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hyperSpec (version 0.98-20120713)

Interface for hyperspectral data, i.e. spectra + meta info (spatial, time, concentration, ...)

Description

This package is an interface to handle hyperspectral data sets in R. 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

1,454

Version

0.98-20120713

License

GPL (>= 3)

Maintainer

Claudia Beleites

Last Published

July 14th, 2012

Functions in hyperSpec (0.98-20120713)

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

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

Convert Principal Component Decomposition or the like into a hyperSpec Object Decomposition of the spectra matrix is a common procedure in chemometrix data analysis. decomposition converts the result matrices into new 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.

aggregate hyperSpec objects

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

Extract and Replace parts of hyperSpec objects

Plot multivariate data into colour channels

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.

Comparison of hyperSpec objects

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

Normalize numbers -> [0, 1]

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

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.

Distance based on Pearson's $R^2$

.DollarNames.hyperSpec

command line completion for $

Plot spectra matrix

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

rbind.fill.matrix

Bind matrices by row, and fill missing columns with NA

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

Function evaluation on hyperSpec objects

Math Functions for hyperSpec Objects

qplotmap with colour mixing for multivariate overlay

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

Merge hyperSpec objects

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

spc.NA.linapprox

Impute missing data points

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

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.

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.

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.

Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%

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

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

Covariance matrices for hyperSpec objects

Logging the processing ot a hyperSpec Object Extracts the slot @log of a hyperSpec object.

Interactively select a polygon (grid graphics)

read.spc.KaiserMap

read.spc.KaiserMap imports sets of .spc files of Raman maps written by Kaiser Optical Systems' Hologram software. It may also serve as an example how to write wrapper functions for read.spc to conveniently import specialized sets of .spc files.

read.jdx.Shimadzu

JCAMP-DX Import for Shimadzu Library Spectra

File Import Witec Raman

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

Append a Row to the logbook of a hyperSpec Object A log entry is generated and appended to the log of x.

Spectra plotting with ggplot2

Evaluate function on wavelengths of 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.

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.

Collapse hyperSpec objects

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

Empty hyperSpec object

hyperSpec-package

Package hyperSpec

Laser Emission A time series of an unstable laser emission.

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

Polynomial Baseline Fitting These functions fit polynomal baselines.

Validation of hyperSpec objects

functions for hyperSpec objects

hyperSpec-class

Class "hyperSpec"

Spectra plotting with ggplot2

Spectra plotting with ggplot2

read.txt.Shimadzu

Reads Shimadzu Spectra Files (.txt) as exported by Shimadzu Chrome Solution (v. 2.73)

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.

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

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

read.ENVI.Nicolet

Nicolet uses some more keywords in their header file. read.ENVI.Nicolet therefore appends "description", "z plot titles", and "pixel size" to keys.hdr2log before calling read.ENVI. They are then interpreted as follows: ll{ description giving the position of the first spectrum z plot titles wavelength and intensity axis units, comma separated pixel size interpreted as x and y step size }

wc word count of ASCII files

Interactively select a polygon (grid graphics) and highlight points

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.

Dimnames for hyperSpec objects

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.

mark.dendrogram

Mark groups in hclust dendrograms

Plotting 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.

scan.txt.Renishaw

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

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.