Distance based on Pearson's $R^2$
Package hyperSpec
apply
Computes summary statistics for the spectra of a hyperSpec
object.
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.
Creating a hyperSpec Object
Like other S4 objects, a hyperSpec object can be created by new
. The
hyperSpec object is then initialize
d using the given parameters.
Options for package hyperSpec
Functions to access and set hyperSpec's options.
Quinine Fluorescence Spectra
Fluorescence spectra of different dilutions of quinine forming a
calibration set.
Paracetamol Spectrum
A Raman spectrum of a paracetamol tablet.
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
Spectra plotting with ggplot2
Validation of hyperSpec objects
Merge hyperSpec objects
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
}
Interactively select a polygon (grid graphics) and highlight points
Math Functions for 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
.
Plot multivariate data into colour channels
Interactively select a polygon (grid graphics)
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. Covariance matrices for hyperSpec objects
Normalize numbers -> [0, 1]
Append a Row to the logbook of a hyperSpec Object
A log entry is generated and appended to the log of x
.
Mark groups in hclust
dendrograms 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. Spectra plotting with ggplot2
Sorting the Wavelengths of a hyperSpec Object
Rearranges the hyperSpec
object so that the wavelength vector is in increasing (or
decreasing) order.
import Raman measurements from Renishaw ASCII-files
import Raman measurements from Renishaw (possibly compressed) .txt file.
Reads Shimadzu GCxGC - Spectra Files (.txt) as exported by Shimadzu Chrome Solution (v. 2.73)
Mass Spectrometer: Shimadzu GCMS-QP 2010 Ultra (www.shimadzu.com)
Multivariate normal random numbers
Extract and Replace parts of 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. 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.
Random Samples and Permutations
Take a sample of the specified size from the elements of x with or without
replacement.
qplotmap with colour mixing for multivariate overlay
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.
Import and Export of hyperSpec objects
Besides save
and load
, two general
ways to import and export data into hyperSpec
objects exist. 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. Sweep Summary Statistic out of an hyperSpec Object
sweep
for hyperSpec
objects. Evaluate function on wavelengths of hyperSpec object
The functions
Comparison of hyperSpec objects
Function evaluation on hyperSpec objects
makeraster
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.
hyperSpec unit tests
If svUnit
is available, run the unit tests and
display the results. 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.
Plotting hyperSpec Objects
Convert a hyerSpec object to character strings for Display
print
, show
, and summary
show the result of
as.character
.
Collapse hyperSpec objects
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
.
Empty hyperSpec object
Laser Emission
A time series of an unstable laser emission.
Getting and Setting the Wavelength Axis
wl
returns the wavelength axis, wl<-
sets it.
subset
aggregate hyperSpec objects
Polynomial Baseline Fitting
These functions fit polynomal baselines.
functions for hyperSpec objects
Impute missing data points
The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an
hyperSpec Object)
Logging the processing ot a hyperSpec Object
Extracts the slot @log
of a hyperSpec
object.
Spectra plotting with ggplot2
Sequence generation along spectra or wavelengths
This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.
loess smoothing interpolation for spectra
Spectra can be smoothed and interpolated on a new wavelength axis using
loess
. Barbiturates Spectra from .spc example files
A time series of mass spectra in a list of hyperSpec objects.
Dimnames for hyperSpec objects
Class "hyperSpec"
JCAMP-DX Import for Shimadzu Library Spectra
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.
Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
Raman spectra of 2 Chondrocytes in Cartilage
A Raman-map (laterally resolved Raman spectra) of chondrocytes in
cartilage.
command line completion for $
Mean and Standard Deviation
Calculate mean and standard deviation, and mean, mean $\pm$ one
standard deviation, respectively.
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.
Plot spectra matrix
Bind matrices by row, and fill missing columns with NA
File Import Witec Raman
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
. wc
word count of ASCII files