hsdar: Manage, Analyse and Simulate Hyperspectral Data
Version 0.5.1

Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.

AuthorLukas W. Lehnert [cre, aut], Hanna Meyer [aut], Joerg Bendix [aut]
Date of publication2016-12-09 16:43:14
MaintainerLukas W. Lehnert <lukaslehnert@googlemail.com>
LicenseGPL
Version0.5.1
URL http://vhrz669.hrz.uni-marburg.de:8070/lcrs/ http://teledetection.ipgp.jussieu.fr/prosail/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hsdar")

Getting started

Package overview

Popular man pages

addcp: Add fix point
caret_createFolds-methods: Methods for Function 'createFolds' and 'createMultiFolds'
caret_rfe: Methods for Function 'rfe'
hsdar-package: Manage, analyse and simulate hyperspectral data in R
rededge: Red edge parameter
smgm: SMGM
spectralResampling: Spectral resampling
See all...

All man pages Function index File listing

Man pages

addcp: Add fix point
applyDistMat3D: Apply function for class DistMat3D
applySpeclib: Apply function for class Speclib
as_hyperSpec: hyperSpec
attributes_speclib: Handling attributes of spectra
bandnames: Handling names of bands
bdri: Band depth ratio indices
cancer_spectra: Hyperspectral samples
caret_createDataPartition-methods: Methods for Function 'createDataPartition'
caret_createFolds-methods: Methods for Function 'createFolds' and 'createMultiFolds'
caret_createResample-methods: Methods for Function 'createResample'
caret_featurePlot-methods: Methods for Function 'featurePlot'
caret_gafs: Methods for Function 'gafs'
caret_preProcess-methods: Methods for Function 'preProcess'
caret_rfe: Methods for Function 'rfe'
caret_safs: Methods for Function 'safs'
caret_setPredictor: Set predictor variable(s)
caret_setResponse: Set response variable
caret_sfb: Methods for Function 'sbf'
caret_showCaretParameters: Show caret related parameters
caret_train-methods: Methods for Function 'train'
checkhull: Check continuum line
clman: * Clman class
Clman-class: * Clman class
Clman-methods: Methods to create, manipulate and query objects of class...
cor.test.normalized.ratio.index: Test for association/correlation between nri values and...
cubePlot: cubePlot
cut.specfeat: Cut absorption features
define.features: Definition of absorption features
deletecp: Delete fix point
derivative_speclib: Derivation
dim_speclib: Dimensions of Speclib
DistMat3D-class: * DistMat3D class
DistMat3D-methods: Methods to create, manipulate and query objects of class...
dist_speclib: Distance between spectra
feature_properties: Calculation of properties of features
getcp: Get fix points
get.gaussian.response: Gaussian response function
getNRI: Return nri-values
get_reflectance: Get reflectance values
get_response: Satellite response functions
get_sensor_name: Satellite sensor name
glm.normalized.ratio.index: (Generalised) Linear models from normalised ratio indices
hsdardocs: Load additional documents
hsdar-package: Manage, analyse and simulate hyperspectral data in R
hsdar_parallel: hsdar_parallel
HyperSpecRaster: Handle hyperspectral cubes using raster package
HyperSpecRaster-class: HyperSpecRaster* class
id_speclib: Handling IDs of spectra
makehull: Check continuum line
mask: Mask spectra
meanfilter: Apply mean filter
merge_speclib: Merge speclibs
normalized.ratio.index: Normalised ratio index
normalized.ratio.index.best.perfomance: Best performing model(s) with NRI
normalized.ratio.index-methods: Methods for * Nri-class
Nri-class: * Nri class
plot.glm.normalized.ratio.index: Plot function for (g)lm.nri and cor.test.nri
plot.specfeat: Plot function for class Specfeat
plot.speclib: Plot speclib
PROSAIL2R: Simulate canopy spectrum
PROSPECT2R: Simulate plant spectrum
rastermeta: Create list containing rastermeta-information
raster-methods: Rasterbased methods for spectra
rededge: Red edge parameter
response_functions: Satellite sensor response functions
sensorCharacteristics: Sensor characteristics
smgm: SMGM
smooth_speclib: Smooth spectra
soilindex: soilindex
specfeat: Function to isolate spectral features
Specfeat-class: * Specfeat class
speclib: Methods to create objects of class Speclib
Speclib-class: * Speclib class
spectra: Handling spectra
spectral_data: Hyperspectral samples
spectralResampling: Spectral resampling
subset_nri: Subsetting 'Nri'-objects
subset_speclib: Subsetting speclibs
transform: Transform spectra
t.test.nri: t-test for nri values
unmix: Unmix spectra
updatecl: Check continuum line
usagehistory: History of usage
USGS: import USGS spectra
vegindex: vegindex
wavelength: Handling wavelength and fwhm

