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_rawfails because the raw file is still being acquired - provide
orbi_get_example_filesfunction as a one-point stop to get both system package test files as well as downloadable test files -
orbi_find_rawnow 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 flexibleCNandRNparameters - 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()replacesorbi_set_settings()andorbi_get_options()/orbi_get_option()replacesorbi_get_settings()) - improved functionality for options loading and defaults
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:
Enhancements
-
orbi_simplify_isox()now includesintensityby default and allows addition of user-specified columns -
orbi_flag_satellite_peaks(),orbi_flag_weak_isotopocules()andorbi_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()andorbi_flag_outliers()supersedeorbi_filter_satellite_peaks(),orbi_filter_weak_isotopocules()andorbi_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 .isoxfilepathin the resulting tibble
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()andorbi_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 onmagrittr - added
.byparameter fororbi_summarize_results()for option to manually adjust grouping
