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Changelog

Source: NEWS.md

metabodecon 1.4.0

  • Improved Github Workflow (GWF) to test installation on a clean Windows/Linux/Mac OS with R pre-installed, but without R-tools and any packages.
  • Added use_rust option to deconvolute(). If use_rust is TRUE, the deconvolution is done using the implementation from Rust package metabodecon-rust. Using the Rust backend requires R package mdrb (Metabodecon Rust Backend) to be installed first. For this purpose the following additional functions are provided:

metabodecon 1.3.0

  • Added Github Workflow (GWF) to test installation on a clean Windows/Linux/Mac OS with R pre-installed, but without R-tools and any packages. Closes Todo Test Install on clean OS.
  • Fixed GWF for testing code coverage script
  • Improved formatting for R-CMD-check-GWF and pkgdown-GWF
  • Improved align(). The new implementation is faster and returns more information. In particular, the chemical shifts of the aligned peaks centers as well as the superposition of the aligned peaks are returned.
  • Improved documentation and defaults for speaq_align() and combine_peaks().
  • Improved draw_spectrum():
    • Added parameters bt_text, lt_text, tp_text and rt_text to plot_spectrum() to allow for full control over the text labels at the plot margins.
    • Added parameter sf_vert to plot_spectrum() to allow configuration of the height of the vertical lines drawn at the peak centers.
    • Added the option to fill the area under lorentzian curves with color.
    • Improved the legend of the plot.

metabodecon 1.2.6

CRAN release: 2025-01-21

  • Fixed a bug in MetaboDecon1D() that caused argument file_path to be interpreted as a relative path, even if it was an absolute path.

metabodecon 1.2.5

  • Fixed a bug in read_spectrum() that caused argument raw to not be passed on to read_jcampdx().

metabodecon 1.2.4

  • Documentation updates

metabodecon 1.2.3

  • Documentation updates

metabodecon 1.2.2

  • Documentation updates

metabodecon 1.2.1

  • Documentation updates

metabodecon 1.2.0

Finished the following tasks. For details about each task, see TODOS.md.

  • CRAN-0: Omit “Functions for” in title
  • CRAN-1: Omit “Functions for” in DESCRIPTION
  • CRAN-2: Explain acronyms like NMR
  • CRAN-3: Use correct reference format in DESCRIPTION
  • CRAN-4: Explain return value in function docs
  • CRAN-5: Remove examples from unexported functions
  • CRAN-6: Fix vignettes
  • CRAN-7: Check dontrun examples
  • CRAN-8: Functions should not write to disk by default
  • CRAN-9: Functions should not change working dir or global options
  • FEATURE-01: Use temp dirs for example data
  • FEATURE-02: Add minimal example dataset
  • FEATURE-03: Batch Mode
  • FEATURE-04: Parallelize
  • FEATURE-05: Add test suite
  • FEATURE-06: Return lambda in hertz
  • FEATURE-07: Improve return value
  • FEATURE-09 Implement read_spectra()
  • FEATURE-11: Accept dataframes in GLC
  • FEATURE-14: Provide simulated datasets
  • FEATURE-15: Add lifecycle badges
  • FEATURE-16: Improve multiprocessing
  • FEATURE-17: Discard output
  • FEATURE-18: Implement plot_spectrum()
  • FEATURE-20: Implement deconvolute_blood()
  • FIX-1: Prevent crashes for high smoothing
  • REFACTOR-01: Combine load_spectrum functions
  • REFACTOR-02: Improve Text Output (-License, +Timestamps)
  • REFACTOR-04: Plotting speed
  • REFACTOR-05: Speedup smoothing
  • REFACTOR-06: Use a single unit as source of truth
  • REFACTOR-07: Split monolithic functions into smaller parts
  • REFACTOR-08: Improve docs for Metabodecon1D return value
  • REFACTOR-09: Replace glc with generate_lorentz_curves()
  • REFACTOR-10: Replace all md1d with MetaboDecon1D() calls
  • REFACTOR-11: Implement calc_prarp()
  • REFACTOR-12: Write compliance tests
  • REFACTOR-13: Write PRARP tests

metabodecon 1.1.1

API:

  • Fixed a bug in generate_lorentz_curves() that caused the function to always use file format “bruker”, even when file format “jcampdx” was specified.

