Function reference • hyperSpec

1. Package and class "hyperSpec"
`hyperSpec-package`	Package "hyperSpec": Interface for Hyperspectral Data Sets
`hyperSpec-class`	Class `hyperSpec`
2. Utility functions
`chk.hy()`	Validation of `hyperSpec` Objects
`.DollarNames(<hyperSpec>)`	Command Line Completion for `$`
`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 Data Set for Testing & Demonstration
`flu`	Quinine Fluorescence Spectra
`laser`	Laser Emission Dataset
`paracetamol`	Paracetamol Spectrum.
4. Input and output
Create or convert from/into `hyperSpec`
`initialize(<hyperSpec>)`	Creating 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
Read/Write from/to files
`count_lines()`	Count Lines (of an ASCII File)
`.read.spe.xml()`	Read XML footer from SPE file format version 3.0.
`read.ini()`	Read INI files.
`read.spc.Kaiser()` `read.spc.KaiserMap()` `read.spc.KaiserLowHigh()`	read Kaiser `.spc` files
`read.spc()`	Import for Thermo Galactic's `spc` file format.
`read.ENVI()` `read.ENVI.HySpex()` `read.ENVI.Nicolet()`	Import of ENVI data.
`read.asc.Andor()`	Import Raman Spectra/Maps from Andor Cameras/Solis ASCII files.
`read.asc.PerkinElmer()`	File import filter PerkinElmer ASCII spectra.
`read.jdx()`	JCAMP-DX Import for Shimadzu Library Spectra.
`read.mat.Cytospec()`	Import for Cytospec `mat` files.
`read.spe()` `spe.showcalpoints()`	Import WinSpec SPE file.
`read.txt.Horiba()` `read.txt.Horiba.xy()` `read.txt.Horiba.t()`	Import Horiba Labspec exported ASCII files
`read.txt.Renishaw()` `read.zip.Renishaw()`	Import Raman measurements from Renishaw ASCII-files.
`read.txt.Shimadzu()`	Reads Shimadzu GCxGC-qMS - Spectra Files (`.txt`).
`read.txt.Witec()` `read.dat.Witec()` `read.txt.Witec.Graph()`	File Import Witec Raman
`read.txt.long()` `read.txt.wide()` `write.txt.long()` `write.txt.wide()`	Import and Export of `hyperSpec` objects.
5. Plotting
Plots
`plot(<hyperSpec>,<missing>)` `plot(<hyperSpec>,<character>)`	Plotting `hyperSpec` Objects.
`plotmap()` `levelplot(<hyperSpec>,<missing>)` `levelplot(<formula>,<hyperSpec>)` `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
`CB7`	Color Suggestions for `hyperSpec` Users
`matlab.palette()` `matlab.dark.palette()` `alois.palette()`	Matlab-Like Color Palettes
Plotting tools
`plotmap()` `levelplot(<hyperSpec>,<missing>)` `levelplot(<formula>,<hyperSpec>)` `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()`	Spectra Plotting with ggplot2 Was Moved to hySpc.ggplot2 (DEPRECATED)
6. Data manipulation
Summary and data preview
`ncol(<hyperSpec>)` `nrow(<hyperSpec>)` `nwl()` `dim(<hyperSpec>)` `length(<hyperSpec>)`	The Number of Rows (Spectra), Columns, and Data Points per Spectrum of a `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
`.fix_spc_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.
`mergeextra()`	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 for `hyperSpec` object.
`sweep(<hyperSpec>)`	Sweep Summary Statistic out of an hyperSpec Object.
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 Data Set 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 an hyperSpec Object.
Wavelength manipulation
`guess.wavelength()`	Guess wavelengths from Character Vector
`orderwl()`	Sorting the Wavelengths of a `hyperSpec` Object.
`wl()` `wl<-`()	Getting and Setting the Wavelength Axis.
`wl.eval()`	Evaluate function on wavelengths of `hyperSpec` object.
`wl2i()` `i2wl()`	Conversion between Wavelength and Spectra Matrix Column.
`wlconv()` `nm2raman()` `nm2invcm()` `nm2ev()` `nm2freq()` `invcm2raman()` `invcm2nm()` `invcm2ev()` `invcm2freq()` `raman2invcm()` `raman2nm()` `raman2ev()` `raman2freq()` `ev2raman()` `ev2invcm()` `ev2nm()` `ev2freq()` `freq2nm()` `freq2invcm()` `freq2ev()` `freq2raman()`	Convert different wavelength units.
Label manipulation
`labels<-`() `labels(<hyperSpec>)`	Get and Set Labels of a `hyperSpec` Object
8. Other functions Functions not mentioned above.
`as.character(<hyperSpec>)` `show(<hyperSpec>)` `print(<hyperSpec>)` `summary(<hyperSpec>)`	Convert a `hyperSpec` object to character strings for display.
9. Removed or deprecated functions
Functions moved to other packages You should use analogues of these functions from appropriate packages.
`qplotspc()` `qplotmap()` `qplotc()` `qplotmixmap()` `legendright()` `qmixtile()` `normalize.colrange()` `normalize.range()` `normalize.null()` `normalize.minmax()` `qmixlegend()` `colmix.rgb()`	Spectra Plotting with ggplot2 Was Moved to hySpc.ggplot2 (DEPRECATED)
Deprecated, renamed, or defunct functions You should not use these functions any more.
`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
`wc()`	Line/word/character count of ASCII files (DEPRECATED).

Reference

1. Package and class "hyperSpec"

2. Utility functions

3. Datasets

4. Input and output

Create or convert from/into `hyperSpec`

Read/Write from/to files

5. Plotting

Plots

Color palettes

Plotting tools

! Moved to package hySpc.ggplot2

6. 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