Function reference • hyperSpec

1. Package and class "hyperSpec"
`hyperSpec-package`	Package "hyperSpec": interface for hyperspectral datasets
`hyperSpec-class`	Class `hyperSpec`
2. Utility functions
`chk.hy()`	Validation of `hyperSpec` objects
`.DollarNames(<hyperSpec>)`	Command line completion for `$`
`hy_attach()`	Load and attach `hyperSpec` and all installed R hyperSpec family (`hySpc.*`) packages
`hy_browse_homepage()`	Browse homepage of R hyperSpec
`hy_list_available_hySpc_packages()`	List available R hyperSpec family packages
`hy_list_installed_hySpc_packages()`	List installed R hyperSpec family packages
`hy.getOptions()` `hy.getOption()` `hy.setOptions()`	Options for package hyperSpec
3. Datasets Datasets to try functionality of hyperSpec functions.
`barbiturates`	Barbiturates spectra from `.spc` example files
`generate_faux_cell()` `faux_cell`	Faux cell dataset for testing & demonstration
`flu`	Quinine fluorescence spectra
`laser`	Laser emission dataset
`paracetamol`	Paracetamol spectrum
4. Create and convert `hyperSpec` objects
Create or convert from/into `hyperSpec`
`initialize(<hyperSpec>)` `new_hyperSpec()`	Create a `hyperSpec` object
`as.hyperSpec()`	`as.hyperSpec`: convenience conversion functions
`as.data.frame(<hyperSpec>)` `as.matrix(<hyperSpec>)` `as.wide.df()` `as.long.df()` `as.t.df()`	Conversion of a `hyperSpec` object into a data frame or matrix
5. Import and export `hyperSpec` objects
Read/Write from/to files
`read.mat.Cytospec()`	(DEPRECATED) Import for Cytospec `mat` files
`read_txt_long()` `read_txt_wide()`	Import and Export of `hyperSpec` objects
`write_txt_long()` `write_txt_wide()`	Export `hyperSpec` objects to ASCII (text) files
! Moved to package hySpc.read.ENVI You should use analogous functions from package hySpc.read.ENVI as these functions will be removed soon.
`read.ENVI()` `read.ENVI.HySpex()` `read.ENVI.Nicolet()`	(DEPRECATED) Import of ENVI data
! Moved to package hySpc.read.jdx You should use analogous functions from package hySpc.read.jdx as these functions will be removed soon.
`read.jdx()`	(DEPRECATED) JCAMP-DX import for Shimadzu library spectra
! Moved to package hySpc.read.mat You should use analogous functions from package hySpc.read.mat as these functions will be removed soon.
`read.mat.Cytospec()`	(DEPRECATED) Import for Cytospec `mat` files
`read.mat.Witec()`	(DEPRECATED) Read `.mat` file into `hyperSpec` object
! Moved to package hySpc.read.spc You should use analogous functions from package hySpc.read.spc as these functions will be removed soon.
`read.spc.Kaiser()` `read.spc.KaiserMap()` `read.spc.KaiserLowHigh()`	(DEPRECATED) Import functions for Kaiser Optical Systems `.spc` files
`read.spc()`	(DEPRECATED) Import for Thermo Galactic's `spc` file format
! Moved to package hySpc.read.spe You should use analogous functions from package hySpc.read.spe as these functions will be removed soon.
`read.spe()` `spe.showcalpoints()`	(DEPRECATED) Import WinSpec SPE file
`.read.spe.xml()`	(DEPRECATED) Read XML footer from SPE file format version 3.0
