Changelog

Source: NEWS.md

isoorbi 1.5.2

CRAN release: 2025-10-03

This is a minor update to decrease package size for CRAN.

Enhancements

• added orbi_get_example_files() that can download additional example files to provide easier access to test files for users

isoorbi 1.5.1

This is a minor update to enhance usability.

Enhancements

• show panel lables in spectral plots, i.e. M+1, M+2, etc. (#93)
• align x-axes in spectral plots (#98)
• introduce default_tolerance and default_charge parameters for orbi_identify_isotopocules (#95)
• automatically calculate ions during orbi_identify_isotopocules
• provide a stastic of ion counts identified when running orbi_identify_isotopocules (#94)
• provide more informative error when orbi_read_raw fails because the raw file is still being acquired
• provide orbi_get_example_files function as a one-point stop to get both system package test files as well as downloadable test files
• orbi_find_raw now finds both .raw and .RAW extensions (i.e. no longer case-sensitive)

isoorbi 1.5.0

Breaking changes

There are no breaking changes in this release (all changes and new features are backwards compatible).

New features

• implemented an optimized and expanded raw file reader (isoraw) that is packaged with isoorbi and is used in orbi_read_raw()
• implemented versatile isotopocule mapping via orbi_identifiy_isotopocule() from csv, tsv, and excel inputs
• implemented orbi_calculate_ions() to calculate ions from peak intensities and noise with flexible CN and RN parameters
• implemented orbi_plot_spectra() to plot

Enhancements

• upgraded all data processing and plotting functions to be compatible with both isox and raw file datasets
• improved default print outputs for S3 classes used in the package
• improved package structure documentation
• expanded orbi_flag_outliers() functionality (contributed by Florian Rubach)

Bug fixes

• fixed incompatibility with ggplot2 version 4.0.0 (#69)

isoorbi 1.4.0

Breaking changes

There are no breaking changes in this release (all changes and new features are backwards compatible).

New features

• implemented direct reading and caching of orbitrap IRMS raw files (orbi_read_read()) via the rawrr package
• use CLI for clearer and more informative info messages for all functions

Enhancements

• renamed package “settings” to package “options” to be consistent with the naming conventions in base R (orbi_options() replaces orbi_set_settings() and orbi_get_options() / orbi_get_option() replaces orbi_get_settings())
• improved functionality for options loading and defaults

isoorbi 1.3.1

CRAN release: 2024-08-27

This is a patch containing compatibility updates.

isoorbi 1.3.0

CRAN release: 2023-11-09

This is a minor release adding new features.

Breaking changes

There are no breaking changes in this release (all changes and new features are backwards compatible).

New features

Plotting functions:

• orbi_plot_satellite_peaks() implemented
• orbi_plot_isotopocule_coverage() implemented
• orbi_plot_raw_data() implemented

Information functions:

• orbi_get_isotopocule_coverage()

Enhancements

• orbi_simplify_isox() now includes intensity by default and allows addition of user-specified columns
• orbi_flag_satellite_peaks(), orbi_flag_weak_isotopocules() and orbi_flag_outliers() now provide additional information when no data is flagged and how to visualize what was flagged (if anything)

Bug Fixes

• orbi_add_blocks_to_plot() now supports log scale axes

isoorbi 1.2.0

This is a minor release adding new features.

Breaking changes

There are no breaking changes in this release (all changes and new features are backwards compatible).

New features

• orbi_find_isox() added
• orbi_analyze_noise() implemented
• orbi_plot_shot_noise() implemented
• orbi_flag_satellite_peaks(), orbi_flag_weak_isotopocules() and orbi_flag_outliers() supersede orbi_filter_satellite_peaks(), orbi_filter_weak_isotopocules() and orbi_filter_scan_intensity()
• orbi_export_data_to_excel() implemented
• orbi_define_block_for_flow_injection() implemented
• orbi_add_blocks_to_plot() implemented

Enhancements

• all loading and utility functions provide more details in the info message about what has been done, what was affected, and how long it took
• all loading and utility functions catch processing errors and report the information back to the user
• orbi_read_isox() now can read multiple .isox files at once and includes the .isox filepath in the resulting tibble

Bug fixes

• data frame groupings introduced in flagging/filtering functions are now removed again at the end of the function

isoorbi 1.1.0

CRAN release: 2023-06-24

This is a minor release adding new features and fixing a few bugs.

Breaking changes

There are no breaking changes in this release (all changes and new features are backwards compatible).

New features

• implemented functionality for dual inlet data acquisitions, see orbi_define_blocks_for_dual_inlet() and orbi_get_blocks_info()
• implemented package settings, using internal functions isoorbi::orbi_get_settings, isoorbi::orbi_set_settings

Enhancements

• removed dependency on stringr
• implemented native pipe |> (R version requirement increased to 4.1.0) and removed dependency on magrittr
• added .by parameter for orbi_summarize_results() for option to manually adjust grouping

Bug fixes

• dplyr changes to joins with explicit multiple argument. multiple now defaults to “all”, and the options of “error” and “warning” are now deprecated in favor of using relationship.