# Functions to Handle and Preprocess Infrared Spectra

## Documentation for package ‘ir’ version 0.4.1

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

## Help Pages

$.ir | Subsetting 'ir' objects
$<-.ir | Subsetting 'ir' objects
anti_join.ir | Filtering joins for an 'ir' object
arrange.ir | Arrange rows in 'ir' objects by column values
bind | Bind rows of 'ir' objects
cbind.ir | Bind rows of 'ir' objects
distinct.ir | Subset distinct/unique rows in 'ir' objects
extract.ir | Extract a character column in an 'ir' object into multiple columns using regular expression groups
filter-joins | Filtering joins for an 'ir' object
filter.ir | Subset rows in 'ir' objects using column values
full_join.ir | Mutating joins for an 'ir' object
group_by | Group rows in 'ir' objects by one or more variables
group_by.ir | Group rows in 'ir' objects by one or more variables
inner_join.ir | Mutating joins for an 'ir' object
ir_add | Add infrared spectra
ir_as_ir | Converts an object to class 'ir'
ir_as_ir.data.frame | Converts an object to class 'ir'
ir_as_ir.hyperSpec | Converts an object to class 'ir'
ir_as_ir.ir | Converts an object to class 'ir'
ir_as_ir.ir_flat | Converts an object to class 'ir'
ir_as_ir.Spectra | Converts an object to class 'ir'
ir_average | Averages infrared spectra within groups
ir_bc | Performs baseline correction on infrared spectra
ir_bc_polynomial | Performs baseline correction on infrared spectra using a polynomial
ir_bc_rubberband | Performs baseline correction on infrared spectra using a rubberband algorithm
ir_bc_sg | Performs baseline correction on infrared spectra using a Savitzky-Golay baseline
ir_bin | Bins infrared spectra
ir_clip | Clips infrared spectra to new wavenumber ranges
ir_correct_atmosphere | Corrects artifacts in a spectrum based on reference spectra of the artifact compound
ir_divide | Divide infrared spectra or divide infrared spectra by a numeric value
ir_drop_spectra | Drops the column 'spectra' from an object is of class 'ir'
ir_export_prepare | Prepares 'ir' objects for export to 'csv'
ir_flatten | Converts objects of class 'ir' to objects of class 'ir_flat'
ir_flat_clean | Cleans objects of class 'ir_flat'
ir_get_intensity | Extracts intensities from spectra in an 'ir' object for specific spectral channels
ir_get_spectrum | Extracts selected spectra from an object of class 'ir'
ir_get_wavenumberindex | Gets the index of a defined wavenumber value for a spectrum
ir_identify_empty_spectra | Identifies empty spectra in an 'ir' object
ir_import_csv | Imports infrared spectra from various files
ir_import_spc | Imports infrared spectra from Thermo Galactic's files
ir_interpolate | Interpolates intensity values of infrared spectra in an 'ir' object for new wavenumber values
ir_interpolate_region | Interpolates selected regions in infrared spectra in an 'ir' object
ir_multiply | Multiply infrared spectra or multiply infrared spectra with a numeric value
ir_new_ir | Creates an object of class 'ir'
ir_new_ir_flat | Creates an object of class 'ir_flat'
ir_normalise | Normalizes infrared spectra in an 'ir' object
ir_normalize | Normalizes infrared spectra in an 'ir' object
ir_remove_missing | Removes empty data values in an object of class 'ir'
ir_sample_data | Sample object of class 'ir'
ir_sample_prospectr | Wrapper to sampling functions from the 'prospectr' package
ir_scale | Scales spectra in an 'ir' object
ir_smooth | Smooths infrared spectra in an 'ir' object
ir_stack | Stacks a matrix or data frame with spectra into a list column
ir_subtract | Subtract infrared spectra
ir_to_absorbance | Converts absorbance spectra to transmittance spectra or vice versa
ir_to_transmittance | Converts absorbance spectra to transmittance spectra or vice versa
ir_variance_region | Computes the variance of a spectrum in an 'ir' object in a given region
left_join.ir | Mutating joins for an 'ir' object
max.ir | Get the minima/maxima/range/median of x axis values or intensity values of infrared spectra
median.ir | Get the minima/maxima/range/median of x axis values or intensity values of infrared spectra
min.ir | Get the minima/maxima/range/median of x axis values or intensity values of infrared spectra
mutate | Mutate an 'ir' object by adding new or replacing existing columns
mutate-joins | Mutating joins for an 'ir' object
mutate.ir | Mutate an 'ir' object by adding new or replacing existing columns
nest | Nest and un-nest an 'ir' object
nest.ir | Nest and un-nest an 'ir' object
Ops.ir | Arithmetic operations for 'ir' objects
pivot_longer.ir | Pivot an 'ir' object from wide to long
pivot_wider.ir | Pivot an 'ir' object from wide to long
plot.ir | Plots an object of class 'ir'
range | Get the minima/maxima/range/median of x axis values or intensity values of infrared spectra
range.ir | Get the minima/maxima/range/median of x axis values or intensity values of infrared spectra
rbind.ir | Bind rows of 'ir' objects
rename | Rename columns in 'ir' objects
rename.ir | Rename columns in 'ir' objects
rename_with.ir | Rename columns in 'ir' objects
rep.ir | Replicate ir objects
right_join.ir | Mutating joins for an 'ir' object
rowwise.ir | Group input 'ir' objects by rows
select.ir | Subset columns in 'ir' objects using column names and types
semi_join.ir | Filtering joins for an 'ir' object
separate.ir | Separate a character column in an 'ir' object into multiple columns with a regular expression or numeric locations
separate_rows.ir | Separate a collapsed column in an 'ir' object into multiple rows
slice | Subset rows in 'ir' objects using their positions
slice.ir | Subset rows in 'ir' objects using their positions
slice_sample.ir | Subset rows in 'ir' objects using their positions
subsetting | Subsetting 'ir' objects
summarise | Summarize each group in a 'ir' object to fewer rows
summarise.ir | Summarize each group in a 'ir' object to fewer rows
summarize | Summarize each group in a 'ir' object to fewer rows
summarize.ir | Summarize each group in a 'ir' object to fewer rows
transmute.ir | Mutate an 'ir' object by adding new or replacing existing columns
ungroup.ir | Group rows in 'ir' objects by one or more variables
unite.ir | Unite multiple columns in an 'ir' object into one by pasting strings together
unnest.ir | Nest and un-nest an 'ir' object
[.ir | Subsetting 'ir' objects
[<-.ir | Subsetting 'ir' objects
[[.ir | Subsetting 'ir' objects
[[<-.ir | Subsetting 'ir' objects