! Moved to package hySpc.read.txt You should use analogous functions from package hySpc.read.txt as these functions will be removed soon.
`count_lines()` `count_lines()`	(DEPRECATED) Count lines (of an ASCII File)
`read.ini()`	(DEPRECATED) Read INI files
`read.asc.Andor()`	(DEPRECATED) Import Raman spectra/maps from Andor cameras/solis ASCII files
`read.asc.PerkinElmer()`	(DEPRECATED) File import filter PerkinElmer ASCII spectra
`read.txt.Horiba()` `read.txt.Horiba.xy()` `read.txt.Horiba.t()`	(DEPRECATED) Import Horiba Labspec exported ASCII files
`read.txt.Renishaw()` `read.zip.Renishaw()`	(DEPRECATED) Import Raman measurements from Renishaw ASCII-files
`read.txt.Shimadzu()`	(DEPRECATED) Read Shimadzu GCxGC-qMS - spectra files (`.txt`)
`read.txt.Witec()` `read.dat.Witec()` `read.txt.Witec.Graph()`	(DEPRECATED) Import Raman spectra from Witec files
`read.txt.long()` `read.txt.wide()`	(DEPRECATED) Import `hyperSpec` objects from ASCII (text) files
`wc()`	(DEPRECATED) Line/word/character count of ASCII files
6. Plotting
Plots
`plot(<hyperSpec>,<missing>)` `plot(<hyperSpec>,<character>)`	Plotting `hyperSpec` objects
`plotmap()` `levelplot(<formula>,<hyperSpec>)` `levelplot(<hyperSpec>,<missing>)` `map.identify()` `plotvoronoi()`	Plot a map and identify/select spectra in the map
`plotc()`	Calibration plots, timeseries plots, and depth-profiles
`plotmat()`	Plot spectra matrix
`plotspc()` `stacked.offsets()`	Plotting spectra
Color palettes
`palette_colorblind`	Color suggestions for `hyperSpec` users
`palette_matlab()` `palette_matlab_dark()` `palette_alois()`	Matlab-like color palettes
Plotting tools
`plotmap()` `levelplot(<formula>,<hyperSpec>)` `levelplot(<hyperSpec>,<missing>)` `map.identify()` `plotvoronoi()`	Plot a map and identify/select spectra in the map
`map.sel.poly()` `sel.poly()`	Interactively select a polygon (grid graphics) and highlight points
`mark.dendrogram()`	Mark groups in `stats::hclust()` dendrograms
`markpeak()`	Mark peak
`spc.identify()` `spc.point.max()` `spc.point.default()` `spc.point.min()` `spc.point.sqr()` `spc.label.default()` `spc.label.wlonly()`	Identifying spectra and spectral data points
`trellis.factor.key()`	Color coding legend for factors
! Moved to package hySpc.ggplot2 You should use analogous functions from package hySpc.ggplot2 as these functions will be removed soon.
`qplotspc()` `qplotmap()` `qplotc()` `qplotmixmap()` `legendright()` `qmixtile()` `normalize.colrange()` `normalize.range()` `normalize.null()` `normalize.minmax()` `qmixlegend()` `colmix.rgb()`	(DEPRECATED) Spectra plotting with ggplot2 was moved to hySpc.ggplot2
7. Data manipulation
Summary and data preview
`ncol(<hyperSpec>)` `nrow(<hyperSpec>)` `nwl()` `dim(<hyperSpec>)` `length(<hyperSpec>)`	Number of rows (spectra), columns, and data points per spectrum of a `hyperSpec` object
`show(<hyperSpec>)` `print(<hyperSpec>)` `summary(<hyperSpec>)` `as.character(<hyperSpec>)`	Show brief summary of `hyperSpec` object
Manipulation
