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ChangeLog
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------------------------------------------------------------------------------------------
--- 19-Februar-2022, version 1.0.4 (under development)
- Bug fixes:
- .blockwise handles transformSpeclib correctly
- safs can handle variables with zero variance if cutoff value is finite
- Option "difference" added to help page of "transformSpeclib"
- Options for figures included in the man pages changed
------------------------------------------------------------------------------------------
--- 04-August-2020, version 1.0.3
- New functionalities:
- Wrapper for Boruta as feature selection method integrated
- Sentinel-2B integrated
- Bug fixes:
- Mask integration estimates same number of bands as in original data
- Spectral response function of Sentinel-2A updated
------------------------------------------------------------------------------------------
--- 15-May-2020, version 1.0.2
- Compatibility changes for new R version
------------------------------------------------------------------------------------------
--- 04-February-2020, version 1.0.1
- New functionalities:
- PROSPECTinvert now handles lower and upper boundary values for each parameter
- Wrapper function to read ASD files together with package 'asdreader' added
- Function to post-process ASD files added
- Bug fixes:
- Typo in description of transformSpeclib fixed
- Functions to convert to "hyperSpec" removed because package is not longer available
- Code fixed to handle vector of length > 1 returned by class(x)
------------------------------------------------------------------------------------------
--- 25-May-2019, version 1.0.0
- New functionalities:
- Function to read ENVI header files added
- Function to linearly interpolate spectra added
- cubePlot interpolates side textures
- Bug fixes:
- writeStart correctly interprets dots arguments
------------------------------------------------------------------------------------------
--- 21-November-2018, version 0.7.2
- Bug fixes:
- Indexing and IDs are working
- Bug using zlib = TRUE together with range or constraint in plot.NRI fixed
- Feature properties runs if spectra are masked within features
- Other changes:
- plot method for class Specfeat plots all features by default
------------------------------------------------------------------------------------------
--- 20-June-2018, version 0.7.1
- New functionalities:
- Recursive simple ratio index method added
- Logarithmic scale of color in nri-plots
- dim-Method for class Nri added
- Function nspectra accepts object of class Nri
- print and show methods of Speclib return units of wavelength and spectral range
- PROSPECTinvert resamples spectra according to PROSPECT bands
- crop-Method for Speclib added
- Bug fixes:
- Columns and rows correctly shown in cubePlot
- lm.nri and glm.nri accepts object of class Nri in argument preddata
- SI accepts variables of classes POSIXlt and POSIXt
- Bug from PROSPECTinvert fixed (thanks to Collins Kukunda)
- Bug from cubePlot removed
- Indexing in samples dimension works if spectra are stored as Brick
------------------------------------------------------------------------------------------
--- 14-December-2017, version 0.7.0
- New functionalities:
- Parallel processing in 'smoothSpeclic' enabled
- Function meanfilter can process Speclibs and matrix
- Parallel computing supports doMPI package for windows
- Brick method for Speclib added
- Speclib-method for function merge accepts more than two Speclibs
- Apply.speclib works in parallel
- plotRGB automatically selects r, g, b bands
- Print function of Speclib returns SI information
- Function define.features integrated into function specfeat
- spectralResampling accepts a Speclib as spectral response function
- Conversion between wavelength units enabled
- Bug fixes:
- New example for manual continuum line in vignette
- Bug in comparison between values in two DistMat3D-objects fixed
- get.sensor.name renamed in .get.sensor.name since the function is only internally
used
- Help files comprehensively revised
- Bug from hsdardocs removed
- vegindex recognizes decimal seperator in wavelength information if indices are
self-defined
- Other changes:
- smoothSpeclib renamed in noiseFiltering (smoothSpeclib still works as well)
------------------------------------------------------------------------------------------
--- 16-October-2017, version 0.6.0
- Major changes:
- Attributes in the Speclib-objects are called "SI". Functions to get and replace SI
added
- SI data may encompass data from raster files. In this case, the respecive part of
the data is automatically read into memory during any kind of iterative reading/
writing of the main hyperspectral file stored in the spectra-slot.
- PROSPECT version D implemented.
- New functionalities:
- Iterative handling of large raster files using writeStart, writeStop from raster-
package implemented for Speclib-class
- Function predictHyperspec added which is a wrapper for predict but using any kind of
classes provided by the hsdar-package.
- Bug fixes:
- Indexing of Nri-objects now works with attributes encompassing a data.frame with
one single column
- NA values in raster images are removed before data is converted to
Speclib.
- Bug from indexing of Specfeat objects removed
- Derivation function from Fortran into R code converted
- Function vegindex recognizes "..." now correctly to define derivation parameters
- plot.Specfeat-function correctly sets the x- and y-label
------------------------------------------------------------------------------------------
--- 09-December-2016, version 0.5.1
- New functionalities:
- Functions to convert to and from class "hyperSpec" from the hyperSpec-package added
- Bug fixes:
- spectralResampling works with NA values
- subset Speclib works if attributes data.frame only has one column
------------------------------------------------------------------------------------------
--- 09-September-2016, version 0.5.0
- New functionalities:
- subset-method for class Nri
- Sentinel-2A integrated
- Set and replace methods for fwhm-values added
- Functions to handle parallel backend added
- New 'transformSpeclib' allowing parallel processing
- Function 'glm.nri' supports parallel processing
- Bug fixes:
- dist.speclib does not crash any more if speclib is not masked
- Erroneous calculation of REP_Li corrected. Thanks go to Xavier Bailleau for finding
the error.
