Package: spectrolab 0.0.19

spectrolab: Class and Methods for Spectral Data

Input/Output, processing and visualization of spectra taken with different spectrometers, including SVC (Spectra Vista), ASD and PSR (Spectral Evolution). Implements an S3 class spectra that other packages can build on. Provides methods to access, plot, manipulate, splice sensor overlap, vector normalize and smooth spectra.

Authors:Jose Eduardo Meireles [aut, cre], Anna K. Schweiger [aut], Jeannine Cavender-Bares [aut]

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spectrolab.pdf |spectrolab.html✨
spectrolab/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/meireles/spectrolab/issues

Datasets:

On CRAN:

science

7.40 score 16 stars 260 scripts 202 downloads 1 mentions 30 exports 32 dependencies

Last updated 3 days agofrom:147671d288. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 14 2025
R-4.5-winOKJan 14 2025
R-4.5-linuxOKJan 14 2025
R-4.4-winOKJan 14 2025
R-4.4-macOKJan 14 2025
R-4.3-winOKJan 14 2025
R-4.3-macOKJan 14 2025

Exports:apply_by_bandas_spectrabandsbands<-combinedefault_spec_regionsguess_splice_atis_spectramake_fwhmmatch_sensorsmetameta<-normalizepairwise_indicesplot_interactiveplot_quantileplot_regionsread_spectraresamplesdsmoothsmooth_fwhmsmooth_moving_avgsmooth_splinespectrasubset_bytry_keep_txtvaluevalue<-var

Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclemagrittrmemoisemimepromisesR6rappdirsRColorBrewerRcpprlangsassshinyshinyjssourcetoolswithrxtable

Introduction to spectrolab

Jose Eduardo Meireles, Anna K. Schweiger, and Jeannine Cavender-Bares

Rendered fromintroduction_to_spectrolab.Rmdusingknitr::rmarkdownon Jan 14 2025.

Last update: 2025-01-10
Started: 2016-11-15

Matching sensor overlap

Jose Eduardo Meireles

Rendered frommatch_sensors.Rmdusingknitr::rmarkdownon Jan 14 2025.

Last update: 2025-01-10
Started: 2017-07-29

Resampling Spectra

Jose Eduardo Meireles

Rendered fromresample.Rmdusingknitr::rmarkdownon Jan 14 2025.

Last update: 2025-01-02
Started: 2024-12-17

Readme and manuals

Help Manual

Help pageTopics
Subset spectra[.spectra
Assign values to spectra[<-.spectra
Aggregate spectraaggregate.spectra
Apply numeric function by bandapply_by_band apply_by_band.spectra
Convert matrix or data frame to spectraas_spectra
Convert data.frame to spectraas_spectra.data.frame
Convert matrix to spectraas_spectra.matrix
Convert spectra to data.frameas.data.frame.spectra
Convert spectra to matrixas.matrix.spectra
Get spectra band labelsbands bands.spectra
Set band labelsbands<-
Combine spectral datasetscombine combine.spectra
Return default spectral regions matrixdefault_spec_regions
Get dimension of spectradim.spectra
Guess splice bands (bounds between senors)guess_splice_at guess_splice_at.spectra
Is it a spectra object?is_spectra
Resample the FWHM to a new set of bands using a gaussian modelmake_fwhm
Match spectra at sensor transitionsmatch_sensors match_sensors.spectra
Maximum valuemax.spectra
Mean spectrummean.spectra
Median spectrummedian.spectra
Get metadatameta meta.spectra
Set metadatameta<-
Minimum valuemin.spectra
Get spectra sample namesnames.spectra
Set spectra sample namesnames<-.spectra
Vector normalize spectranormalize normalize.spectra
Arithmetic operators for spectraOps.spectra
Pairwise indicespairwise_indices
Plot spectra interactivelyplot_interactive
Plot spectra quantilesplot_quantile
Plot polygons for spectral regionsplot_regions
Plot spectraplot.spectra
Print spectraprint.spectra
Compute spectra quantilesquantile.spectra
Range of spectral valuesrange.spectra
Read files from various formats into `spectra`read_spectra
Resample spectraresample
Standard deviationsd
Default standard deviationsd.default
Standard deviation spectrumsd.spectra
Generic Smoothing functionsmooth
Smooth spectra with a gaussian modelsmooth_fwhm
Smooth moving average for spectrasmooth_moving_avg
Smooth spline functions for spectrasmooth_spline
Default smoothing functionsmooth.default
Smooth spectrasmooth.spectra
Example spectral datasetspec_matrix_example
Spectra object constructorspectra
Split spectrasplit.spectra
Structure of the spectra objectstr.spectra
Subset spectra by factorsubset_by subset_by.spectra
Summarize spectrasummary.spectra
Spectra Transposet.spectra
Wrap function to try to keep texttry_keep_txt
Get spectra valuevalue value.spectra
Set spectra valuevalue<-
Variancevar
Variancevar.default
Variance spectrumvar.spectra