Package: ir 0.3.0

ir: Functions to Handle and Preprocess Infrared Spectra

Functions to import and handle infrared spectra (import from '.csv' and Thermo Galactic's '.spc', baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, plotting).

Authors:Henning Teickner [aut, cre, cph]

ir_0.3.0.tar.gz
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ir_0.3.0.tgz(r-4.4-any)ir_0.3.0.tgz(r-4.3-any)
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ir_0.3.0.tgz(r-4.4-emscripten)ir_0.3.0.tgz(r-4.3-emscripten)
ir.pdf |ir.html✨
ir/json (API)
NEWS

# Install 'ir' in R:

install.packages('ir', repos = c('https://henningte.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/henningte/ir/issues

Datasets:

ir_sample_data - Sample object of class 'ir'

On CRAN:

chemometrics infrared infrared-spectra ir-package mid-infrared-spectra spectroscopy

35 exports 6 stars 1.18 score 110 dependencies 35 scripts 187 downloads

Last updated 2 years agofrom:fb317d5284. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 24 2024
R-4.5-win	NOTE	Aug 24 2024
R-4.5-linux	NOTE	Aug 24 2024
R-4.4-win	NOTE	Aug 24 2024
R-4.4-mac	NOTE	Aug 24 2024
R-4.3-win	NOTE	Aug 24 2024
R-4.3-mac	NOTE	Aug 24 2024

Exports:%>%ir_add ir_as_ir ir_average ir_bc ir_bc_polynomial ir_bc_rubberband ir_bc_sg ir_bin ir_clip ir_correct_atmosphere ir_divide ir_drop_spectra ir_export_prepare ir_flat_clean ir_flatten ir_get_intensity ir_get_spectrum ir_get_wavenumberindex ir_import_csv ir_import_spc ir_interpolate ir_interpolate_region ir_multiply ir_new_ir ir_new_ir_flat ir_normalise ir_normalize ir_remove_missing ir_smooth ir_stack ir_subtract ir_to_absorbance ir_to_transmittance ir_variance_region

Dependencies:askpass base64enc baseline brio bslib cachem callr ChemoSpec ChemoSpecUtils cli colorspace cpp11 crayon crosstalk curl data.table deldir desc diffobj digest dplyr errors evaluate fansi farver fastmap fontawesome fs generics ggplot2 ggrepel glue gtable highr htmltools htmlwidgets httr hyperSpec interp isoband jpeg jquerylib jsonlite knitr labeling later lattice latticeExtra lazyeval lifecycle limSolve lpSolve magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgbuild pkgconfig pkgload plotly plyr png praise processx promises ps purrr quadprog quantities R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack readJDX rematch2 reshape2 rlang rmarkdown rprojroot sass scales signal SparseM stringi stringr sys testthat tibble tidyr tidyselect tinytex units utf8 vctrs viridisLite waldo withr xfun xml2 yaml

Introduction to the 'ir' package

Henning Teickner

Rendered fromir-introduction.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2022-06-13
Started: 2022-06-13

Introduction to the irclass

Henning Teickner

Rendered fromir-class.Rmdusingknitr::rmarkdownon Aug 24 2024.

Last update: 2022-06-13
Started: 2022-06-13

Citation

Development and contributors

Readme and manuals

Help Manual

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