Package: alkahest 1.2.0
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:
alkahest_1.2.0.tar.gz
alkahest_1.2.0.zip(r-4.5)alkahest_1.2.0.zip(r-4.4)alkahest_1.2.0.zip(r-4.3)
alkahest_1.2.0.tgz(r-4.4-any)alkahest_1.2.0.tgz(r-4.3-any)
alkahest_1.2.0.tar.gz(r-4.5-noble)alkahest_1.2.0.tar.gz(r-4.4-noble)
alkahest_1.2.0.tgz(r-4.4-emscripten)alkahest_1.2.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/tesselle/alkahest/issues
Pkgdown:https://packages.tesselle.org
Last updated 5 months agofrom:ecd85e40ae (on v1.2.0). Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 04 2024 |
| R-4.5-win | OK | Dec 04 2024 |
| R-4.5-linux | OK | Dec 04 2024 |
| R-4.4-win | NOTE | Dec 04 2024 |
| R-4.4-mac | NOTE | Dec 04 2024 |
| R-4.3-win | NOTE | Dec 04 2024 |
| R-4.3-mac | NOTE | Dec 04 2024 |
Exports:baseline_aslsbaseline_linearbaseline_peakfillingbaseline_polynomialbaseline_rollingballbaseline_rubberbandbaseline_snipintegrate_rectangleintegrate_trapezoidka2_strip_penalizedpeaks_findpeaks_fwhmreplace_negativereplace_thresholdresample_binresample_downresample_interpolaterescale_arearescale_maxrescale_minrescale_rangerescale_snvrescale_totalrescale_transformsignal_bindsignal_correctsignal_driftsignal_meansignal_selectsignal_shiftsignal_slicesmooth_likelihoodsmooth_loesssmooth_rectangularsmooth_savitzkysmooth_triangularsmooth_whittakerwindow_slidingwindow_tumbling
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Asymmetric Least Squares Smoothing | baseline_asls baseline_asls,ANY,missing-method baseline_asls,numeric,numeric-method baseline_asls-method |
| Linear Baseline Estimation | baseline_linear baseline_linear,ANY,missing-method baseline_linear,numeric,numeric-method baseline_linear-method |
| 4S Peak Filling | baseline_peakfilling baseline_peakfilling,ANY,missing-method baseline_peakfilling,numeric,numeric-method baseline_peakfilling-method |
| Polynomial Baseline Estimation | baseline_polynomial baseline_polynomial,ANY,missing-method baseline_polynomial,numeric,numeric-method baseline_polynomial-method |
| Rolling Ball Baseline Estimation | baseline_rollingball baseline_rollingball,ANY,missing-method baseline_rollingball,numeric,numeric-method baseline_rollingball-method |
| Rubberband Baseline Estimation | baseline_rubberband baseline_rubberband,ANY,missing-method baseline_rubberband,numeric,numeric-method baseline_rubberband-method |
| SNIP Baseline Estimation | baseline_snip baseline_snip,ANY,missing-method baseline_snip,numeric,numeric-method baseline_snip-method |
| Gamma-Ray Spectrometry | BEGe |
| Rectangle Rule | integrate_rectangle integrate_rectangle,ANY,missing-method integrate_rectangle,numeric,numeric-method integrate_rectangle-method |
| Trapezoidal Rule | integrate_trapezoid integrate_trapezoid,ANY,missing-method integrate_trapezoid,numeric,numeric-method integrate_trapezoid-method |
| Strip XRD ka2 | ka2_strip_penalized ka2_strip_penalized,ANY,missing-method ka2_strip_penalized,numeric,numeric-method ka2_strip_penalized-method |
| Gamma-Ray Spectrometry | LaBr |
| Find Peaks | peaks_find peaks_find,ANY,missing-method peaks_find,numeric,numeric-method peaks_find-method |
| Half-Width at Half-Maximum | peaks_fwhm peaks_fwhm,ANY,missing-method peaks_fwhm,numeric,numeric-method peaks_fwhm-method |
| Raman Spectroscopy | Raman |
| Replace Negative Values | replace_negative replace_negative,ANY,missing-method replace_negative,numeric,numeric-method replace_negative-method |
| Replace Values Below a Given Threshold | replace_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 |
| Bin | resample_bin resample_bin,ANY,missing-method resample_bin,numeric,numeric-method resample_bin-method |
| Downsample | resample_down resample_down,ANY,missing-method resample_down,numeric,numeric-method resample_down-method |
| Linearly Interpolate | resample_interpolate resample_interpolate,ANY,missing-method resample_interpolate,numeric,numeric-method resample_interpolate-method |
| Normalize intensities by AUC | rescale_area rescale_area,ANY,missing-method rescale_area,numeric,numeric-method rescale_area-method |
| Rescales intensities to have specified minimum and maximum | rescale_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 |
| Standard Normal Variate (SNV) Transformation | rescale_snv rescale_snv,ANY,missing-method rescale_snv,numeric,numeric-method rescale_snv-method |
| Rescale intensities to sum to a specified value | rescale_total rescale_total,ANY,missing-method rescale_total,numeric,numeric-method rescale_total-method |
| Transform Intensities | rescale_transform rescale_transform,ANY,missing-method rescale_transform,numeric,numeric-method rescale_transform-method |
| Bind | signal_bind signal_bind,ANY-method signal_bind-method |
| Baseline Correction | signal_correct signal_correct,ANY,missing-method signal_correct,numeric,numeric-method signal_correct-method |
| Drift Intensities | signal_drift signal_drift,ANY,missing,ANY-method signal_drift,numeric,numeric,numeric-method signal_drift-method |
| Mean Intensities | signal_mean signal_mean,ANY-method signal_mean-method |
| Shift the X Scale | signal_shift signal_shift,ANY,missing-method signal_shift,numeric,numeric-method signal_shift-method |
| Penalized Likelihood Smoothing | smooth_likelihood smooth_likelihood,ANY,missing-method smooth_likelihood,numeric,numeric-method smooth_likelihood-method |
| Loess Smoothing | smooth_loess smooth_loess,ANY,missing-method smooth_loess,numeric,numeric-method smooth_loess-method |
| Rectangular Smoothing | smooth_rectangular smooth_rectangular,ANY,missing-method smooth_rectangular,numeric,numeric-method smooth_rectangular-method |
| Savitzky-Golay Filter | smooth_savitzky smooth_savitzky,ANY,missing-method smooth_savitzky,numeric,numeric-method smooth_savitzky-method |
| Triangular Smoothing | smooth_triangular smooth_triangular,ANY,missing-method smooth_triangular,numeric,numeric-method smooth_triangular-method |
| Whittaker Smoothing | smooth_whittaker smooth_whittaker,ANY,missing-method smooth_whittaker,numeric,numeric-method smooth_whittaker-method |
| Subset | signal_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 Windows | window_sliding window_sliding,integer,integer-method window_sliding,numeric,numeric-method window_sliding-method |
| Tumbling Windows | window_tumbling window_tumbling,integer,integer-method window_tumbling,numeric,numeric-method window_tumbling-method |
| Powder X-ray Diffraction | XRD |
