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hyperSpec (version 0.98-20140523)

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

1,392

Version

0.98-20140523

License

GPL (>= 3)

Last Published

May 23rd, 2014

Functions in hyperSpec (0.98-20140523)

apply

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

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

.DollarNames.hyperSpec

command line completion for $
makeraster

makeraster
rbind.fill.matrix

Bind matrices by row, and fill missing columns with NA
flu

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

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

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.
merge

Merge hyperSpec objects
sample

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

Plotting hyperSpec Objects
spc.rubberband

Rubberband baseline correction
all.equal

Comparison of hyperSpec objects
quickdf

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.
bind

empty

Empty hyperSpec object
map.sel.poly

Interactively select a polygon (grid graphics) and highlight points
decomposition

Convert Principal Component Decomposition or the like into a hyperSpec Object
scan.txt.Renishaw

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

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

Function evaluation on hyperSpec objects
scan.dat.Witec

File Import Witec Raman
colSums

functions for hyperSpec objects
aggregate

aggregate hyperSpec objects
hyperSpec-package

Package hyperSpec
initialize

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.
rmmvnorm

Multivariate normal random numbers
spc.fit.poly

Polynomial Baseline Fitting These functions fit polynomal baselines.
plotmap

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.
laser

Laser Emission A time series of an unstable laser emission.
dimnames

Dimnames for hyperSpec objects
ncol

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

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.
Math2

Math Functions for hyperSpec Objects
logentry

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

Class "hyperSpec"
plotmat

Plot spectra matrix
spc.bin

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.
hy.getOptions

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

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

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

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

Plot multivariate data into colour channels
mark.dendrogram

pearson.dist

Distance based on Pearson's $R^2$
qplotspc

Spectra plotting with ggplot2
chk.hy

Validation of hyperSpec objects
read.ini

Read INI files
spc.smooth.spline

Spectral smoothing by splines
as.character

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

read Kaiser .spc files
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 }
wl2i

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.
qplotmap

Spectra plotting with ggplot2
split

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.
cov

Covariance matrices for hyperSpec objects
chondro

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

Extract and Replace parts of hyperSpec objects
mean_sd

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

Interactively select a polygon (grid graphics)
qplotc

Spectra plotting with ggplot2
spc.NA.linapprox

Impute missing data points
sweep

wc

wc word count of ASCII files
wl.eval

Evaluate function on wavelengths of hyperSpec object
read.txt.Horiba

Import Horiba Labspec exported ASCII files
read.cytomat

Import for Cytospec mat files
scale,hyperSpec-method

Center and scale hyperSpec object
as.data.frame

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
paracetamol

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.
matlab.palette

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.
normalize01

Normalize numbers -> [0, 1]
qplotmixmap

qplotmap with colour mixing for multivariate overlay
seq.hyperSpec

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

subset
collapse

Collapse hyperSpec objects
read.txt.long

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

Import for Thermo Galactic's spc file format These functions allow to import .spc files. A detailed description of the .spc file format is available at https://ftirsearch.com/features/converters/SPCFileFormat.htm.
read.jdx

JCAMP-DX Import for Shimadzu Library Spectra
spc.loess

Summary

The functions