Package index • OpenSpecy

All functions

Specs() is_Specs() check_Specs() as_Specs() fit_specs_pca() decompress_spec() as_OpenSpecy(<Specs>) encode_specs_hilbert() decode_specs_hilbert() write_specs() read_specs() specs_background_filter() specs_source_count() specs_background_mask() specs_source_values() specs_coordinates() specs_metadata() cor_spec(<Specs>) match_spec(<Specs>) def_features(<Specs>) collapse_spec(<Specs>): Create compressed Specs objects
adj_intens(): Adjust spectral intensities to standard absorbance units.
restrict_range() flatten_range(): Range restriction and flattening for spectra
adj_wave(): Adjust wavelength to wavenumbers for Raman
area_under_band(): Measure the area under band of spectra
as_OpenSpecy() is_OpenSpecy() check_OpenSpecy() OpenSpecy() gen_grid(): Create OpenSpecy objects
assess_spec(): Assess common spectral quality issues
automate_particle_analysis(): Automate particle analysis for spectral maps
build_lib() make_lib_lookup_template() join_lib_metadata() join_material_hierarchy() dedupe_spec() prune_lib() reduce_lib() build_model_lib() assess_lib(): Build spectral libraries
conform_spec(): Conform spectra to a standard wavenumber series
correct_spike(): Detect and correct isolated spikes in spectra
adj_res() conform_res() adj_neg() mean_replace() is_empty_vector(): Normalization and conversion of spectral data
collapse_spec() def_features(): Define features
head(<OpenSpecy>) print(<OpenSpecy>) plot(<OpenSpecy>) summary(<OpenSpecy>) as.data.frame(<OpenSpecy>) as.data.table(<OpenSpecy>): Generic Open Specy Methods
human_ts(): Create human readable timestamps
plotly_spec() heatmap_spec() interactive_plot(): Interactive plots for OpenSpecy objects
write_spec() read_spec() as_hyperSpec(): Read and write spectral data
lib_metadata_name_lookup() lib_clean_name() lib_clean_metadata(): Create and apply metadata-name lookup rules
make_rel(): Make spectral intensities relative
check_lib() get_lib() load_lib() rm_lib(): Manage spectral libraries
manage_na(): Ignore or remove NA intensities
c_spec() sample_spec() merge_map(): Manage spectral objects
cor_spec() match_spec() ident_spec() get_metadata() max_cor_named() filter_spec() ai_classify() fill_spec() os_similarity(): Identify and filter spectra
open_specs() as_Specs(<FileSpecs>) print(<FileSpecs>) check_Specs(<FileSpecs>) decompress_spec(<FileSpecs>) split_spec(<FileSpecs>) cor_spec(<FileSpecs>) match_spec(<FileSpecs>) def_features(<FileSpecs>) collapse_spec(<FileSpecs>): Open a large spectral source as file-backed Specs
particle_image(): Plot particle maps with base graphics
peak_ratio(): Calculate ratios between spectral intensities at two wavenumbers
plot(<OpenSpecyParticleAnalysis>): Plot a recorded particle-analysis diagnostic
point_intensity(): Measure spectral intensity at one wavenumber
predict_class_reference(): Predict blank class-reference values with reviewed regex rules
process_spec(): Process Spectra
raman_hdpe: Sample Raman spectrum
read_envi(): Read ENVI data
read_text() read_asp() read_spa() read_spc() read_jdx() read_extdata() read_h5(): Read spectral data
read_any() read_many() read_zip(): 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
run_app(): Run Open Specy app
sig_noise(): Calculate signal and noise metrics for OpenSpecy objects
smooth_intens() calc_window_points(): Smooth spectral intensities
spatial_smooth(): Spatial Smoothing of OpenSpecy Objects
spec_res(): Spectral resolution
split_spec(): Split Open Specy objects
subtr_baseline(): Automated background subtraction for spectral data
test_lib: Test reference library
crowd_lookup() recovery_rate() minimum_detectable_amount() batch_detection_limit(): Particle analysis validation metrics
add_visual_image() visual_image() detect_image_origin(): Attach visual images to spectral map objects