prospectr

Misc. Functions for Processing and Sample Selection of Spectroscopic Data

Antoine Stevens & Leo Ramirez-Lopez

Last update: 24.09.2020

prospectr provides various utilities for pre--processing and sample selection of visible and near infrared spectral data with R. While similar functions are available in other packages, like signal, the functions in this package works indifferently for data.frame, matrix and vector inputs. Besides, several functions are optimized for speed and use C++ code through the Rcpp and RcppArmadillo packages.

A vignette gives an overview of the main functionalities of the package. Just type vignette("prospectr-intro") in the console to access it. Currently, the following preprocessing functions are available:

continuumRemoval : continuum-removed absorbance or reflectance values
savitzkyGolay : Savitzky-Golay filter (smoothing and derivatives)
gapDer : gap-segment derivative
movav : moving average
standardNormalVariate : standard normal variate (snv)
detrend : detrend normalization
binning : average in column--wise subsets
resample : resample a signal to new coordinates by linear or spline interpolation resample2 : resample a signal to new coordinates using FWHM values
blockScale : block scaling
blockNorm : sum of squares block weighting

The selection of representative samples/observations for calibration of spectral models can be achieved with one of the following functions:

naes : k-means sampling
kenStone : CADEX (Kennard--Stone) algorithm
duplex : DUPLEX algorithm
shenkWest : SELECT algorithm
puchwein : Puchwein sampling
honigs : Unique-sample selection by spectral subtraction

Other useful functions are also available:

read_nircal : read binary files exported from BUCHI NIRCal software
readASD : read binary or text files from an ASD instrument (Indico Pro format)
spliceCorrection : correct spectra for steps at the splice of detectors in an ASD FieldSpec Pro
cochranTest : detects replicate outliers with the Cochran C test

Bug report and development version

You can send an email to the package maintainer (ramirez.lopez.leo@gmail.com) or create an issue on github. To install the development version of prospectr, simply install devtools from CRAN then run install_github("l-ramirez-lopez/prospectr").