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Changelog

Source: NEWS.md

AlpsNMR (development version)

Breaking changes

  • plot_vip_scores(): nbootstrap argument renamed to n_samples, and its threshold line now uses the correct degrees of freedom (df = n_samples - 1), matching the selection bp_VIP_analysis() actually performs.
  • nmr_read_bruker_fid(): endian argument removed (byte order is now auto-detected from acqus), and it now returns a data frame with time_s/fid_complex columns instead of a raw numeric vector. Also fixes silent truncation of the FID to half its length.
  • nmr_baseline_threshold() / nmr_baseline_threshold_plot(): range_without_peaks / chemshift_range no longer default to c(9.5, 10) ppm; must now be given explicitly.
  • nmr_detect_peaks(): range_without_peaks no longer defaults to c(9.5, 10) ppm either; either it or baselineThresh must now be given, or the call aborts with a clear message instead of failing deep inside with a confusing one (#66).
  • download_MTBLS242(): keep_only_preop_and_3months (logical) replaced by timepoints (a character vector of TimePoint values to keep, or NULL for every timepoint), so any two (or more) of the study’s five timepoints can be selected, not just preop and 12 months. timepoints = c("preop", "12 months after surgery") is the new default and reproduces the old keep_only_preop_and_3months = TRUE behavior.
  • nmr_baseline_threshold_plot(): NMRExperiment = NULL now means “every sample” (paginated via new nrow/ncol/page arguments) instead of silently subsampling to 10 random samples when there were more than 20. "all" remains a synonym for NULL. nrow/ncol default to a snug grid for small sample counts, or a fixed 3x3 (paginate with page) for 7 or more.

New features

  • nmr_baseline_threshold_plot(): new nrow/ncol/page arguments paginate the per-sample facets instead of cramming every sample onto one illegible page.
  • bp_VIP_analysis() / bp_kfold_VIP_analysis(): new optional identity_column argument. When given, fold assignment and bootstrap resampling keep every identity_column group (e.g. a subject’s repeated measurements) together, and the fitted plsda models become multilevel, matching what nmr_data_analysis() already did for the same identity_column. Opt-in and backward compatible (defaults to NULL, reproducing the previous behavior).

Bug fixes

  • peaklist_fit_lorentzians() (used by nmr_detect_peaks(fit_lorentzians = TRUE)): its “Fitting lorentzians” progress bar was not gated behind the same interactive/non-knitr check every other progress bar in the package uses, so it always printed, including inside notebooks/vignettes.
  • nmr_identify_regions_blood() / nmr_identify_regions_urine() / nmr_identify_regions_cell(): each ppm_to_assign query always contributed exactly num_proposed_compounds rows, padding with NA when fewer candidate metabolites were found within tolerance; those NA-only rows are now dropped instead of returned.
  • models_stability_plot_plsda() / models_stability_plot_bootstrap(): the loadings-correlation heatmap now uses a fixed, sign-agnostic color scale (-1 and +1 both render as the same dark blue, 0 as white; a latent variable’s sign is arbitrary, so -1 and +1 indicate equally strong agreement) instead of a plain sequential palette that auto-scaled to whatever range the data happened to have. Also fixes self-correlation cells (expected to be exactly 1) intermittently rendering as blank/white: a loading vector’s self dot-product can come out as e.g. 1.0000000000000002 due to floating-point rounding, which fell just outside the (-1, 1) scale limits and was dropped to NA by ggplot2’s default out-of-bounds handling; now clamped to the nearest limit instead.
  • bp_VIP_analysis(): VIP scores were indexed by the requested ncomp rather than the fitted model’s actual model$ncomp; on data where mixOmics silently fits fewer components than requested (e.g. a degenerate bootstrap resample), this caused subscript out of bounds.
  • bp_kfold_VIP_analysis(): fixed fold partitioning, which assigned samples to folds with a deterministic x %% k split instead of the intended random shuffle.
  • bp_VIP_analysis(): a degenerate (single-class) bootstrap resample is now redrawn instead of being patched with a fixed, non-random replacement, which biased a fraction of the bootstrap replicates.
  • read_bruker_param(): fixed a wrong regex capture-group index causing subscript out of bounds on some Bruker parameter files.
  • parse_title_file(): fixed a gsub() call missing perl = TRUE, which left trailing whitespace untrimmed from Bruker pdata title fields.
  • choose_best_nlv(): fixed a key-name mismatch that made diagnostic_plot, diagnostic_box_plot, and model_performances always NULL for models built with plsda_auroc_vip_method().
  • models_stability_plot_plsda() / models_stability_plot_bootstrap() / plot_bootstrap_multimodel(): fixed two ggplot2 arguments deprecated since ggplot2 3.3.4/3.4.0, which warned on every call.
  • create_sample_names(): disambiguates samples sharing a leaf directory name (e.g. Bruker EXPNO 10) by stripping the full common path prefix, instead of only one parent level. Collisions more than one level deep now get readable names instead of vctrs-generated ...N suffixes (#62).
  • tidy.nmr_dataset_1D() (and thus plot() / nmr_baseline_threshold_plot()): an unknown NMRExperiment value now warns and is excluded (if some values are valid) or errors (if none are), instead of silently returning rows with NA intensities (#69).

