NEWS

isoorbi 1.5.3

This is a minor update to support the latest version of testthat and address a few small bugs.

Bug fixes & improvements

updated snapshots for continuous integration tests to work with testthat 3.3.0
changed orbi_export_data_to_excel() to only export file_info and summary by default to avoid uintentionally enormous excel files when exporting large datasets (#106)
fixed issue with orbi_define_basepeak() not correctly handling unidentified peaks, they are now automatically filtered out when this function is called (#114)
improved error messages in functions that need an isotopocule defintion ifisotopocules have not yet been identified
clarified installation instructions

isoorbi 1.5.2 (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 (2024-08-27)

This is a patch containing compatibility updates.

isoorbi 1.3.0 (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 (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.

isoorbi 1.0.0 (2022-10-17)

First public release.