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Overview

Pacakge overview

ir-package
ir: Functions to Handle and Preprocess Infrared Spectra

ir-class

Create ir-objects, subset ir objects

ir_new_ir()
Creates an object of class ir
ir_as_ir()
Generic to convert objects to class ir
ir_drop_spectra()
Drops the column spectra from an object is of class ir
ir_get_intensity()
Extracts intensities from spectra in an ir object for specific spectral channels
ir_get_wavenumberindex()
Gets the index of a defined wavenumber value for a spectrum
ir_get_spectrum()
Extracts selected spectra from an object of class ir
ir_remove_missing()
Removes empty data values in an object of class ir
ir_flatten()
Converts objects of class ir to objects of class ir_flat
rep(<ir>)
Replicate ir objects
rbind(<ir>) cbind(<ir>)
Bind rows of ir objects
`[`(<ir>) `$`(<ir>) `[[`(<ir>) `$<-`(<ir>) `[<-`(<ir>) `[[<-`(<ir>)
Subsetting ir objects

Plotting spectra

Plotting spectra

plot(<ir>)
Plots an object of class ir

Import

Import of spectra

ir_import_csv()
Imports infrared spectra from various files
ir_import_spc()
Imports infrared spectra from Thermo Galactic's files

Export

Export of spectra

ir_export_prepare()
Prepares ir objects for export to csv

Spectral processing

Spectral preprocessing

ir_average()
Averages infrared spectra within groups
ir_bc()
Performs baseline correction on infrared spectra
ir_bin()
Bins infrared spectra
ir_clip()
Clips infrared spectra to new wavenumber ranges
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_normalize() ir_normalise()
Normalizes infrared spectra in an ir object
ir_smooth()
Smooths infrared spectra in an ir object
ir_correct_atmosphere()
Corrects artifacts in a spectrum based on reference spectra of the artifact compound
ir_to_transmittance() ir_to_absorbance()
Converts absorbance spectra to transmittance spectra or vice versa

Spectral analysis

Spectral analysis

Ops(<ir>)
Arithmetic operations for ir objects
ir_add()
Add infrared spectra
ir_subtract()
Subtract infrared spectra
ir_multiply()
Multiply infrared spectra or multiply infrared spectra with a numeric value
ir_divide()
Divide infrared spectra or divide infrared spectra by a numeric value
ir_variance_region()
Computes the variance of a spectrum in an ir object in a given region
range(<ir>) min(<ir>) max(<ir>) median(<ir>)
Get the minima/maxima/range/median of x axis values or intensity values of infrared spectra

tidyverse methods

tidyverse methods for ir objects

arrange.ir()
Arrange rows in ir objects by column values
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
semi_join.ir() anti_join.ir()
Filtering joins for an ir object
filter.ir()
Subset rows in ir objects using column values
group_by.ir() ungroup.ir()
Group rows in ir objects by one or more variables
inner_join.ir() left_join.ir() right_join.ir() full_join.ir()
Mutating joins for an ir object
mutate.ir() transmute.ir()
Mutate an ir object by adding new or replacing existing columns
nest.ir() unnest.ir()
Nest and un-nest an ir object
pivot_longer.ir()
Pivot an ir object from wide to long
pivot_wider.ir()
Pivot an ir object from wide to long
rename.ir() rename_with.ir()
Rename columns in ir objects
rowwise.ir()
Group input ir objects by rows
select.ir()
Subset columns in ir objects using column names and types
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.ir() slice_sample.ir()
Subset rows in ir objects using their positions
summarize.ir() summarise.ir()
Summarize each group in a ir object to fewer rows
unite.ir()
Unite multiple columns in an ir object into one by pasting strings together

Sample data

Sample dataset

ir_sample_data
Sample object of class ir