Other changes

  • download_MTBLS242(): validate downloaded files against MetaboLights’ published SHA-256 checksums for the MTBLS242 dataset (#72).
  • Bumped several dependency version floors to roughly their versions from a year ago. Packages with a recent major release are pinned to the last minor of the previous major instead, to avoid forcing an upgrade: ggplot2 (>= 3.5.2), fs (>= 1.6.7), curl (>= 6.4.0), zip (>= 2.3.3), progressr (>= 0.19.0).

AlpsNMR 4.11.1 (2025-09-24)

  • Compatibility with ggplot2-4.0.

AlpsNMR 4.7.2 (2024-08-10)

AlpsNMR 4.7.1 (2024-06-02)

  • Added nmr_autophase() for automated phase correction using the NMRphasing package (#68).
  • Added to_ASICS function to export dataset for ASICS quantification (#68).

AlpsNMR 4.1.6 (2023-02-16)

  • Download improvements:
    • Progress bar
    • Detect user interruptions
    • Sleep 3 seconds between retrying failed downloads

AlpsNMR 4.1.5 (2023-02-10)

  • Replace deprecated dplyr::select() calls.
  • Remove workaround for mixOmics bug, bump mixOmics dependency
  • Simplify implementation (same algorithm) for determining the optimal number of latent variables in the plsda models.
  • Bump dplyr dependency version.

AlpsNMR 4.1.4 (2022-11-08)

  • Disable nested parallelization
  • Update workaround Biocparallel bpmapply
  • Revert bpstop to sleep

AlpsNMR 4.1.3 (2022-11-07)

  • Closer to the fix

AlpsNMR 4.1.2 (2022-11-04)

AlpsNMR 4.1.1 (2022-11-02)

  • Remove archive dependency
  • Try fixing build on palomino4, due to race condition in R CMD check

AlpsNMR 3.99.7 (2022-10-27)

Minor changes

  • Fix build issue on palomino4, simplifying helper function

AlpsNMR 3.99.6 (2022-10-26)

Minor changes

  • When saving, normalize extra information is saved as well.
  • Updated downsampled demo data for examples.
  • More robust nmr_baseline_threshold()
  • Faster examples

AlpsNMR 3.99.5 (2022-10-26)

Minor changes

AlpsNMR 3.99.4 (2022-10-19)

Major changes

  • Improved the download_MTBLS242() function, allowing to either download the parts of MTBLS242 needed for the tutorial or the whole dataset, which may be nice to have if you want to play beyond the tutorial.

  • When reading a Bruker sample from a zip file, you now can specify in the file name the zip subdirectory. For instance, “/path/to/sample.zip!/sample/3”, when sample.zip contains a folder named sample with a subfolder named 3 that includes the sample data you want to actually read.

Minor changes

AlpsNMR 3.99.3 (2022-10-17)

  • Add libarchive as a SystemRequirement to workaround a limitation of the Bioconductor build system (BBS), that can’t pick system requirements recursively. Thanks to Jennifer Wokaty for checking the BBS and providing this suggestion.

AlpsNMR 3.99.2 (2022-10-14)

Breaking changes

  • Set fix_baseline = FALSE in nmr_integrate_regions() as default. The former TRUE approach here did not make much sense if peak boundaries were not perfectly established.

