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

## Documentation for package ‘OpenSpecy’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D F G H I L M O P R S T W

## -- A --

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
as.data.frame.OpenSpecy | Generic Open Specy Methods
as.data.table.OpenSpecy | Generic Open Specy Methods
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

## -- C --

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
collapse_spec | Define features
collapse_spec.default | Define features
collapse_spec.OpenSpecy | Define features
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
cor_spec | Identify and filter spectra
cor_spec.default | Identify and filter spectra
cor_spec.OpenSpecy | Identify and filter spectra
c_spec | Manage spectral objects
c_spec.default | Manage spectral objects
c_spec.list | Manage spectral objects
c_spec.OpenSpecy | Manage spectral objects

## -- D --

def_features | Define features
def_features.default | Define features
def_features.OpenSpecy | Define features

## -- 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
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
is_empty_vector | Normalization and conversion of spectral data
is_OpenSpecy | Create 'OpenSpecy' objects

## -- L --

lines.OpenSpecy | Generic Open Specy Methods
load_lib | Manage spectral libraries

## -- M --

make_rel | Make spectral intensities relative
make_rel.default | 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.OpenSpecy | Identify and filter spectra
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

## -- O --

OpenSpecy | Create 'OpenSpecy' objects
os_similarity | Identify and filter spectra
os_similarity.default | Identify and filter spectra
os_similarity.OpenSpecy | Identify and filter spectra

## -- P --

plot.OpenSpecy | Generic Open Specy Methods
plotly_spec | Interactive plots for OpenSpecy objects
plotly_spec.default | Interactive plots for OpenSpecy objects
plotly_spec.OpenSpecy | Interactive plots for OpenSpecy objects
print.OpenSpecy | Generic Open Specy Methods
process_spec | Process Spectra
process_spec.default | Process Spectra
process_spec.OpenSpecy | Process Spectra

## -- 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_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_text | Read spectral data
read_zip | Read spectral data from multiple files
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
spec_res | Spectral resolution
spec_res.default | Spectral resolution
spec_res.OpenSpecy | Spectral resolution
split_spec | Split Open Specy objects
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

## -- W --

write_spec | Read and write spectral data
write_spec.default | Read and write spectral data
write_spec.OpenSpecy | Read and write spectral data