isoorbi 1.5.2

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

This is a patch containing compatibility updates.

isoorbi 1.3.0

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

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

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.

isorbi 1.0.0

First public release.