Major changes

  • Baseline estimation: We now offer nmr_baseline_estimation() besides nmr_baseline_removal(). The estimation function computes the baseline and saves it instead of subtracting it from the signal. This is a better approach because it lets each step of the pipeline decide whether it makes sense to subtract the baseline or not. The nmr_baseline_removal() is for now still available, but it will be deprecated in a future version.

  • For the baselineThresh argument in nmr_detect_peaks() we now suggest using nmr_baseline_threshold(dataset, method = "median3mad"). This is more robust than the former (but still the default) method.

  • Peak detection and integration: We want to approach the peak detection, clustering an integration in a different way. While the old pipeline still works as expected, we have introduced new arguments to peak detection, with backwards compatible defaults and a peak clustering function. We still provide the vignette with the former workflow, because it is still relevant but we may deprecate it in a future version, once we are confident the changes we are making are robust across several datasets.

  • Parallellization: We are switching from the future package to BiocParallel, to better integrate in the Bioconductor ecosystem. In this version, if you use a different future plan you may get a warning to switch to BiocParallel. In a future version we will remove our dependency with the (awesome) future package.

Minor changes

  • You can now set experiment names (NMRExperiment) with names(dataset) <- c("Sample1", "Sample2").
  • You can now pass a named vector with the sample names to the nmr_read_samples function. The names will be used as the sample names.
  • Peak detection has a more robust baseline threshold estimation
  • Peak detection estimates the baseline threshold on each sample individually. The threshold is calculated using only the sample where we are currently detecting the peaks.
  • Peak detection includes a simple but effective lorentzian fitting (for area and width estimation)
  • Add functions to evaluate the quality of the peak detection using plots
  • More fine grained interpolation axis if axis = NULL is given in nmr_interpolate_1D()
  • Save list of excluded regions in the nmr_dataset object.
  • Drop MassSpecWavelet workaround on partial argument matching since it was fixed upstream
  • Documentation: Start providing verbose messages with tips in functions
  • Remove unused deprecated imports from the future package (#65, thanks to @HenrikBengtsson)
  • Add URL and BugReports to the DESCRIPTION (#64, thanks to @HenrikBengtsson)
  • Reading bruker samples is now a bit more robust and gives detailed tracebacks in case of error.

AlpsNMR 3.5.1 (2022-04-07)

  • plot_interactive now accepts an overwrite argument to avoid asking the user interactively
  • Improve nmr_detect_peaks_tune_snr to tune the SNR threshold with the right other parameters
  • Documentation improvements
    • Split Peak_detection page into smaller and more specific pages
  • Let the user choose how code is parallellized, as suggested by BiocParallel documentation.
  • Replace furr/future parallellization loops with BiocParallel. Provides a warning in case a future::plan() has been set.
  • Demote Imports to Suggests: SummarizedExpriment, S4Vectors, ggrepel, GGally
  • Remove dependencies: tidyselect, assertthat, plyr, furrr
  • Add download_MTBLS242() function to help download the data for the tutorial
  • Skip mixOmics test if affected by https://github.com/mixOmicsTeam/mixOmics/pull/199
  • Fix auto setting of the baseline threshold for the peak detection

AlpsNMR 3.3.4 (2021-09-16)

  • Fix issue with PCA plots not working as expected
  • Ensure NMRExperiment names are not duplicated in a dataset (closes #44)
  • Fix issue with some title file formatting in Bruker samples (closes #46)
  • Export groups in to_ChemoSpec
  • License since AlpsNMR was released has alwayd been MIT as stated in the bioinformatics paper

AlpsNMR 3.1.5 (2021-3-31)

  • Removed warning about future_options deprecation

AlpsNMR 3.1.4 (2021-1-20)

  • bug fix loading bruker files

AlpsNMR 3.1.3 (2020-11-19)

  • Added instructions to follow a longer tutorial
  • nmr_pca_outliers_plot modified to show names in all boundaries of the plot

AlpsNMR 3.1.2 (2020-11-04)

  • Bug fix related with Bioconductor Renviron variable R_CHECK_LENGTH_1_CONDITION

AlpsNMR 3.1.1 (2020-10-30)