- Plot-method for Nri sets figure window correctly and allows to start a new plot.
- IDs of spectra are correctly set after subsetting Speclib.
- In function merge: IDs in Speclibs are linked together.
- Argument "upperdiag" changed to "uppertriang" in plot method for Nri (for compatibility,
the old argument still works)
- Functions for indexing and masking of Speclibs now consider 'bandnames'
- Functions for indexing and masking of Speclibs now consider 'fwhm'
- Function 'feature_properties' works if initial object does not contain attributes
- Tabs in Fortran code replaced by whitespaces
- Vignettes:
- Hsdar-intro: Example for manual hull changed.
------------------------------------------------------------------------------------------
--- 23-February-2016, version 0.4.1
- New functionalities:
- Soil spectrum may be passed to PROSAIL
- Function "transform_speclib" renamed as "transformSpeclib"
- Class Nri contains usagehistory
- Inversion of PROSPECT
- Bug fixes:
- Dependency on texi2dvi for vignettes removed
------------------------------------------------------------------------------------------
--- 12-January-2016, version 0.4.0
- New functionalities:
- Index-method for class Nri
- Class Nri may contain attributes data.frame
- Set- and replace-methods for attributes in Nri-Objects added
- New internal class '.CaretHyperspectral' added.
- New functions for caret support added:
* setResponse
* setPredictor
* showCaretParameters
- New wrapper methods for caret functions added:
* preProcess
* gafs
* sfb
* safs
* rfe
* createDataPartition
* createResample
* createFolds
* createMultiFolds
* featurePlot
* train
* train.formula
- More efficient way of reading subset of spectra implemented if spectra are
stored as RasterBrick.
- print, show and [-methods for class .Spectra added
- Download function for spectra from USGS added
- Example datasets changed
- Bug fixes:
- Bandnames are correctly used
- Integration of indexing into history of Speclibs
- Actualize usagehistory after masking
------------------------------------------------------------------------------------------
--- 6-October-2015, version 0.3.1
- New functionalities:
- as.data.frame-method for class Nri
- Bug fixes:
- Spectral.resampling searches for names "lb" and "ub" in data.frames of user
defined sensors
- Bounds error in apply_response.f90 fixed
------------------------------------------------------------------------------------------
--- 27-July-2015, version 0.3.0
- New functionalities:
- '.Spectra' class to handle spectra added
- '.Spectra' now may contain spectral data eiter as a matrix or as a RasterBrick
object.
- smoothSpeclib accepts now all available filter functions from the signal-package
- unmix accepts NA values and scales spectra to [0, 1] on demand
- Blockwise calculation if spectra are read from RasterBrick-object in following
functions:
* sam
* rededge
* soilindex
* vegindex
* mask
* spectral.resampling
* unmix
* smoothSpeclib
* transform_speclib
* derivative.speclib
- extract- and writeRaster-methods added for spectra from RasterBrick-object.
- Bug fixes:
- plot.Speclib accepts xaxt and yaxt settings
- get.response correctly accepts center and fwhm values
- transform_speclib get correct upper hull if method = "ch"
- Indexing of speclibs works if only one band or only one spectrum is remaining
- transform_speclib returns interpolated spectra if input speclib is masked
------------------------------------------------------------------------------------------
--- 19-June-2015, version 0.2.1
- Bug fixes:
- Memmory access error in unmix fixed
------------------------------------------------------------------------------------------
--- 18-June-2015, version 0.2
- New functionalities:
- Tutorial added
- nri accepts vector of bands to calculate nri-indices
- Bug fixes:
- plot.Nri accepts NAs in coefficients to be plotted
------------------------------------------------------------------------------------------
--- 22-May-2015, version 0.1.5
- Bug fixes:
- Memory access error in fortran subroutine smgm fixed
------------------------------------------------------------------------------------------
--- 21-May-2015, version 0.1.4
- New functionalities:
- new function cubePlot to produce a 3D plot of a HyperSpecRaster
- brick method for Speclib
- wavelength method for HyperSpecRaster
- Bug fixes:
- HyperSpecRaster-method for Speclib returns HyperSpecRaster-object
(instead of RasterBrick)
- row.names of spectra are correctly used as ID in speclib
(for createspeclib-function)
- r.squared value is returned by lm.nri if NRI-values are predictors
- constraint in plot.Nri selects correct layer in respective
coefficient
------------------------------------------------------------------------------------------
--- 30-April-2015, version 0.1.3
- New functionalities (suggested and supported by André Große-Stoltenberg):
- Function for soil indices implemented (soilindex)
- In soilindex and vegindex, user defined indices can be passed
- Gaussian model on soil spectra implemented (Special thanks to Michael Whiting
for providing his IDL code and helping on the development of the FORTRAN implemention)
- Bug fixes:
- transform_speclib: The bugs only affected the continuum hull
- vegindex: Some indices were missing or calculation was faulty
------------------------------------------------------------------------------------------
--- 08-April-2015, version 0.1.2
Starting this log