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:
OpenSpecy_1.4.0.tar.gz
OpenSpecy_1.4.0.tar.gz(r-4.5-noble)OpenSpecy_1.4.0.tar.gz(r-4.4-noble)
OpenSpecy_1.4.0.tgz(r-4.4-emscripten)OpenSpecy_1.4.0.tgz(r-4.3-emscripten)
OpenSpecy.pdf |OpenSpecy.html✨
OpenSpecy/json (API)
NEWS
# Install 'OpenSpecy' in R: |
install.packages('OpenSpecy', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wincowgerdev/openspecy-package/issues
- raman_hdpe - Sample Raman spectrum
- test_lib - Test reference library
Last updated 20 days agofrom:c146b16d35. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 05 2024 |
R-4.5-linux | OK | Nov 05 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
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Adjust spectral intensities to standard absorbance units. | adj_intens adj_intens.default adj_intens.OpenSpecy |
Normalization and conversion of spectral data | adj_neg adj_res conform_res is_empty_vector mean_replace |
Adjust wavelength to wavenumbers for Raman | adj_wave adj_wave.default adj_wave.OpenSpecy |
Create 'OpenSpecy' objects | as_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 objects | c_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 libraries | check_lib get_lib load_lib rm_lib |
Define features | collapse_spec collapse_spec.default collapse_spec.OpenSpecy def_features def_features.default def_features.OpenSpecy |
Conform spectra to a standard wavenumber series | conform_spec conform_spec.default conform_spec.OpenSpecy |
Identify and filter spectra | ai_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 Methods | as.data.frame.OpenSpecy as.data.table.OpenSpecy head.OpenSpecy lines.OpenSpecy plot.OpenSpecy print.OpenSpecy summary.OpenSpecy |
Create human readable timestamps | human_ts |
Make spectral intensities relative | make_rel make_rel.default make_rel.OpenSpecy |
Ignore or remove NA intensities | manage_na manage_na.default manage_na.OpenSpecy |
Interactive plots for OpenSpecy objects | heatmap_spec heatmap_spec.default heatmap_spec.OpenSpecy interactive_plot interactive_plot.default interactive_plot.OpenSpecy plotly_spec plotly_spec.default plotly_spec.OpenSpecy |
Process Spectra | process_spec process_spec.default process_spec.OpenSpecy |
Sample Raman spectrum | raman_hdpe |
Read spectral data from multiple files | read_any read_many read_zip |
Read ENVI data | read_envi |
Read spectral data from Bruker OPUS binary files | read_opus |
Read a Bruker OPUS spectrum binary raw string | read_opus_raw |
Read spectral data | read_asp read_extdata read_jdx read_spa read_spc read_text |
Range restriction and flattening for spectra | flatten_range flatten_range.default flatten_range.OpenSpecy restrict_range restrict_range.default restrict_range.OpenSpecy |
Run Open Specy app | run_app |
Calculate signal and noise metrics for OpenSpecy objects | sig_noise sig_noise.default sig_noise.OpenSpecy |
Smooth spectral intensities | calc_window_points calc_window_points.default calc_window_points.OpenSpecy smooth_intens smooth_intens.default smooth_intens.OpenSpecy |
Spatial Smoothing of OpenSpecy Objects | spatial_smooth |
Spectral resolution | spec_res spec_res.default spec_res.OpenSpecy |
Split Open Specy objects | split_spec |
Automated background subtraction for spectral data | subtr_baseline subtr_baseline.default subtr_baseline.OpenSpecy |
Test reference library | test_lib |
Read and write spectral data | as_hyperSpec read_spec write_spec write_spec.default write_spec.OpenSpecy |