  • Modified order of author list

AlpsNMR 3.1.0 (2020-10-22)

  • Package accepted in bioconductor

AlpsNMR 2.99.93 (2020-10-22)

  • Héctor removed as maintainer to ensure a single point of contact

AlpsNMR 2.99.92 (2020-10-22)

  • Héctor added as maintainer

AlpsNMR 2.99.91 (2020-10-22)

  • test changed

AlpsNMR 2.99.9 (2020-10-22)

  • Added Héctor ass author
  • Bug fix in nmr_read_bruker_fid

AlpsNMR 2.99.8 (2020-10-22)

  • Deletion of tutorial and download_MTBLS242_demo.R

AlpsNMR 2.99.7 (2020-10-19)

  • Bugs in import/export functions to SummarizedExperiment solved

AlpsNMR 2.99.6 (2020-10-19)

  • Added import/export options form nmr_dataset_1D to SummarizedExperiment
  • Added import/export options form nmr_dataset_peak_table to SummarizedExperiment

AlpsNMR 2.99.5 (2020-10-14)

  • Bug in bp_kfold_VIP_analysis solved
  • Several packages moved from import to depends
  • Reexport of some functions removed
  • to_rDolphin_blood code reorganized
  • Typos removed from tutorial
  • norm_pqn_diagnostic$norm_factor used in tutorial instead of plot it
  • Parallel changed for BiocParallel

AlpsNMR 2.99.4 (2020-09-28)

  • Warning in plot_interactive function added
  • Suppressed other warnings of plot_interactive function

AlpsNMR 2.99.3 (2020-09-21)

  • sapply calls changed for vapply
  • Bioconductor installation instructions included
  • MIT license removed
  • LazyData: TRUE removed
  • Excessive print statements removed from vignettes
  • sessionInfo() added to end of vignettes
  • Created inst/script directoy to describe inst/extdata source and creation #TODO falta rellenar el archivo
  • Commented out code removed

AlpsNMR 2.99.2 (2020-08-26)

  • AlpsNMR.Rproj removed from git repository
  • Reduced demo dataset to avoid package size > 5 MB
  • Modified introduction to alpsnmr vignette and some tests to work with reduced demo dataset

AlpsNMR 2.99.1 (2020-08-25)

  • AlpsNMR.Rproj added to gitignore
  • Modified examples to avoid create files in main package folder

AlpsNMR 2.99.0 (2020-08-24)

  • Added bootstrap and permutation method and some plots related to it
  • Minor modifications for bioconductor submision

AlpsNMR 2.5.9002 (2020-05-25)

  • Changes to pass BiocCheck
  • Added permutation test and permutation test plot to nmr_data_analysis

AlpsNMR 2.4.9002 (2020-05-13)

  • Changes to pass checks for R4

AlpsNMR 2.3.3.9002

  • NIHS_specific removed
  • Tests coverage up to 30%
  • Update of save_profiling_plots
  • Add tutorial
  • Remotes installation
  • nmr_diagnose is deprecated. Since nmr_diagnose was only used for getting extra normalization information, it was been replaced with nmr_normalize_extra_info that offers a less confusing name.

AlpsNMR 2.3.3.9001

  • Add nmr_identify_regions_cell function
  • Add documentation of HMDB_cell
  • Vignettes updated
  • New functions to apply multilevel statistics
  • Update of README file

AlpsNMR 2.3.3

  • Change of nmr_identify_regions_blood function
  • Add nmr_identify_regions_urine function
  • Add documentation of HMDB_urine
  • Add computes_peak_width_ppmfunction for nmr_integrate_peak_positions
  • New get_integration_with_metadata
  • Vignettes updated
  • New functions to apply machine learning to proccessed datasets

AlpsNMR 2.3.2

  • Inclusion of baseline removal using assymetric least squares
  • Change the baselineThresh to NULL so it is autodetected
  • Vignettes updated including baseline removal
  • Bug correction in nmr_baseline_threshold
  • Elimination of package vignettes (there is an error to be solved there)
  • New nmr_identify_regions function
  • Add documentation of HMDB_blood
  • New files_to_rDolphin function

AlpsNMR 2.3.1.9000

  • Rename package from NIHSnmr to AlpsNMR