Speclib
Speclib-class | * Speclib class
speclib-method | Methods to create objects of class Speclib
spectra | Handling spectra
spectra-method | Methods to create, manipulate and query objects of class 'Clman'.
spectra-method | Handling spectra
spectra.Speclib | Handling spectra
spectra<- | Handling spectra
spectra<--method | Methods to create, manipulate and query objects of class 'Clman'.
spectra<--method | Handling spectra
spectral.resampling | Spectral resampling
spectralInterpolation | Interpolate spectra
spectralResampling | Spectral resampling
spectral_data | Hyperspectral samples
sr | Simple ratio index
subset-method | Subsetting 'Nri'-objects
subset-method | Subsetting speclibs
subset.nri | Subsetting 'Nri'-objects
subset.speclib | Subsetting speclibs

## -- T --

t.test-method | t-test for nri values
t.test.nri | t-test for nri values
train-method | Methods for Function 'train'
train-methods | Methods for Function 'train'
transformSpeclib | Transform spectra

## -- U --

unmix | Unmix spectra
updatecl | Check transformed Speclib
usagehistory | History of usage
usagehistory<- | History of usage
USGS_get_available_files | import USGS spectra
USGS_retrieve_files | import USGS spectra

## -- V --

vegindex | vegindex

## -- W --

wavelength | Handling wavelength and fwhm
wavelength-method | Methods for * Nri-class
wavelength-method | Handling wavelength and fwhm
wavelength<- | Handling wavelength and fwhm
wavelength<--method | Handling wavelength and fwhm
writeRaster-method | Rasterbased methods for spectra
writeStart-method | Handle hyperspectral cubes using raster package (deprecated)
writeStart-method | Functions for processing large hyperspectral raster files
writeStop-method | Functions for processing large hyperspectral raster files
writeValues-method | Handle hyperspectral cubes using raster package (deprecated)
writeValues-method | Functions for processing large hyperspectral raster files
WV_2_8_response | Spectral resampling

## -- misc --

$-method | Methods for * Nri-class
$-method | Methods to create objects of class Speclib
<-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
<=-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
==-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
>-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
>=-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
[-method | Methods to create, manipulate and query objects of class 'DistMat3D'.
[-method | Handling supplementary information (SI) of spectra
[-method | Methods for * Nri-class
[-method | Function to isolate absorption features
[-method | Indexing Speclib
[-method | Handling spectra
[<--method | Methods to create, manipulate and query objects of class 'DistMat3D'.