Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
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Documentation for package ‘OpenSpecy’ version 2.0.1
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A B C D E F G H I J L M O P R S T V W
-- A --
| add_visual_image | Attach visual images to spectral map objects |
| adj_intens | Adjust spectral intensities to standard absorbance units. |
| adj_intens.default | Adjust spectral intensities to standard absorbance units. |
| adj_intens.OpenSpecy | Adjust spectral intensities to standard absorbance units. |
| adj_neg | Normalization and conversion of spectral data |
| adj_res | Normalization and conversion of spectral data |
| adj_wave | Adjust wavelength to wavenumbers for Raman |
| adj_wave.default | Adjust wavelength to wavenumbers for Raman |
| adj_wave.OpenSpecy | Adjust wavelength to wavenumbers for Raman |
| ai_classify | Identify and filter spectra |
| ai_classify.default | Identify and filter spectra |
| ai_classify.OpenSpecy | Identify and filter spectra |
| area_under_band | Measure the area under band of spectra |
| area_under_band.default | Measure the area under band of spectra |
| area_under_band.OpenSpecy | Measure the area under band of spectra |
| as.data.frame.OpenSpecy | Generic Open Specy Methods |
| as.data.table.OpenSpecy | Generic Open Specy Methods |
| assess_lib | Build spectral libraries |
| assess_spec | Assess common spectral quality issues |
| assess_spec.default | Assess common spectral quality issues |
| assess_spec.OpenSpecy | Assess common spectral quality issues |
| as_hyperSpec | Read and write spectral data |
| as_OpenSpecy | Create 'OpenSpecy' objects |
| as_OpenSpecy.data.frame | Create 'OpenSpecy' objects |
| as_OpenSpecy.default | Create 'OpenSpecy' objects |
| as_OpenSpecy.hyperSpec | Create 'OpenSpecy' objects |
| as_OpenSpecy.list | Create 'OpenSpecy' objects |
| as_OpenSpecy.OpenSpecy | Create 'OpenSpecy' objects |
| as_OpenSpecy.Specs | Create compressed Specs objects |
| as_Specs | Create compressed Specs objects |
| as_Specs.default | Create compressed Specs objects |
| as_Specs.FileSpecs | Open a large spectral source as file-backed Specs |
| as_Specs.OpenSpecy | Create compressed Specs objects |
| as_Specs.Specs | Create compressed Specs objects |
| automate_particle_analysis | Automate particle analysis for spectral maps |
| automate_particle_analysis.default | Automate particle analysis for spectral maps |
| automate_particle_analysis.FileSpecs | Automate particle analysis for spectral maps |
-- B --
| batch_detection_limit | Particle analysis validation metrics |
| build_lib | Build spectral libraries |
| build_model_lib | Build spectral libraries |
-- C --
| calculate_emissivity | Calculate spectral emissivity at supplied material temperatures |
| calculate_emissivity.default | Calculate spectral emissivity at supplied material temperatures |
| calculate_emissivity.OpenSpecy | Calculate spectral emissivity at supplied material temperatures |
| calc_window_points | Smooth spectral intensities |
| calc_window_points.default | Smooth spectral intensities |
| calc_window_points.OpenSpecy | Smooth spectral intensities |
| check_lib | Manage spectral libraries |
| check_OpenSpecy | Create 'OpenSpecy' objects |
| check_Specs | Create compressed Specs objects |
| check_Specs.default | Create compressed Specs objects |
| check_Specs.FileSpecs | Open a large spectral source as file-backed Specs |
| check_Specs.Specs | Create compressed Specs objects |
| collapse_spec | Define features |
| collapse_spec.default | Define features |
| collapse_spec.FileSpecs | Open a large spectral source as file-backed Specs |
| collapse_spec.OpenSpecy | Define features |
| collapse_spec.Specs | Create compressed Specs objects |
| conform_res | Normalization and conversion of spectral data |
| conform_spec | Conform spectra to a standard wavenumber series |
| conform_spec.default | Conform spectra to a standard wavenumber series |
| conform_spec.OpenSpecy | Conform spectra to a standard wavenumber series |
| correct_spike | Detect and correct isolated spikes in spectra |
| correct_spike.default | Detect and correct isolated spikes in spectra |
| correct_spike.OpenSpecy | Detect and correct isolated spikes in spectra |
| cor_spec | Identify and filter spectra |
| cor_spec.default | Identify and filter spectra |
| cor_spec.FileSpecs | Open a large spectral source as file-backed Specs |
| cor_spec.OpenSpecy | Identify and filter spectra |
| cor_spec.Specs | Create compressed Specs objects |
| crowd_lookup | Particle analysis validation metrics |
| c_spec | Manage spectral objects |
| c_spec.default | Manage spectral objects |
