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hyperSpec (version 0.99-20200115)

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

1,452

Version

0.99-20200115

License

GPL (>= 3)

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Repository

https://github.com/cbeleites/hyperSpec

Maintainer

Claudia Beleites

Last Published

January 17th, 2020

Functions in hyperSpec (0.99-20200115)

Polynomial Baseline Fitting These functions fit polynomal baselines.

.collapse.equal

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

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.

mark.dendrogram

Mark groups in hclust dendrograms

guess.wavelength

guess wavelengths from character vector

.cluster.wavelengths

Find clusters of approximately equal wavelengths

Interactively select a polygon (grid graphics) and highlight points

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.

[,hyperSpec-method

Extract and Replace parts of hyperSpec objects

Plotting hyperSpec Objects

Convert Principal Component Decomposition or the like into a hyperSpec Object

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

droplevels,hyperSpec-method

droplevels for hyperSpec object

ncol,hyperSpec-method

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

Empty hyperSpec object

normalization for mixed colors

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

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

dimnames,hyperSpec-method

dimnames for hyperSpec objects

Collapse 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.

mean_sd,numeric-method

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

cov,hyperSpec,missing-method

Covariance matrices for hyperSpec objects

Laser Emission A time series of an unstable laser emission.

merge,hyperSpec,hyperSpec-method

Merge hyperSpec objects

hyperSpec-package

Package hyperSpec

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

Creating a hyperSpec Object

.DollarNames.hyperSpec

command line completion for $

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.

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

File Import Witec Raman

sample,hyperSpec-method

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

Multivariate normal random numbers

scale,hyperSpec-method

Center and scale hyperSpec object

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.

qplotmap with colour mixing for multivariate overlay

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.

Import of ENVI data as hyperSpec object

Plot multivariate data into colour channels

Plot spectra matrix

File Import Andor Solis

read.asc.PerkinElmer

File import filter PerkinElmer ASCII spectra

scan.txt.Renishaw

import Raman measurements from Renishaw ASCII-files

Math2,hyperSpec-method

Math Functions for hyperSpec Objects

Spectra plotting with ggplot2

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

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.

JCAMP-DX Import for Shimadzu Library Spectra

read.spc.Kaiser

read Kaiser .spc files

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

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

Read XML footer from SPE file format version 3.0

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)

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

read.txt.Horiba

Import Horiba Labspec exported ASCII files

Rubberband baseline correction

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.

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

Spectra plotting with ggplot2

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.

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.

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.

Import WinSpec SPE file

hyperSpec unit tests

Convert different wavelength units

Function evaluation on 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.

spc.smooth.spline

Spectral smoothing by splines

Impute missing data points

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

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.

wc word count of ASCII files

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

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.

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

Comparison of hyperSpec objects

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

aggregate hyperSpec objects

as.hyperSpec: convenience conversion functions

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

Arithmetical Operators for hyperSpec objects

Validation of hyperSpec objects

Binding hyperSpec Objects