`Arith(<hyperSpec>,<hyperSpec>)` `Arith(<hyperSpec>,<missing>)` `Arith(<hyperSpec>,<numeric>)` `Arith(<hyperSpec>,<matrix>)` `Arith(<numeric>,<hyperSpec>)` `Arith(<matrix>,<hyperSpec>)` `%%`(<hyperSpec>,<hyperSpec>) `%%`(<hyperSpec>,<matrix>) `%*%`(<matrix>,<hyperSpec>)	Arithmetical operators: `+`, `-`, ``, `/`, `^`, `%%`, `%/%`, `%%` for `hyperSpec` objects
`Compare(<hyperSpec>,<hyperSpec>)` `Compare(<hyperSpec>,<numeric>)` `Compare(<hyperSpec>,<matrix>)` `Compare(<numeric>,<hyperSpec>)` `Compare(<matrix>,<hyperSpec>)` `all.equal(<hyperSpec>,<hyperSpec>)`	Comparison of `hyperSpec` objects
`aggregate(<hyperSpec>)`	Aggregate `hyperSpec` objects
`apply(<hyperSpec>)`	Compute summary statistics for the spectra of a `hyperSpec` object
`bind()` `cbind(<hyperSpec>)` `rbind(<hyperSpec>)` `cbind2(<hyperSpec>,<hyperSpec>)` `cbind2(<hyperSpec>,<missing>)` `rbind2(<hyperSpec>,<hyperSpec>)` `rbind2(<hyperSpec>,<missing>)`	Binding `hyperSpec` objects
`collapse()`	Collapse/bind several `hyperSpec` objects into one object
`decomposition()`	Convert principal component decomposition or the like into a `hyperSpec` object
`dimnames(<hyperSpec>)` `rownames(<hyperSpec>)` `rownames<-`(<hyperSpec>) `colnames(<hyperSpec>)` `colnames<-`(<hyperSpec>)	Dimnames for `hyperSpec` objects
`.spc_fix_colnames()`	Ensure that the spectra matrix has the wavelengths in column names
`droplevels(<hyperSpec>)`	Droplevels for `hyperSpec` objects
`empty()`	Empty `hyperSpec` object
`[`(<hyperSpec>) `[[`(<hyperSpec>) `$`(<hyperSpec>) `[<-`(<hyperSpec>) `[[<-`(<hyperSpec>) `$<-`(<hyperSpec>)	Extract and replace parts of `hyperSpec` objects
`makeraster()` `fitraster()`	Find an evenly spaced grid for x
`Math2(<hyperSpec>)` `log(<hyperSpec>)` `Math(<hyperSpec>)`	Mathematical functions for `hyperSpec` objects
`mean_sd(<numeric>)` `mean_sd(<matrix>)` `mean_sd(<hyperSpec>)` `mean_pm_sd(<numeric>)` `mean_pm_sd(<matrix>)` `mean_pm_sd(<hyperSpec>)` `mean(<hyperSpec>)` `quantile(<hyperSpec>)`	Mean and standard deviation
`merge(<hyperSpec>,<hyperSpec>)` `merge(<hyperSpec>,<data.frame>)` `merge(<data.frame>,<hyperSpec>)`	Merge `hyperSpec` objects
`merge_data()`	Merge additional extra data into an object
`normalize01()`	Normalize numbers to interval [0, 1]
`rbind.fill(<matrix>)` `rbind(<fill>)`	Bind matrices by row, and fill missing columns with `NA`.
`scale(<hyperSpec>)`	Center and scale `hyperSpec` object
`seq(<hyperSpec>)`	Sequence generation along spectra or wavelengths
`spc_na_approx()`	Impute missing data points
`split(<hyperSpec>)`	Split a `hyperSpec` object according to groups
`subset(<hyperSpec>)`	Subset `hyperSpec` object
`sweep(<hyperSpec>)`	Sweep summary statistic out of `hyperSpec` objects
Baseline manipulation
`spc_fit_poly()` `spc_fit_poly_below()`	Polynomial baseline fitting
`spc_rubberband()`	Rubberband baseline correction
Binning and smoothing
`spc_bin()`	Wavelength binning
`spc_loess()`	LOESS smoothing interpolation for spectra
`spc_smooth_spline()`	Spectral smoothing by splines
Data generation functions
`generate_faux_cell()` `faux_cell`	Faux cell dataset for testing & demonstration
`generate_hy_spectra()` `generate_hy_profile()` `generate_hy_map()`	Generate spectroscopic data
`rmmvnorm()`	Multivariate normal random numbers