| c_spec.list | Manage spectral objects |
| c_spec.OpenSpecy | Manage spectral objects |
-- D --
| decode_specs_hilbert | Create compressed Specs objects |
| decompress_spec | Create compressed Specs objects |
| decompress_spec.default | Create compressed Specs objects |
| decompress_spec.FileSpecs | Open a large spectral source as file-backed Specs |
| decompress_spec.Specs | Create compressed Specs objects |
| dedupe_spec | Build spectral libraries |
| def_features | Define features |
| def_features.default | Define features |
| def_features.FileSpecs | Open a large spectral source as file-backed Specs |
| def_features.OpenSpecy | Define features |
| def_features.Specs | Create compressed Specs objects |
| detect_image_origin | Attach visual images to spectral map objects |
-- E --
| encode_specs_hilbert | Create compressed Specs objects |
| estimate_temperature | Estimate material temperature and an emissivity diagnostic |
| estimate_temperature.default | Estimate material temperature and an emissivity diagnostic |
| estimate_temperature.FileSpecs | Estimate material temperature and an emissivity diagnostic |
| estimate_temperature.OpenSpecy | Estimate material temperature and an emissivity diagnostic |
-- F --
| fill_spec | Identify and filter spectra |
| fill_spec.default | Identify and filter spectra |
| fill_spec.OpenSpecy | Identify and filter spectra |
| filter_spec | Identify and filter spectra |
| filter_spec.default | Identify and filter spectra |
| filter_spec.OpenSpecy | Identify and filter spectra |
| fit_specs_pca | Create compressed Specs objects |
| flatten_range | Range restriction and flattening for spectra |
| flatten_range.default | Range restriction and flattening for spectra |
| flatten_range.OpenSpecy | Range restriction and flattening for spectra |
-- G --
| gen_grid | Create 'OpenSpecy' objects |
| get_lib | Manage spectral libraries |
| get_metadata | Identify and filter spectra |
| get_metadata.default | Identify and filter spectra |
| get_metadata.OpenSpecy | Identify and filter spectra |
-- H --
| head.OpenSpecy | Generic Open Specy Methods |
| heatmap_spec | Interactive plots for OpenSpecy objects |
| heatmap_spec.default | Interactive plots for OpenSpecy objects |
| heatmap_spec.OpenSpecy | Interactive plots for OpenSpecy objects |
| human_ts | Create human readable timestamps |
-- I --
| ident_spec | Identify and filter spectra |
| interactive_plot | Interactive plots for OpenSpecy objects |
| interactive_plot.default | Interactive plots for OpenSpecy objects |
| interactive_plot.OpenSpecy | Interactive plots for OpenSpecy objects |
| io_spec | Read and write spectral data |
| is_empty_vector | Normalization and conversion of spectral data |
| is_OpenSpecy | Create 'OpenSpecy' objects |
| is_Specs | Create compressed Specs objects |
-- J --
| join_lib_metadata | Build spectral libraries |
| join_material_hierarchy | Build spectral libraries |
-- L --
| lib_clean_metadata | Create and apply metadata-name lookup rules |
| lib_clean_name | Create and apply metadata-name lookup rules |
| lib_metadata_name_lookup | Create and apply metadata-name lookup rules |
| load_lib | Manage spectral libraries |
-- M --
| make_lib_lookup_template | Build spectral libraries |
| make_rel | Make spectral intensities relative |
| make_rel.default | Make spectral intensities relative |
| make_rel.matrix | Make spectral intensities relative |
| make_rel.OpenSpecy | Make spectral intensities relative |
| manage_na | Ignore or remove NA intensities |
| manage_na.default | Ignore or remove NA intensities |
| manage_na.OpenSpecy | Ignore or remove NA intensities |
| match_spec | Identify and filter spectra |
| match_spec.default | Identify and filter spectra |
| match_spec.FileSpecs | Open a large spectral source as file-backed Specs |
| match_spec.OpenSpecy | Identify and filter spectra |
| match_spec.Specs | Create compressed Specs objects |
| material_percentage_uncertainty | Calculate material percentage uncertainty from observed particle counts |
| max_cor_named | Identify and filter spectra |
| mean_replace | Normalization and conversion of spectral data |
| merge_map | Manage spectral objects |
| merge_map.default | Manage spectral objects |
| merge_map.list | Manage spectral objects |
| merge_map.OpenSpecy | Manage spectral objects |
| minimum_detectable_amount | Particle analysis validation metrics |
| model_class_weights | Interactive plots for OpenSpecy objects |
-- O --
| OpenSpecy | Create 'OpenSpecy' objects |
| open_specs | Open a large spectral source as file-backed Specs |
| os_similarity | Identify and filter spectra |
| os_similarity.default | Identify and filter spectra |
