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Changelog

Source: NEWS.md

metabodecon 1.2.6

  • 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.