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hyperSpec (version 0.99-20201127)

Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Description

Comfortable ways to work with hyperspectral data sets. I.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f (wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.

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Install

install.packages('hyperSpec')

Monthly Downloads

1,493

Version

0.99-20201127

License

GPL (>= 3)

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Repository

https://github.com/cbeleites/hyperSpec

Maintainer

Claudia Beleites

Last Published

November 29th, 2020

Functions in hyperSpec (0.99-20201127)

Binding hyperSpec Objects

Conversion of a hyperSpec object into a data.frame or matrix as.data.frame returns x@data (as data.frame) as.matrix returns the spectra matrix x@data$spc as matrix

colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects

Raman spectra of 2 Chondrocytes in Cartilage A Raman-map (laterally resolved Raman spectra) of chondrocytes in cartilage.

.read.spe.xml_string

.read.spe.xml_string

aggregate hyperSpec objects

dimnames,hyperSpec-method

dimnames for hyperSpec objects

Read XML footer from SPE file format version 3.0

.fix_spc_colnames

Ensure that the spectra matrix has the wavelengths in column names

.cluster.wavelengths

Find clusters of approximately equal wavelengths

ncol,hyperSpec-method

The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)

apply Computes summary statistics for the spectra of a hyperSpec object.

.DollarNames.hyperSpec

command line completion for $

droplevels,hyperSpec-method

droplevels for hyperSpec object

Mark peak Marks location of the first spectrum at the data point closest to the specified position on the current plot.

mark.dendrogram

Mark groups in hclust dendrograms

Empty hyperSpec object

Barbiturates Spectra from .spc example files A time series of mass spectra in a list of hyperSpec objects.

count lines (of an ASCII file)

.collapse.equal

Try finding groups of hyperSpec objects with (approximately) equal wavelength axes

Collapse hyperSpec objects

Polynomial Baseline Fitting These functions fit polynomal baselines.

[,hyperSpec-method

Extract and Replace parts of hyperSpec objects

Get and Set Labels of a hyperSpec Object value may be a list or vector of labels giving the new label for each of the entries specified by which.

Creating a hyperSpec Object

Plotting Spectra Plot the spectra of a hyperSpec object, i.e. intensity over wavelength. Instead of the intensity values of the spectra matrix summary values calculated from these may be used.

.fileio.optional

Helper function to harmonize treatment of file import results

normalization for mixed colors

merge,hyperSpec,hyperSpec-method

Merge hyperSpec objects

mean_sd,numeric-method

Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean \(\pm\) one standard deviation, respectively.

Spectra plotting with ggplot2

Plot multivariate data into colour channels

Math2,hyperSpec-method

Math Functions for hyperSpec Objects

Laser Emission A time series of an unstable laser emission.

Quick data frame. Experimental version of as.data.frame that converts a list to a data frame, but doesn't do any checks to make sure it's a valid format. Much faster.

Comparison of hyperSpec objects

Import WinSpec SPE file

Arithmetical Operators for hyperSpec objects

Spectra plotting with ggplot2

read.txt.Horiba

Import Horiba Labspec exported ASCII files

Plot a Map and Identify/Select Spectra in the Map levelplot functions for hyperSpec objects. An image or map of a summary value of each spectrum is plotted. Spectra may be identified by mouse click.

cov,hyperSpec,missing-method

Covariance matrices for hyperSpec objects

Convert Principal Component Decomposition or the like into a hyperSpec Object

File Import Andor Solis

File Import Witec Raman

Quinine Fluorescence Spectra Fluorescence spectra of different dilutions of quinine forming a calibration set.

Multivariate normal random numbers

hyperSpec-class

Class "hyperSpec" This class handles hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with the spectra.

read.spc.Kaiser

read Kaiser .spc files

read.asc.PerkinElmer

File import filter PerkinElmer ASCII spectra

hyperSpec-package

Package hyperSpec

line/word/character count of ASCII files

rbind.fill.matrix

Bind matrices by row, and fill missing columns with NA

Getting and Setting the Wavelength Axis wl returns the wavelength axis, wl<- sets it.

Rubberband baseline correction

loess smoothing interpolation for spectra Spectra can be smoothed and interpolated on a new wavelength axis using loess.

Wavelength Binning In order to reduce the spectral resolution and thus gain signal to noise ratio or to reduce the dimensionality of the spectral data set, the spectral resolution can be reduced.

Sorting the Wavelengths of a hyperSpec Object Rearranges the hyperSpec object so that the wavelength vector is in increasing (or decreasing) order.

Identifying Spectra and Spectral Data Points This function allows to identify the spectrum and the wavelength of a point in a plot produced by plotspc.

guess.wavelength

guess wavelengths from character vector

Matlab-like Palettes Two palettes going from blue over green to red, approximately as the standard palette of Matlab does. The second one has darker green values and is better suited for plotting lines on white background.

qplotmap with colour mixing for multivariate overlay

Spectra plotting with ggplot2

Calibration- and Timeseries Plots, Depth-Profiles and the like plotc plots intensities of a hyperSpec object over another dimension such as concentration, time, or a spatial coordinate.

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.

Options for package hyperSpec Functions to access and set hyperSpec's options.

Plot spectra matrix

scale,hyperSpec-method

Center and scale hyperSpec object

sample,hyperSpec-method

Random Samples and Permutations Take a sample of the specified size from the elements of x with or without replacement.

Convert different wavelength units

spc.smooth.spline

Spectral smoothing by splines

Sweep Summary Statistic out of an hyperSpec Object sweep for hyperSpec objects.

Impute missing data points

Interactively select a polygon (grid graphics) and highlight points

Import of ENVI data as hyperSpec object

Import for Thermo Galactic's spc file format These functions allow to import Thermo Galactic/Grams .spc files.

read.txt.Shimadzu

Reads Shimadzu GCxGC-qMS - Spectra Files (.txt) as exported by Shimadzu Chrome Solution (v. 2.72) Mass Spectrometer: Shimadzu GCMS-QP 2010 Ultra (www.shimadzu.com)

scan.txt.Renishaw

import Raman measurements from Renishaw ASCII-files

trellis.factor.key

Color coding legend for factors Modifies a list of lattice arguments (as for levelplot, etc.) according to the factor levels. The colorkey will shows all levels (including unused), and the drawing colors will be set accordingly.

Import and Export of hyperSpec objects Besides save and load, two general ways to import and export data into hyperSpec objects exist.

hyperSpec unit tests

Function evaluation on hyperSpec objects

Distance based on Pearson's \(R^2\)

Plotting hyperSpec Objects

JCAMP-DX Import for Shimadzu Library Spectra

Sequence generation along spectra or wavelengths This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.

Import for Cytospec mat files

as.character,hyperSpec-method

Convert a hyperSpec object to character strings for Display print, show, and summary show the result of as.character.

Evaluate function on wavelengths of hyperSpec object

Conversion between Wavelength and Spectra Matrix Column Index wl2i returns the column indices for the spectra matrix for the given wavelengths. i2wl converts column indices into wavelengths.

Split a hyperSpec object according to groups split divides the hyperSpec object into a list of hyperSpec objects according to the groups given by f.

as.hyperSpec: convenience conversion functions

Validation of hyperSpec objects