Functions

$,Nri-method Man page
$,Speclib-method Man page
<,ANY,DistMat3D-method Man page
<,DistMat3D,ANY-method Man page
<,DistMat3D,DistMat3D-method Man page
<=,ANY,DistMat3D-method Man page
<=,DistMat3D,ANY-method Man page
<=,DistMat3D,DistMat3D-method Man page
==,ANY,DistMat3D-method Man page
==,DistMat3D,ANY-method Man page
==,DistMat3D,DistMat3D-method Man page
>,ANY,DistMat3D-method Man page
>,DistMat3D,ANY-method Man page
>,DistMat3D,DistMat3D-method Man page
>=,ANY,DistMat3D-method Man page
>=,DistMat3D,ANY-method Man page
>=,DistMat3D,DistMat3D-method Man page
Clman Man page
Clman-class Man page
DistMat3D-class Man page
HyperSpecRaster Man page
HyperSpecRaster,HyperSpecRaster-method Man page
HyperSpecRaster,RasterBrick,numeric-method Man page
HyperSpecRaster,RasterLayer,numeric-method Man page
HyperSpecRaster,Speclib,ANY-method Man page
HyperSpecRaster,character,numeric-method Man page
HyperSpecRaster-class Man page
Landsat_4_response Man page
Landsat_5_response Man page
Landsat_7_response Man page
Landsat_8_response Man page
Nri-class Man page
PROSAIL Man page Source code
PROSPECT Man page Source code
PROSPECTinvert Man page Source code
Quickbird_response Man page
RapidEye_response Man page
Raster-methods Man page
Sentinel2A_response Man page
Specfeat-class Man page
Speclib-class Man page
TerraModis_response Man page Man page
USGS_get_available_files Man page Source code
USGS_retrieve_files Man page Source code
WV_2_8_response Man page
[,.Spectra,ANY,ANY,ANY-method Man page
[,DistMat3D,ANY,ANY,ANY-method Man page
[,DistMat3D,ANY,ANY-method Man page
[,Nri,ANY,ANY,ANY-method Man page
[,Nri,ANY,ANY-method Man page
[,Speclib,ANY,ANY,ANY-method Man page
[,Speclib,ANY,ANY-method Man page
[<-,DistMat3D,ANY,ANY,ANY-method Man page
[<-,DistMat3D,ANY,ANY-method Man page
addcp Man page Source code
adopt_dotsvar Source code
alignSpeclibs Source code
allocateOutput Source code
apply,DistMat3D-method Man page
apply,Speclib-method Man page
apply.DistMat3D Man page
apply.Speclib Man page
area.specfeat Source code
as.array,DistMat3D-method Man page
as.data.frame,Nri-method Man page
as.hyperSpec Man page Source code
as.matrix,DistMat3D-method Man page
as.matrix,Nri-method Man page
as.matrix.nri Man page Man page
as.speclib.specfeat Source code
attribute Man page
attribute,Nri-method Man page
attribute,Speclib-method Man page
attribute.speclib Man page
attribute<- Man page
attribute<-,Nri,data.frame-method Man page
attribute<-,Nri,matrix-method Man page
attribute<-,Speclib,data.frame-method Man page
attribute<-,Speclib,matrix-method Man page
attributes Source code
bandnames Man page Source code
bandnames<- Man page
bdri Man page Source code
blockwise Source code
brick,Speclib,ANY-method Man page
cancer_spectra Man page
cellFromCol,Speclib-method Man page
cellFromLine,Speclib-method Man page
cellFromPolygon,Speclib-method Man page
cellFromRow,Speclib-method Man page
cellFromRowCol,Speclib-method Man page
cellFromRowColCombine,Speclib-method Man page
cellFromXY,Speclib-method Man page
checkhull Man page Source code
coerce2Speclib Source code
colFromX,Speclib-method Man page
cor.test,Nri-method Man page
cor.test.nri Man page
createDataPartition,.CaretHyperspectral-method Man page
createDataPartition,ANY-method Man page
createDataPartition-methods Man page
createFolds,.CaretHyperspectral-method Man page
createFolds,ANY-method Man page
createFolds-methods Man page
createMultiFolds,.CaretHyperspectral-method Man page
createMultiFolds,ANY-method Man page
createMultiFolds-methods Man page
createResample,.CaretHyperspectral-method Man page
createResample,ANY-method Man page
createResample-methods Man page
createspeclib Man page Source code
cubePlot Man page Source code
cut_specfeat Man page Source code
define.features Man page Source code
deletecp Man page Source code
derivative.speclib Man page Source code
dim,DistMat3D-method Man page
