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hyperSpec (version 0.99-20180627)

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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Version

Install

install.packages('hyperSpec')

Monthly Downloads

1,119

Version

0.99-20180627

License

GPL (>= 3)

Maintainer

Claudia Beleites

Last Published

June 28th, 2018

Functions in hyperSpec (0.99-20180627)

as.hyperSpec: convenience conversion functions

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

droplevels,hyperSpec-method

droplevels for hyperSpec object

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

Polynomial Baseline Fitting These functions fit polynomal baselines.

Empty hyperSpec object

guess.wavelength

guess wavelengths from character vector

.DollarNames.hyperSpec

command line completion for $

colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects

Comparison of hyperSpec objects

Interactively select a polygon (grid graphics) and highlight points

hyperSpec-package

Package hyperSpec

Creating a hyperSpec Object Like other S4 objects, a hyperSpec object can be created by new. The hyperSpec object is then initialized using the given parameters.

Arithmetical Operators for hyperSpec objects

Collapse hyperSpec objects

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

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.

mark.dendrogram

Mark groups in hclust dendrograms

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.

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.

Spectra plotting with ggplot2

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.

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.

Binding hyperSpec Objects

Import WinSpec SPE file

Read XML footer from SPE file format version 3.0

read.txt.Horiba

Import Horiba Labspec exported ASCII files

Plot spectra matrix

rbind.fill.matrix

Bind matrices by row, and fill missing columns with NA

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

scan.txt.Renishaw

import Raman measurements from Renishaw ASCII-files

cov,hyperSpec,missing-method

Covariance matrices for hyperSpec objects

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.

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.

Validation of hyperSpec objects

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.

Convert Principal Component Decomposition or the like into a hyperSpec Object

Rubberband baseline correction

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

Convert different wavelength units

spc.smooth.spline

Spectral smoothing by splines

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

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

ncol,hyperSpec-method

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

normalization for mixed colors

[,hyperSpec-method

Extract and Replace parts of hyperSpec objects

Function evaluation on hyperSpec objects

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

wc word count of ASCII files

mean_sd,numeric-method

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

Math2,hyperSpec-method

Math Functions for hyperSpec Objects

merge,hyperSpec,hyperSpec-method

Merge hyperSpec objects

Spectra plotting with ggplot2

Plot multivariate data into colour channels

Spectra plotting with ggplot2

Import for Cytospec mat files

JCAMP-DX Import for Shimadzu Library Spectra

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)

Plotting hyperSpec Objects

File Import Witec Raman

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.

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.

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

as.character,hyperSpec-method

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

read.spc.Kaiser

read Kaiser .spc files

Multivariate normal random numbers

qplotmap with colour mixing for multivariate overlay

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

read.ENVI.Nicolet

Import of ENVI data as hyperSpec object

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

sample,hyperSpec-method

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

File Import Andor Solis

scale,hyperSpec-method

Center and scale hyperSpec object

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

Impute missing data points

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

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.

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.

Evaluate function on wavelengths of hyperSpec object

hyperSpec unit tests

aggregate 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

dimnames,hyperSpec-method

dimnames for hyperSpec objects

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

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.

Laser Emission A time series of an unstable laser emission.