| os_similarity.OpenSpecy | Identify and filter spectra |
-- P --
| particle_image | Plot particle maps with base graphics |
| peak_ratio | Calculate ratios between spectral intensities at two wavenumbers |
| peak_ratio.default | Calculate ratios between spectral intensities at two wavenumbers |
| peak_ratio.OpenSpecy | Calculate ratios between spectral intensities at two wavenumbers |
| plot.OpenSpecy | Generic Open Specy Methods |
| plot.OpenSpecyParticleAnalysis | Plot a recorded particle-analysis diagnostic |
| plotly_spec | Interactive plots for OpenSpecy objects |
| plotly_spec.default | Interactive plots for OpenSpecy objects |
| plotly_spec.OpenSpecy | Interactive plots for OpenSpecy objects |
| point_intensity | Measure spectral intensity at one wavenumber |
| point_intensity.default | Measure spectral intensity at one wavenumber |
| point_intensity.OpenSpecy | Measure spectral intensity at one wavenumber |
| predict_class_reference | Predict blank class-reference values with reviewed regex rules |
| print.FileSpecs | Open a large spectral source as file-backed Specs |
| print.OpenSpecy | Generic Open Specy Methods |
| process_spec | Process Spectra |
| process_spec.default | Process Spectra |
| process_spec.OpenSpecy | Process Spectra |
| prune_lib | Build spectral libraries |
-- R --
| raman_hdpe | Sample Raman spectrum |
| read_any | Read spectral data from multiple files |
| read_asp | Read spectral data |
| read_envi | Read ENVI data |
| read_extdata | Read spectral data |
| read_h5 | Read spectral data |
| read_jdx | Read spectral data |
| read_many | Read spectral data from multiple files |
| read_opus | Read spectral data from Bruker OPUS binary files |
| read_opus_raw | Read a Bruker OPUS spectrum binary raw string |
| read_spa | Read spectral data |
| read_spc | Read spectral data |
| read_spec | Read and write spectral data |
| read_specs | Create compressed Specs objects |
| read_text | Read spectral data |
| read_zip | Read spectral data from multiple files |
| rebuild_lib_artifacts | Build spectral libraries |
| recovery_rate | Particle analysis validation metrics |
| reduce_lib | Build spectral libraries |
| restrict_range | Range restriction and flattening for spectra |
| restrict_range.default | Range restriction and flattening for spectra |
| restrict_range.OpenSpecy | Range restriction and flattening for spectra |
| rm_lib | Manage spectral libraries |
| run_app | Run Open Specy app |
-- S --
| sample_spec | Manage spectral objects |
| sample_spec.default | Manage spectral objects |
| sample_spec.OpenSpecy | Manage spectral objects |
| sig_noise | Calculate signal and noise metrics for OpenSpecy objects |
| sig_noise.default | Calculate signal and noise metrics for OpenSpecy objects |
| sig_noise.OpenSpecy | Calculate signal and noise metrics for OpenSpecy objects |
| smooth_intens | Smooth spectral intensities |
| smooth_intens.default | Smooth spectral intensities |
| smooth_intens.OpenSpecy | Smooth spectral intensities |
| spatial_smooth | Spatial Smoothing of OpenSpecy Objects |
| Specs | Create compressed Specs objects |
| specs_background_filter | Create compressed Specs objects |
| specs_background_mask | Create compressed Specs objects |
| specs_coordinates | Create compressed Specs objects |
| specs_metadata | Create compressed Specs objects |
| specs_source_count | Create compressed Specs objects |
| specs_source_values | Create compressed Specs objects |
| spec_res | Spectral resolution |
| spec_res.default | Spectral resolution |
| spec_res.OpenSpecy | Spectral resolution |
| split_h5 | Split a large HDF5 spectral map by metadata category |
| split_spec | Split Open Specy objects |
| split_spec.default | Split Open Specy objects |
| split_spec.FileSpecs | Open a large spectral source as file-backed Specs |
| subtr_baseline | Automated background subtraction for spectral data |
| subtr_baseline.default | Automated background subtraction for spectral data |
| subtr_baseline.OpenSpecy | Automated background subtraction for spectral data |
| summary.OpenSpecy | Generic Open Specy Methods |
-- T --
| test_lib | Test reference library |
| train_spec_model | Build spectral libraries |
-- V --
| visual_image | Attach visual images to spectral map objects |
-- W --
| write_spec | Read and write spectral data |
| write_spec.default | Read and write spectral data |
| write_spec.FileSpecs | Read and write spectral data |
| write_spec.OpenSpecy | Read and write spectral data |
| write_specs | Create compressed Specs objects |
| write_specs.default | Create compressed Specs objects |
| write_specs.FileSpecs | Create compressed Specs objects |
| write_specs.Specs | Create compressed Specs objects |