dim,Speclib-method Man page
dim.speclib Man page
dist.speclib Man page Source code
distMat3D Man page
distMat3D,array-method Man page
distMat3D,matrix-method Man page
distMat3D,numeric-method Man page
doExtract Source code
doReplace Source code
extract,Speclib,ANY-method Man page
featurePlot,.CaretHyperspectral-method Man page
featurePlot,ANY-method Man page
featurePlot-methods Man page
feature_properties Man page Source code
fourCellsFromXY,Speclib-method Man page
fwhm Man page
fwhm,Speclib-method Man page
fwhm<- Man page
fwhm<-,Speclib,numeric-method Man page
gafs,Nri-method Man page
gafs,Specfeat-method Man page
gafs,Speclib-method Man page
gafs-methods Man page
get.feature.wavelength Source code
get.gaussian.response Man page Source code
get.rep.feature.parts Source code
get.rep.wavelength Source code
get.response Man page Source code
get.sensor.characteristics Man page Source code
get.sensor.name Man page Source code
getAllPredictors Source code
getAttrParameters Source code
getCaretCompatibleClasses Source code
getCaretParameter Source code
getFiniteNri Man page Source code
getImgMatrix_SpatialGridDataFrame Source code
getNRI Man page Source code
getParallel Source code
getPredicantVar Source code
getResponseVar Source code
getValuesBlock,HyperSpecRaster Man page
getValuesBlock,HyperSpecRaster-method Man page
get_RapidEye_response Man page Source code
get_args Source code
get_gafs Man page Source code
get_landsat4_response Man page Man page Source code
get_landsat5_response Man page Man page Source code
get_landsat7_response Man page Man page Source code
get_landsat8_response Man page Source code
get_quickbird_response Man page Man page Source code
get_reflectance Man page Source code
get_reflectance,Speclib-method Man page
get_reflectance.speclib Man page
get_response_function Man page Source code
get_rfe Man page Source code
get_safs Man page Source code
get_sbf Man page Source code
get_sentinel2_response Man page Source code
get_transformation Source code
get_wv2_4_response Man page Man page Source code
get_wv2_8_response Man page Man page Source code
getcp Man page Source code
glm.nri Man page Source code
glm_apply_lh Source code
glm_apply_rh Source code
hsdar Man page
hsdar-package Man page
hsdar_parallel Man page Source code
hsdardocs Man page Source code
idSpeclib Man page Source code
idSpeclib<- Man page
initialize,Clman-method Man page
initialize,Speclib-method Man page
interpolate.mask Man page Source code
is.speclib Man page Source code
legendSpeclib Man page Source code
list.available.sensors Man page Source code
lm.nri Man page Source code
makehull Man page Source code
mark_nri_best_performance Man page Source code
mask Man page Source code
mask,Speclib-method Man page
mask<- Man page
mask<-,Speclib,data.frame-method Man page
mask<-,Speclib,list-method Man page
mask<-,Speclib,matrix-method Man page
mask<-,Speclib,numeric-method Man page
maskSpeclib Man page Source code
max.specfeat Source code
maxwl.specfeat Source code
meanfilter Man page Source code
merge,Speclib,Speclib-method Man page
nbands Man page Source code
ncol,.Spectra-method Man page
ncol,DistMat3D-method Man page
nri Man page Source code
nri_best_performance Man page Source code
nrow,.Spectra-method Man page
nrow,DistMat3D-method Man page
nspectra Man page Source code
nversionFUN Source code
onAttach Source code
plot,Clman,ANY-method Man page
plot,Clman-method Man page
plot,Nri,ANY-method Man page
plot,Nri-method Man page
plot,Specfeat,ANY-method Man page
plot,Specfeat-method Man page
plot,Speclib,ANY-method Man page
plot.Nri Man page
plot.Speclib Man page
plotRGB_temp Source code
plot_side_cube Source code
plot_spec_curves Source code
preProcess,.CaretHyperspectral-method Man page
preProcess,ANY-method Man page
preProcess-class Man page
preProcess-methods Man page
print,.Spectra-method Man page
print,Nri-method Man page
print,Speclib-method Man page
