Package: alkahest 1.1.1

Nicolas Frerebeau

alkahest: Pre-Processing XY Data from Experimental Methods

A lightweight, dependency-free toolbox for pre-processing XY data from experimental methods (i.e. any signal that can be measured along a continuous variable). This package provides methods for baseline estimation and correction, smoothing, normalization, integration and peaks detection. Baseline correction methods includes polynomial fitting as described in Lieber and Mahadevan-Jansen (2003) <doi:10.1366/000370203322554518>, Rolling Ball algorithm after Kneen and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>, SNIP algorithm after Ryan et al. (1988) <doi:10.1016/0168-583X(88)90063-8>, 4S Peak Filling after Liland (2015) <doi:10.1016/j.mex.2015.02.009> and more.

Authors:Nicolas Frerebeau [aut, cre], Brice Lebrun [ctb]

alkahest_1.1.1.tar.gz
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alkahest_1.1.1.tgz(r-4.4-any)alkahest_1.1.1.tgz(r-4.3-any)
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alkahest.pdf |alkahest.html
alkahest/json (API)
NEWS

# Install alkahest in R:
install.packages('alkahest', repos = c('https://tesselle.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tesselle/alkahest/issues

Datasets:
  • BEGe - Gamma-Ray Spectrometry
  • LaBr - Gamma-Ray Spectrometry
  • XRD - Powder X-ray Diffraction

On CRAN:

archaeometryspectroscopy

37 exports 4 stars 1.10 score 0 dependencies 239 downloads

Last updated 1 years agofrom:df22cfc7cd25edb00bfbe50d95a41ab526f0b007 (via v1.1.1)

Exports:baseline_linearbaseline_peakfillingbaseline_polynomialbaseline_rollingballbaseline_rubberbandbaseline_snipintegrate_rectangleintegrate_trapezoidka2_strip_penalizedpeaks_findpeaks_fwhmreplace_negativereplace_thresholdresample_binresample_downresample_interpolaterescale_arearescale_maxrescale_minrescale_rangerescale_totalrescale_transformsignal_bindsignal_correctsignal_driftsignal_meansignal_selectsignal_shiftsignal_slicesmooth_likelihoodsmooth_loesssmooth_rectangularsmooth_savitzkysmooth_triangularsmooth_whittakerwindow_slidingwindow_tumbling

Dependencies:

Bibliography

Rendered frombibliography.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2022-09-02
Started: 2022-09-02