`vanderMonde()`	Function evaluation on `hyperSpec` objects
Statistics, analysis, randomization
`aggregate(<hyperSpec>)`	Aggregate `hyperSpec` objects
`apply(<hyperSpec>)`	Compute summary statistics for the spectra of a `hyperSpec` object
`colMeans(<hyperSpec>)` `colSums(<hyperSpec>)` `rowMeans(<hyperSpec>)` `rowSums(<hyperSpec>)`	Functions `colSums()`, `colMeans()`, `rowSums()`, and `rowMeans()` for `hyperSpec` objects
`cov(<hyperSpec>,<missing>)` `pooled.cov()`	Covariance matrices for `hyperSpec` objects
`mean_sd(<numeric>)` `mean_sd(<matrix>)` `mean_sd(<hyperSpec>)` `mean_pm_sd(<numeric>)` `mean_pm_sd(<matrix>)` `mean_pm_sd(<hyperSpec>)` `mean(<hyperSpec>)` `quantile(<hyperSpec>)`	Mean and standard deviation
`pearson.dist()`	Distance based on Pearson's $R^2$
`sample(<hyperSpec>)` `isample()` `sample(<data.frame>)` `sample(<matrix>)`	Random samples and permutations
`Summary(<hyperSpec>)` `is.na(<hyperSpec>)` `all_wl()` `any_wl()`	Statistical summary and other functions for `hyperSpec`
`sweep(<hyperSpec>)`	Sweep summary statistic out of `hyperSpec` objects
Wavelength manipulation
`extract_numbers()`	Guess wavelengths from character vector
`wl()` `wl<-`()	Getting and setting the wavelength axis
`wl2i()` `i2wl()`	Conversion between Wavelength and Spectra Matrix Column.
`wl_convert_units()`	Convert between different wavelength units
`wl_eval()`	Evaluate function on wavelengths of `hyperSpec` object
`wl_sort()`	Sorting the wavelengths of a `hyperSpec` object
Label manipulation
`labels(<hyperSpec>)` `labels<-`()	Get and set labels of a `hyperSpec` object
8. Other functions Functions not mentioned above.
`skip_if_not_fileio_available()`	Helper function for unit testing
9. Removed or deprecated functions
Functions moved to other packages The following functions were moved to other r-hyperspec family packages. In most cases, the functions were also renamed. Please, use the analogues of these functions, which are in appropriate packages.
`qplotspc()` `qplotmap()` `qplotc()` `qplotmixmap()` `legendright()` `qmixtile()` `normalize.colrange()` `normalize.range()` `normalize.null()` `normalize.minmax()` `qmixlegend()` `colmix.rgb()`	(DEPRECATED) Spectra plotting with ggplot2 was moved to hySpc.ggplot2
`read.ENVI()` `read.ENVI.HySpex()` `read.ENVI.Nicolet()`	(DEPRECATED) Import of ENVI data
`read.jdx()`	(DEPRECATED) JCAMP-DX import for Shimadzu library spectra
`read.mat.Cytospec()`	(DEPRECATED) Import for Cytospec `mat` files
`read.mat.Witec()`	(DEPRECATED) Read `.mat` file into `hyperSpec` object
`read.spc.Kaiser()` `read.spc.KaiserMap()` `read.spc.KaiserLowHigh()`	(DEPRECATED) Import functions for Kaiser Optical Systems `.spc` files
`read.spc()`	(DEPRECATED) Import for Thermo Galactic's `spc` file format
`read.spe()` `spe.showcalpoints()`	(DEPRECATED) Import WinSpec SPE file
`.read.spe.xml()`	(DEPRECATED) Read XML footer from SPE file format version 3.0
`count_lines()` `count_lines()`	(DEPRECATED) Count lines (of an ASCII File)
`read.ini()`	(DEPRECATED) Read INI files
`read.asc.Andor()`	(DEPRECATED) Import Raman spectra/maps from Andor cameras/solis ASCII files