print.cortestnri Man page
print.getNRI Man page
print.glmnri Source code
print.nri Man page
print.ttestnri Man page
printUsagehistory Source code
process_parallel Source code
range.specfeat Source code
rastermeta Man page Source code
read.USGS.asc Source code
readAll,Speclib-method Man page
rededge Man page Source code
rededge_apply Source code
response_functions Man page Man page
restoreParallel Source code
rfe,Nri-method Man page
rfe,Specfeat-method Man page
rfe,Speclib-method Man page
rfe-methods Man page
rowFromY,Speclib-method Man page
s.rastermeta Source code
sMasked Source code
safs,Nri-method Man page
safs,Specfeat-method Man page
safs,Speclib-method Man page
safs-methods Man page
sam Man page Source code
sam_distance Man page Source code
sbf,Nri-method Man page
sbf,Specfeat-method Man page
sbf,Speclib-method Man page
sbf-methods Man page
setCaretParameter Source code
setPredictor Man page
setPredictor,.CaretHyperspectral,character-method Man page
setPredictor-methods Man page
setResponse Man page
setResponse,.CaretHyperspectral,character-method Man page
setResponse-methods Man page
setattributes Man page
show,.Spectra-method Man page
show,.preProcessHyperspectral-method Man page
show,DistMat3D-method Man page
show,HyperSpecRaster-method Man page
show,Nri-method Man page
show,Speclib-method Man page
showCaretParameters Man page
showCaretParameters,.CaretHyperspectral-method Man page
smgm Man page Source code
smgm_lsa_wrapper Source code
smoothSpeclib Man page Source code
soilindex Man page Source code
specfeat Man page Source code
speclib Man page
speclib,HyperSpecRaster,ANY-method Man page
speclib,RasterBrick,data.frame-method Man page
speclib,RasterBrick,matrix-method Man page
speclib,RasterBrick,numeric-method Man page
speclib,SpatialGridDataFrame,data.frame-method Man page
speclib,SpatialGridDataFrame,matrix-method Man page
speclib,SpatialGridDataFrame,numeric-method Man page
speclib,hyperSpec,ANY-method Man page
speclib,matrix,data.frame-method Man page
speclib,matrix,matrix-method Man page
speclib,matrix,numeric-method Man page
speclib,numeric,data.frame-method Man page
speclib,numeric,matrix-method Man page
speclib,numeric,numeric-method Man page
spectra Man page Source code
spectra,Clman-method Man page
spectra,Speclib-method Man page
spectra.Speclib Man page
spectra<- Man page
spectra<-,Clman,data.frame-method Man page
spectra<-,Clman,matrix-method Man page
spectra<-,Clman,numeric-method Man page
spectra<-,Speclib,RasterBrick-method Man page
spectra<-,Speclib,data.frame-method Man page
spectra<-,Speclib,matrix-method Man page
spectra<-,Speclib,numeric-method Man page
spectral.resampling Man page
spectralResampling Man page Source code
spectral_data Man page
subset,Nri-method Man page
subset,Speclib-method Man page
subset.nri Man page Source code
subset.speclib Man page Source code
t.test,Nri-method Man page
t.test.nri Man page
t.test_nri.formula Man page
train,.CaretHyperspectral-method Man page
train,ANY-method Man page
train-methods Man page
train.formula,formula,Speclib-method Man page
transformSpeclib Man page Source code
unmix Man page Source code
updateCaretParameters Source code
updatecl Man page Source code
usagehistory Man page Source code
usagehistory<- Man page
vegindex Man page Source code
wavelength Man page
wavelength,HyperSpecRaster-method Man page
wavelength,Nri-method Man page
wavelength,Speclib-method Man page
wavelength<- Man page
wavelength<-,HyperSpecRaster,numeric-method Man page
wavelength<-,Speclib,data.frame-method Man page
wavelength<-,Speclib,numeric-method Man page
wlhm.specfeat Source code
writeRaster,Speclib,character-method Man page
writeStart,HyperSpecRaster,Speclib-method Man page
writeStart,HyperSpecRaster,character-method Man page
writeValues,HyperSpecRaster,Speclib-method Man page
writeValues,RasterBrick,Speclib-method Man page
writeValues,RasterLayer,Speclib-method Man page