Readme and manuals

Help Manual

Help pageTopics
Linear Baseline Estimationbaseline_linear baseline_linear,ANY,missing-method baseline_linear,numeric,numeric-method baseline_linear-method
4S Peak Fillingbaseline_peakfilling baseline_peakfilling,ANY,missing-method baseline_peakfilling,numeric,numeric-method baseline_peakfilling-method
Polynomial Baseline Estimationbaseline_polynomial baseline_polynomial,ANY,missing-method baseline_polynomial,numeric,numeric-method baseline_polynomial-method
Rolling Ball Baseline Estimationbaseline_rollingball baseline_rollingball,ANY,missing-method baseline_rollingball,numeric,numeric-method baseline_rollingball-method
Rubberband Baseline Estimationbaseline_rubberband baseline_rubberband,ANY,missing-method baseline_rubberband,numeric,numeric-method baseline_rubberband-method
SNIP Baseline Estimationbaseline_snip baseline_snip,ANY,missing-method baseline_snip,numeric,numeric-method baseline_snip-method
Gamma-Ray SpectrometryBEGe
Rectangle Ruleintegrate_rectangle integrate_rectangle,ANY,missing-method integrate_rectangle,numeric,numeric-method integrate_rectangle-method
Trapezoidal Ruleintegrate_trapezoid integrate_trapezoid,ANY,missing-method integrate_trapezoid,numeric,numeric-method integrate_trapezoid-method
Strip XRD ka2ka2_strip_penalized ka2_strip_penalized,ANY,missing-method ka2_strip_penalized,numeric,numeric-method ka2_strip_penalized-method
Gamma-Ray SpectrometryLaBr
Find Peakspeaks_find peaks_find,ANY,missing-method peaks_find,numeric,numeric-method peaks_find-method
Half-Width at Half-Maximumpeaks_fwhm peaks_fwhm,ANY,missing-method peaks_fwhm,numeric,numeric-method peaks_fwhm-method
Replace Negative Valuesreplace_negative replace_negative,ANY,missing-method replace_negative,numeric,numeric-method replace_negative-method
Replace Values Below a Given Thresholdreplace_threshold replace_threshold,ANY,missing,function-method replace_threshold,ANY,missing,numeric-method replace_threshold,numeric,numeric,function-method replace_threshold,numeric,numeric,numeric-method replace_threshold-method
Binresample_bin resample_bin,ANY,missing-method resample_bin,numeric,numeric-method resample_bin-method
Downsampleresample_down resample_down,ANY,missing-method resample_down,numeric,numeric-method resample_down-method
Linearly Interpolateresample_interpolate resample_interpolate,ANY,missing-method resample_interpolate,numeric,numeric-method resample_interpolate-method
Normalize intensities by AUCrescale_area rescale_area,ANY,missing-method rescale_area,numeric,numeric-method rescale_area-method
Rescales intensities to have specified minimum and maximumrescale_max rescale_max,ANY,missing-method rescale_max,numeric,numeric-method rescale_max-method rescale_min rescale_min,ANY,missing-method rescale_min,numeric,numeric-method rescale_min-method rescale_range rescale_range,ANY,missing-method rescale_range,numeric,numeric-method rescale_range-method
Rescale intensities to sum to a specified valuerescale_total rescale_total,ANY,missing-method rescale_total,numeric,numeric-method rescale_total-method
Transform Intensitiesrescale_transform rescale_transform,ANY,missing-method rescale_transform,numeric,numeric-method rescale_transform-method
Bindsignal_bind signal_bind,ANY-method signal_bind-method
Baseline Correctionsignal_correct signal_correct,ANY,missing-method signal_correct,numeric,numeric-method signal_correct-method
Drift Intensitiessignal_drift signal_drift,ANY,missing,ANY-method signal_drift,numeric,numeric,numeric-method signal_drift-method
Mean Intensitiessignal_mean signal_mean,ANY-method signal_mean-method
Shift the X Scalesignal_shift signal_shift,ANY,missing-method signal_shift,numeric,numeric-method signal_shift-method
Penalized Likelihood Smoothingsmooth_likelihood smooth_likelihood,ANY,missing-method smooth_likelihood,numeric,numeric-method smooth_likelihood-method
Loess Smoothingsmooth_loess smooth_loess,ANY,missing-method smooth_loess,numeric,numeric-method smooth_loess-method
Rectangular Smoothingsmooth_rectangular smooth_rectangular,ANY,missing-method smooth_rectangular,numeric,numeric-method smooth_rectangular-method
Savitzky-Golay Filtersmooth_savitzky smooth_savitzky,ANY,missing-method smooth_savitzky,numeric,numeric-method smooth_savitzky-method
Triangular Smoothingsmooth_triangular smooth_triangular,ANY,missing-method smooth_triangular,numeric,numeric-method smooth_triangular-method
Whittaker Smoothingsmooth_whittaker smooth_whittaker,ANY,missing-method smooth_whittaker,numeric,numeric-method smooth_whittaker-method
Subsetsignal_select signal_select,ANY,missing-method signal_select,numeric,numeric-method signal_select-method signal_slice signal_slice,ANY,missing-method signal_slice,numeric,numeric-method signal_slice-method subset
Sliding Windowswindow_sliding window_sliding,integer,integer-method window_sliding,numeric,numeric-method window_sliding-method
Tumbling Windowswindow_tumbling window_tumbling,integer,integer-method window_tumbling,numeric,numeric-method window_tumbling-method
Powder X-ray DiffractionXRD