Package: OpenSpecy 1.4.0

OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available via run_app() or online at <https://openanalysis.org/openspecy/>.

Authors:Win Cowger [cre, aut, dtc], Zacharias Steinmetz [aut], Hazel Vaquero [aut], Nick Leong [aut], Andrea Faltynkova [aut, dtc], Hannah Sherrod [aut], Andrew B Gray [ctb], Hannah Hapich [ctb], Jennifer Lynch [ctb, dtc], Hannah De Frond [ctb, dtc], Keenan Munno [ctb, dtc], Chelsea Rochman [ctb, dtc], Sebastian Primpke [ctb, dtc], Orestis Herodotou [ctb], Mary C Norris [ctb], Christine M Knauss [ctb], Aleksandra Karapetrova [ctb, dtc, rev], Vesna Teofilovic [ctb], Laura A. T. Markley [ctb], Shreyas Patankar [ctb, dtc], Rachel Kozloski [ctb, dtc], Samiksha Singh [ctb], Katherine Lasdin [ctb], Cristiane Vidal [ctb], Clare Murphy-Hagan [ctb], Philipp Baumann [ctb], Pierre Roudier [ctb], National Renewable Energy Laboratory [fnd], Possibility Lab [fnd]

OpenSpecy_1.4.0.tar.gz
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OpenSpecy.pdf |OpenSpecy.html✨
OpenSpecy/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/wincowgerdev/openspecy-package/issues

Datasets:

On CRAN:

7.38 score 27 stars 17 scripts 514 downloads 63 exports 106 dependencies

Last updated 4 days agofrom:ab372bed5e. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winNOTENov 14 2024
R-4.4-macNOTENov 14 2024
R-4.3-winNOTENov 14 2024
R-4.3-macNOTENov 14 2024

Exports:adj_intensadj_negadj_resadj_waveai_classifyas_hyperSpecas_OpenSpecyc_speccalc_window_pointscheck_libcheck_OpenSpecycollapse_specconform_resconform_speccor_specdef_featuresfill_specfilter_specflatten_rangegen_gridget_libget_metadataheatmap_spechuman_tsident_specinteractive_plotis_empty_vectoris_OpenSpecyload_libmake_relmanage_namatch_specmax_cor_namedmean_replacemerge_mapOpenSpecyos_similarityplotly_specprocess_specread_anyread_aspread_enviread_extdataread_jdxread_manyread_opusread_opus_rawread_sparead_spcread_specread_textread_ziprestrict_rangerm_librun_appsample_specsig_noisesmooth_intensspatial_smoothspec_ressplit_specsubtr_baselinewrite_spec

Dependencies:askpassbase64encbitopsbriobslibcachemcallrcaToolsclicodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledeldirdescdiffobjdigestdplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsggplot2glmnetgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrhyperSpecinterpisobanditeratorsjpegjquerylibjsonliteknitrlabelinglaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemmandmunsellnlmeopensslpillarpkgbuildpkgconfigpkgloadplotlypngpraiseprocessxpromisespspurrrR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrprojrootsassscalesshapeshinysignalsourcetoolsstringistringrsurvivalsystestthattibbletidyrtidyselecttinytexutf8vctrsviridisLitewaldowithrxfunxml2xtableyaml

Open Specy Package Tutorial

Win Cowger, Zacharias Steinmetz, Rachel Kozloski, Aleksandra Karapetrova

Rendered fromsop.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-06-13
Started: 2021-03-22

Readme and manuals

Help Manual

Help pageTopics
Adjust spectral intensities to standard absorbance units.adj_intens adj_intens.default adj_intens.OpenSpecy
Normalization and conversion of spectral dataadj_neg adj_res conform_res is_empty_vector mean_replace
Adjust wavelength to wavenumbers for Ramanadj_wave adj_wave.default adj_wave.OpenSpecy
Create 'OpenSpecy' objectsas_OpenSpecy as_OpenSpecy.data.frame as_OpenSpecy.default as_OpenSpecy.hyperSpec as_OpenSpecy.list as_OpenSpecy.OpenSpecy check_OpenSpecy gen_grid is_OpenSpecy OpenSpecy
Manage spectral objectsc_spec c_spec.default c_spec.list c_spec.OpenSpecy merge_map merge_map.default merge_map.list merge_map.OpenSpecy sample_spec sample_spec.default sample_spec.OpenSpecy
Manage spectral librariescheck_lib get_lib load_lib rm_lib
Define featurescollapse_spec collapse_spec.default collapse_spec.OpenSpecy def_features def_features.default def_features.OpenSpecy
Conform spectra to a standard wavenumber seriesconform_spec conform_spec.default conform_spec.OpenSpecy
Identify and filter spectraai_classify ai_classify.default ai_classify.OpenSpecy cor_spec cor_spec.default cor_spec.OpenSpecy fill_spec fill_spec.default fill_spec.OpenSpecy filter_spec filter_spec.default filter_spec.OpenSpecy get_metadata get_metadata.default get_metadata.OpenSpecy ident_spec match_spec match_spec.default match_spec.OpenSpecy max_cor_named os_similarity os_similarity.default os_similarity.OpenSpecy
Generic Open Specy Methodsas.data.frame.OpenSpecy as.data.table.OpenSpecy head.OpenSpecy lines.OpenSpecy plot.OpenSpecy print.OpenSpecy summary.OpenSpecy
Create human readable timestampshuman_ts
Make spectral intensities relativemake_rel make_rel.default make_rel.OpenSpecy
Ignore or remove NA intensitiesmanage_na manage_na.default manage_na.OpenSpecy
Interactive plots for OpenSpecy objectsheatmap_spec heatmap_spec.default heatmap_spec.OpenSpecy interactive_plot interactive_plot.default interactive_plot.OpenSpecy plotly_spec plotly_spec.default plotly_spec.OpenSpecy
Process Spectraprocess_spec process_spec.default process_spec.OpenSpecy
Sample Raman spectrumraman_hdpe
Read spectral data from multiple filesread_any read_many read_zip
Read ENVI dataread_envi
Read spectral data from Bruker OPUS binary filesread_opus
Read a Bruker OPUS spectrum binary raw stringread_opus_raw
Read spectral dataread_asp read_extdata read_jdx read_spa read_spc read_text
Range restriction and flattening for spectraflatten_range flatten_range.default flatten_range.OpenSpecy restrict_range restrict_range.default restrict_range.OpenSpecy
Run Open Specy apprun_app
Calculate signal and noise metrics for OpenSpecy objectssig_noise sig_noise.default sig_noise.OpenSpecy
Smooth spectral intensitiescalc_window_points calc_window_points.default calc_window_points.OpenSpecy smooth_intens smooth_intens.default smooth_intens.OpenSpecy
Spatial Smoothing of OpenSpecy Objectsspatial_smooth
Spectral resolutionspec_res spec_res.default spec_res.OpenSpecy
Split Open Specy objectssplit_spec
Automated background subtraction for spectral datasubtr_baseline subtr_baseline.default subtr_baseline.OpenSpecy
Test reference librarytest_lib
Read and write spectral dataas_hyperSpec read_spec write_spec write_spec.default write_spec.OpenSpecy