Files

inst
inst/CITATION
inst/COPYRIGHTS
inst/doc
inst/doc/References.Rnw
inst/doc/Hsdar-intro.pdf
inst/doc/Hsdar-intro.R
inst/doc/References.pdf
inst/doc/Hsdar-intro.Rnw
src
src/prospect_5B.f90
src/main_PROSAIL.f90
src/Makevars
src/adminparallel.f90
src/c2lablas.f
src/apply_response.f90
src/c2lablas.h
src/meanfilter.f90
src/checkhull.f90
src/dataSpec_P5B_PROSPECT.f90
src/pt2f.c
src/bandDepthRatioIndices.f90
src/recursiveNRI.f90
src/dladgen.f
src/main_PROSPECT.f90
src/tav_abs.f90
src/MODULE_PRO4SAIL.f90
src/dataSpec_P5B_PROSAIL.f90
src/unmix.c
src/sam.f90
src/volscatt.f90
src/LIDF.f90
src/localMaxima.f90
src/smgm.f90
src/differenciate.f90
src/Makevars.win
src/PRO4SAIL.f90
src/suh.f90
NAMESPACE
data
data/Quickbird_response.csv.gz
data/Sentinel2A_response.csv.xz
data/Landsat_5_response.csv.gz
data/Landsat_7_response.csv.gz
data/RapidEye_response.csv.gz
data/spectral_data.RData
data/Landsat_8_response.csv.gz
data/WV_2_8_response.csv.gz
data/cancer_spectra.RData
data/Landsat_4_response.csv.gz
R
R/spectral_resampling_gaussian.R
R/PROSPECT.R
R/PROSPECTinvert.R
R/speclib_mask.R
R/hyperSpec_conversion.R
R/caret_train.R
R/nri_print.R
R/speclib_spectra.R
R/speclib_plot.R
R/nri_attributes.R
R/continuum_features_properties.R
R/caret_safs.R
R/speclib_usagehistory.R
R/speclib_merge.R
R/speclib_bandnames.R
R/speclib_id.R
R/speclib_raster-methods.R
R/speclib_subset.R
R/continuum_transform.R
R/HyperSpecRaster_methods.R
R/USGS_speclib.R
R/spectral_resampling_sensorCharacteristics.R
R/plot_HyperSpec_cube.R
R/speclib_fwhm.R
R/caret_gafs.R
R/speclib_index.R
R/continuum_clman.R
R/nri_t_test.R
R/nri_glm.R
R/nri_index.R
R/rastermeta.R
R/nri_cor_test.R
R/nri_multivariate.R
R/PROSAIL.R
R/speclib_wavelength.R
R/hsdardocs.R
R/speclib_differenciate.R
R/speclib_get_reflectance.R
R/spectral_resampling_response.R
R/caret_preProcess.R
R/caret_createDataPartition.R
R/speclib_apply.R
R/distMat3D_methods.R
R/caret_rfe.R
R/unmix.R
R/smgm.R
R/nri_subset.R
R/blockwise_functions.R
R/nri_plot.R
R/raster-methods.R
R/nri_lm.R
R/getFiniteNri.R
R/speclib_dim.R
R/spectral_resampling.R
R/caret_utils.R
R/speclib_attributes.R
R/soilindex.R
R/speclib.R
R/Spectra-class.R
R/nri_methods.R
R/vegindex.R
R/caret_sbf.R
R/rededge.R
R/nri.R
R/multicore_funtions.R
R/caret_featurePlot.R
R/AAAClasses.R
R/spectral_resampling_response_functions.R
R/speclib_print.R