`read.asc.PerkinElmer()`	(DEPRECATED) File import filter PerkinElmer ASCII spectra
`read.txt.Horiba()` `read.txt.Horiba.xy()` `read.txt.Horiba.t()`	(DEPRECATED) Import Horiba Labspec exported ASCII files
`read.txt.Renishaw()` `read.zip.Renishaw()`	(DEPRECATED) Import Raman measurements from Renishaw ASCII-files
`read.txt.Shimadzu()`	(DEPRECATED) Read Shimadzu GCxGC-qMS - spectra files (`.txt`)
`read.txt.Witec()` `read.dat.Witec()` `read.txt.Witec.Graph()`	(DEPRECATED) Import Raman spectra from Witec files
`read.txt.long()` `read.txt.wide()`	(DEPRECATED) Import `hyperSpec` objects from ASCII (text) files
`wc()`	(DEPRECATED) Line/word/character count of ASCII files
Deprecated, renamed, or defunct functions You should not use these functions any more.
`spc.fit.poly()` `spc.fit.poly.below()`	(DEPRECATED) Polynomial baseline fitting
`.fix_spc_colnames()`	(DEPRECATED) Ensure that the spectra matrix has the wavelengths in column names
`guess.wavelength()`	(DEPRECATED) Guess wavelengths from character vector
`orderwl()`	(DEPRECATED) Sorting the wavelengths of a `hyperSpec` object
`spc.rubberband()`	(DEPRECATED) Rubberband baseline correction
`spc.NA.approx()`	(DEPRECATED) Impute missing data points
`spc.bin()`	(DEPRECATED) Wavelength binning
`spc.loess()`	(DEPRECATED) LOESS smoothing interpolation for spectra
`spc.smooth.spline()`	(DEPRECATED) Spectral smoothing by splines
`read.txt.long()` `read.txt.wide()`	(DEPRECATED) Import `hyperSpec` objects from ASCII (text) files
`wl.eval()`	(DEPRECATED) Evaluate function on wavelengths of `hyperSpec` object
`wlconv()` `nm2raman()` `nm2invcm()` `nm2ev()` `nm2freq()` `invcm2raman()` `invcm2nm()` `invcm2ev()` `invcm2freq()` `raman2invcm()` `raman2nm()` `raman2ev()` `raman2freq()` `ev2raman()` `ev2invcm()` `ev2nm()` `ev2freq()` `freq2nm()` `freq2invcm()` `freq2ev()` `freq2raman()`	(DEPRECATED) Convert different wavelength units
`write.txt.long()` `write.txt.wide()`	(DEPRECATED) Export `hyperSpec` objects to ASCII (text) files
`scan.asc.Andor()` `scan.txt.Renishaw()` `scan.zip.Renishaw()` `scan.txt.Witec()` `scan.dat.Witec()` `scan.txt.Witec.Graph()` `read.cytomat()`	Deprecated and defunct functions

Reference

1. Package and class "hyperSpec"

2. Utility functions

3. Datasets

4. Create and convert `hyperSpec` objects

Create or convert from/into `hyperSpec`

5. Import and export `hyperSpec` objects

Read/Write from/to files

! Moved to package hySpc.read.ENVI

! Moved to package hySpc.read.jdx

! Moved to package hySpc.read.mat

! Moved to package hySpc.read.spc

! Moved to package hySpc.read.spe

! Moved to package hySpc.read.txt

6. Plotting

Plots

Color palettes

Plotting tools

! Moved to package hySpc.ggplot2

7. Data manipulation

Summary and data preview

Manipulation

Baseline manipulation

Binning and smoothing

Data generation functions

Statistics, analysis, randomization

Wavelength manipulation

Label manipulation

8. Other functions

9. Removed or deprecated functions

Functions moved to other packages

Deprecated, renamed, or defunct functions