Datasets:

  • Fixed filenames of samples in blood dataset (renamed from Bood_<nr> to blood_<nr>).
  • Renamed example_datasets/jcampdx/urine/urine.dx to example_datasets/jcampdx/urine/urine_1.dx and renamed example_datasets/bruker/urine/urine/ to example_datasets/bruker/urine/urine_1/. This was done because list.files seems to return different orderings for urine.dx and urine_2.dx in different operating systems, whereas urine_1.dx and urine_2.dx are sorted the same way everywhere. This makes it easier to write clear and concise test cases, because we don’t need to check for file ordering.

Documentation:

Testing:

  • Added unit tests for generate_lorentz_curves().
  • Enabled parallel processing for unit tests.
  • Created initial versions of tests/testthat/test-generate_lorentz_curves-[1-4].R.
  • Added generate_lorentz_curves_v2() to DESCRIPTION/Config/testthat/start-first.
  • Adjusted existing tests to use the updated version of example_datasets (sample urine was renamed to urine_1, as mentioned in above in section Datasets)

Internal:

  • Added functions %||%, msg() and msgf to R/util.R.
  • Added elements range_water_signal_ppm and signal_free_region to returned list of function deconvolute_spectrum.
  • Function with now prints error messages to stderr even if the message stream is redirected.
  • Copied function deconvolution() from R/MetaboDecon1D.R to R/main_v2.R as .deconvolute_spectrum.
  • Fixed order of params in deconvolution.
  • Fixed download_example_datasets(). Argument overwrite is passed correctly on to cache_example_datasets().
  • Changed URL of example datasets xds$url from https://github.com/spang-lab/metabodecon/releases/download/v1.0.2/example_datasets.zip to https://github.com/spang-lab/metabodecon/releases/download/v1.1.0/example_datasets.zip.
  • Improved cache_example_datasets(). Extraction now only is done if extract == TRUE AND the resulting folder does not yet exist (saves approx. 2-3s on each call). To overwrite a possible existing folder, argument overwrite can be set to TRUE.
  • Fixed formatting of test_helpers.R
  • Added linter config .lintr

metabodecon 1.1.0

API:

Documentation:

Datasets:

  • Moved misc/datasets to misc/example_datasets
  • Moved misc/examples/usage_example.R to misc/code_examples/sage_example.R

Internal:

  • Added unit tests
  • Removed script check_package.R
  • Moved functions from util.R to datadir.R
  • Added grDevices, stats and utils as internal imports
  • Added lots of test helper functions in R/test_helpers.R
  • Added function generate_lorentz_curves_v2() which will replace generate_lorentz_curves() as soon as we have new features AND 100% backwards compatibility
  • Fixed bug in with() that caused get_datadir_mock() to be called after redirection took place causing unexpected message output
  • Fixed bug in datadir() that caused the resulting path to end with a slash on Unix-like systems and without a slash on Windows, if file was not specified
  • RUN_SLOW_TESTS is now set to TRUE for the CI pipeline

metabodecon 1.0.3

API:

Documentation:

  • Removed table of contents from README.md as it’s a bit overkill for approx. 50 lines of text
  • Improved documentation

Internal:

  • Switched from MIT License to GPL-3 to match the license of the predecessor package MetaboDecon1D
  • Added docs folder to .gitignore. Reason: we changed all vignettes to pkgdown articles which will be displayed only at our Github Pages website and can be regenerated from folder vignettes upon deployment.
  • Created TODOS.md and added it to .Rbuildignore
  • Improved .gitignore

metabodecon 1.0.2

  • Minor URL and spelling adjustments to pass CRAN checks

metabodecon 1.0.1

  • Fixed some spelling errors.
  • Removed unused CONTRIBUTE.md (instead a section within README.md is used)

metabodecon 1.0.0

  • Initial CRAN submission.