Function reference • hyperSpec

Package and class “hyperSpec”
`hyperSpec-package` `_PACKAGE`	Package "hyperSpec": interface for hyperspectral datasets
`hyperSpec-class`	Class `hyperSpec`
Utility functions
`.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
`is_hyperSpec()` `assert_hyperSpec()`	Check and validate `hyperSpec` objects
`hy_get_options()` `hy_get_option()` `hy_set_options()`	Options for package hyperSpec
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
Create and convert `hyperSpec` objects
Create or convert from/into `hyperSpec`
`hyperSpec()` `initialize(<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()`	Convert `hyperSpec` object into a data frame or matrix
Import and export `hyperSpec` objects
Read/Write from/to 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()`	(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
Plotting
Plots
`plot(<hyperSpec>,<missing>)` `plot(<hyperSpec>,<character>)`	Plot `hyperSpec` objects
`calculate_offsets()`	Y offsets for stacked plots
`plot_map()` `levelplot(<formula>,<hyperSpec>)` `levelplot(<hyperSpec>,<missing>)` `map.identify()` `plot_voronoi()`	Plot a map and identify/select spectra in the map
`plot_c()`	Calibration plots, timeseries plots, and depth-profiles
`plot_matrix()`	Plot spectra matrix
`plot_spc()`	Plotting spectra
Color palettes
`palette_colorblind` `colors,palette_colorblind`	Color suggestions for `hyperSpec` users
`palette_matlab()` `palette_matlab_dark()` `palette_alois()`	Matlab-like color palettes
Plotting tools
`identify_spc()` `locate_spc_point_max()` `locate_spc_point_clicked()` `locate_spc_point_min()` `locate_spc_point_parabola_max()` `format_label_ispc_wl()` `format_label_wl_only()`	Identifying spectra and spectral data points
`plot_map()` `levelplot(<formula>,<hyperSpec>)` `levelplot(<hyperSpec>,<missing>)` `map.identify()` `plot_voronoi()`	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_groups_in_dendrogram()`	Mark groups in `stats::hclust()` dendrograms
`mark_peak()`	Mark peak
`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
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>)`	Bind `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
`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
`normalize_01()`	Normalize numbers to interval [0, 1]
`raster_make()` `raster_fit()`	Find an evenly spaced grid for x
`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>)` `cov_pooled()`	Covariance matrices for `hyperSpec` objects
`dist_pearson()`	Distance based on Pearson's $R^2$
`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
`sample(<hyperSpec>)` `sample(<data.frame>)` `sample(<matrix>)`	Sample or permute rows of `hyperSpec`, `data.frame`, or `matrix`
`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<-`()	Get and set the wavelength axis
`wl2i()` `i2wl()`	Conversion between Wavelength and spectra matrix column
`wl_convert_units()`	Convert between different wavelength units
`wl_create_label_from_units()`	Create label from units for wavelength axis
`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
Other functions Functions not mentioned above.
`.wl_fix_unit_name()`	Bring argument to a conventional name
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()`	(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
`chk.hy()`	(DEPRECATED) Validate `hyperSpec` objects
`.fix_spc_colnames()`	(DEPRECATED) Ensure that the spectra matrix has the wavelengths in column names
`guess.wavelength()`	(DEPRECATED) Guess wavelengths from character vector
`isample()`	(DEPRECATED) Return vector of row indices
`mark.dendrogram()`	(DEPRECATED) Identifying spectra and spectral data points
`markpeak()`	(DEPRECATED) Find an evenly spaced grid for x
`normalize01()`	(DEPRECATED) Normalize numbers to interval [0, 1]
`hy.getOptions()` `hy.getOption()` `hy.setOptions()`	(DEPRECATED) Options for package hyperSpec
`orderwl()`	(DEPRECATED) Sorting the wavelengths of a `hyperSpec` object
`pearson.dist()`	(DEPRECATED) Distance based on Pearson's $R^2$
`plotc()`	(DEPRECATED) Plotting spectra
`plotmap()`	(DEPRECATED) Plotting spectra
`plotmat()`	(DEPRECATED) Plotting spectra
`plotspc()`	(DEPRECATED) Plotting spectra
`plotvoronoi()`	(DEPRECATED) Plotting spectra
`pooled.cov()`	(DEPRECATED) Pooled covariance matrix
`makeraster()` `fitraster()`	(DEPRECATED) Find an evenly spaced grid for x
`spc.rubberband()`	(DEPRECATED) Rubberband baseline correction
`spc.NA.approx()`	(DEPRECATED) Impute missing data points
`spc.bin()`	(DEPRECATED) Wavelength binning
`spc.identify()` `spc.label.wlonly()` `spc.label.default()` `spc.point.sqr()` `spc.point.min()` `spc.point.max()` `spc.point.default()`	(DEPRECATED) Identifying spectra and spectral data points
`spc.loess()`	(DEPRECATED) LOESS smoothing interpolation for spectra
`spc.smooth.spline()`	(DEPRECATED) Spectral smoothing by splines
`stacked.offsets()`	(DEPRECATED) Calculate y-axis offsets
`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) Deprecated and defunct functions

Reference

Create or convert from/into `hyperSpec`

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

Plots

Color palettes

Plotting tools

! Moved to package hySpc.ggplot2

Summary and data preview

Manipulation

Baseline manipulation

Binning and smoothing

Data generation functions

Statistics, analysis, randomization

Wavelength manipulation

Label manipulation

Functions moved to other packages

Deprecated, renamed, or defunct functions

Reference

Create or convert from/into hyperSpec

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

Plots

Color palettes

Plotting tools

! Moved to package hySpc.ggplot2

Summary and data preview

Manipulation

Baseline manipulation

Binning and smoothing

Data generation functions

Statistics, analysis, randomization

Wavelength manipulation

Label manipulation

Functions moved to other packages

Deprecated, renamed, or defunct functions

Create or convert from/into `hyperSpec`