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hyperSpec (version 0.98-20150304)

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

1,452

Version

0.98-20150304

License

GPL (>= 3)

Maintainer

Claudia Beleites

Last Published

March 5th, 2015

Functions in hyperSpec (0.98-20150304)

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

aggregate hyperSpec objects

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

dimnames,hyperSpec-method

Dimnames for hyperSpec objects

Arithmetical Operators for hyperSpec objects

qplotmap with colour mixing for multivariate overlay

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.

rbind.fill.matrix

Bind matrices by row, and fill missing columns with NA

hyperSpec-class

Class "hyperSpec"

Laser Emission A time series of an unstable laser emission.

Collapse hyperSpec objects

.DollarNames.hyperSpec

command line completion for $

cov,hyperSpec,missing-method

Covariance matrices for hyperSpec objects

merge,hyperSpec,hyperSpec-method

Merge hyperSpec objects

Plotting hyperSpec Objects

mark.dendrogram

Mark groups in hclust dendrograms

Comparison of hyperSpec objects

Convert Principal Component Decomposition or the like into a hyperSpec Object

Binding hyperSpec Objects Two S3 functions cbind.hyperSpec and rbind.hyperSpec act as an interfaces to cbind2 and rbind2 because neither rBind and cBind nor S4 versions of cbind and rbind do work at the moment.

Interactively select a polygon (grid graphics) and highlight points

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

Polynomial Baseline Fitting These functions fit polynomal baselines.

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.

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

[,hyperSpec-method

Extract and Replace parts of hyperSpec objects

Spectra plotting with ggplot2

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.

colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects

ncol,hyperSpec-method

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

Rubberband baseline correction

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.

levelplot,hyperSpec,missing-method

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.

Math2,hyperSpec-method

Math Functions for hyperSpec Objects

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

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.

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.

read.txt.Horiba

Import Horiba Labspec exported ASCII files

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.

Evaluate function on wavelengths of hyperSpec object

Spectra plotting with ggplot2

File Import Witec Raman

JCAMP-DX Import for Shimadzu Library Spectra

hyperSpec unit tests If svUnit is available, run the unit tests and display the results.

scale,hyperSpec-method

Center and scale hyperSpec object

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

as.character,hyperSpec-method

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

Plot spectra matrix

Import for Cytospec mat files

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.

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.

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.

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.

wc word count of ASCII files

read.spc.Kaiser

read Kaiser .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)

sample,hyperSpec-method

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

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 import Raman measurements from Renishaw (possibly compressed) .txt file.

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

Multivariate normal random numbers

Spectra plotting with ggplot2

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.

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

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

Validation of hyperSpec objects

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

mean_sd,numeric-method

Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean $+-$ one standard deviation, respectively.

hyperSpec-package

Package hyperSpec

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

read.ENVI.Nicolet

Nicolet uses some more keywords in their header file. They are interpreted as follows:

giving the position of the first spectrum

wavelength and intensity axis units, comma separated

These parameters can be overwritten by giving a list with the respective elements in parameter header.

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

Function evaluation on hyperSpec objects

spc.NA.linapprox

Impute missing data points

normalization for mixed colors

Empty hyperSpec object

Plot multivariate data into colour channels

Distance based on Pearson's $R squared$

spc.smooth.spline

Spectral smoothing by splines