R/zzz.R
R/continuum_features.R
R/caret_parameters.R
R/distance.R
R/speclib_smooth.R
vignettes
vignettes/References.Rnw
vignettes/hsdar.bib
vignettes/Hsdar-intro.Rnw
MD5
build
build/vignette.rds
build/hsdar.pdf
DESCRIPTION
ChangeLog
man
man/transform.Rd
man/plot.specfeat.Rd
man/Specfeat-class.Rd
man/figures
man/figures/classes.png
man/figures/classes.pdf
man/figures/classes.svg
man/clman.Rd
man/get_sensor_name.Rd
man/hsdar-package.Rd
man/bandnames.Rd
man/id_speclib.Rd
man/addcp.Rd
man/cancer_spectra.Rd
man/caret_gafs.Rd
man/unmix.Rd
man/specfeat.Rd
man/updatecl.Rd
man/applySpeclib.Rd
man/PROSPECT2R.Rd
man/caret_safs.Rd
man/wavelength.Rd
man/vegindex.Rd
man/PROSAIL2R.Rd
man/subset_speclib.Rd
man/Clman-methods.Rd
man/meanfilter.Rd
man/applyDistMat3D.Rd
man/get_response.Rd
man/bdri.Rd
man/attributes_speclib.Rd
man/plot.glm.normalized.ratio.index.Rd
man/HyperSpecRaster.Rd
man/caret_train-methods.Rd
man/normalized.ratio.index-methods.Rd
man/getcp.Rd
man/caret_preProcess-methods.Rd
man/spectra.Rd
man/caret_createFolds-methods.Rd
man/define.features.Rd
man/getNRI.Rd
man/hsdardocs.Rd
man/subset_nri.Rd
man/caret_createResample-methods.Rd
man/plot.speclib.Rd
man/rededge.Rd
man/sensorCharacteristics.Rd
man/rastermeta.Rd
man/normalized.ratio.index.best.perfomance.Rd
man/caret_setResponse.Rd
man/DistMat3D-methods.Rd
man/raster-methods.Rd
man/get_reflectance.Rd
man/derivative_speclib.Rd
man/caret_showCaretParameters.Rd
man/as_hyperSpec.Rd
man/Speclib-class.Rd
man/caret_featurePlot-methods.Rd
man/t.test.nri.Rd
man/deletecp.Rd
man/normalized.ratio.index.Rd
man/Nri-class.Rd
man/get.gaussian.response.Rd
man/dim_speclib.Rd
man/spectral_data.Rd
man/HyperSpecRaster-class.Rd
man/smooth_speclib.Rd
man/USGS.Rd
man/DistMat3D-class.Rd
man/cor.test.normalized.ratio.index.Rd
man/caret_sfb.Rd
man/checkhull.Rd
man/caret_createDataPartition-methods.Rd
man/cut.specfeat.Rd
man/response_functions.Rd
man/Clman-class.Rd
man/mask.Rd
man/soilindex.Rd
man/dist_speclib.Rd
man/speclib.Rd
man/cubePlot.Rd
man/caret_rfe.Rd
man/hsdar_parallel.Rd
man/usagehistory.Rd
man/makehull.Rd
man/glm.normalized.ratio.index.Rd
man/smgm.Rd
man/caret_setPredictor.Rd
man/spectralResampling.Rd
man/merge_speclib.Rd
man/feature_properties.Rd
.Rinstignore
hsdar documentation built on May 20, 2017, 4:03 a.m.

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