Function reference • ir

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