apply
Computes summary statistics for the spectra of a hyperSpec object.
Barbiturates Spectra from .spc example files
A time series of mass spectra in a list of 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 command line completion for $
makeraster
Bind matrices by row, and fill missing columns with NA
Quinine Fluorescence Spectra
Fluorescence spectra of different dilutions of quinine forming a
calibration set.
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)
Logging the processing ot a hyperSpec Object
Extracts the slot @log of a hyperSpec object.
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 hyperSpec objects
Random Samples and Permutations
Take a sample of the specified size from the elements of x with or without
replacement.
Plotting hyperSpec Objects
Rubberband baseline correction
Comparison of hyperSpec objects
Quick data frame.
Experimental version of as.data.frame Binding hyperSpec Objects
Two S3 functions cbind.hyperSpec and rbind.hyperSpec act as
an interfaces to cbind2 and rbind2 because neither
rBind cBind cbind and rbind do work at the moment. Empty hyperSpec object
Interactively select a polygon (grid graphics) and highlight points
Convert Principal Component Decomposition or the like into a hyperSpec Object
import Raman measurements from Renishaw ASCII-files
import Raman measurements from Renishaw (possibly compressed) .txt file.
Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
Function evaluation on hyperSpec objects
File Import Witec Raman
functions for hyperSpec objects
aggregate hyperSpec objects
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.
Multivariate normal random numbers
Polynomial Baseline Fitting
These functions fit polynomal baselines.
Plot a Map and Identify/Select Spectra in the Map
levelplot Laser Emission
A time series of an unstable laser emission.
Dimnames for hyperSpec objects
The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an
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.
Math Functions for hyperSpec Objects
Append a Row to the logbook of a hyperSpec Object
A log entry is generated and appended to the log of x.
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.
Class "hyperSpec"
Plot spectra matrix
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.
Options for package hyperSpec
Functions to access and set hyperSpec's options.
Getting and Setting the Wavelength Axis
wl returns the wavelength axis, wl<- sets it.
Sorting the Wavelengths of a hyperSpec Object
Rearranges the hyperSpec object so that the wavelength vector is in increasing (or
decreasing) order.
hyperSpec unit tests
If svUnit Plot multivariate data into colour channels
Mark groups in hclust Distance based on Pearson's $R^2$
Spectra plotting with ggplot2
Validation of hyperSpec objects
Read INI files
Spectral smoothing by splines
Convert a hyerSpec object to character strings for Display
print, show, and summary show the result of
as.character.
read Kaiser .spc files
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
}
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.
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.
Covariance matrices for hyperSpec objects
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 and Standard Deviation
Calculate mean and standard deviation, and mean, mean $\pm$ one
standard deviation, respectively.
Interactively select a polygon (grid graphics)
Spectra plotting with ggplot2
Impute missing data points
Sweep Summary Statistic out of an hyperSpec Object
sweep hyperSpec objects. wc
word count of ASCII files
Evaluate function on wavelengths of hyperSpec object
Import Horiba Labspec exported ASCII files
Import for Cytospec mat files
Center and scale hyperSpec object
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 Spectrum
A Raman spectrum of a paracetamol tablet.
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.
Normalize numbers -> [0, 1]
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.
Color coding legend for factors
Modifies a list of lattice arguments (as for levelplot subset
Collapse hyperSpec objects
Import and Export of hyperSpec objects
Besides save load hyperSpec objects exist. 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 .
JCAMP-DX Import for Shimadzu Library Spectra
loess smoothing interpolation for spectra
Spectra can be smoothed and interpolated on a new wavelength axis using
loess The functions