Changes in version 4.7.2 (2024-08-10) - Disable nested parallellization in nmr_detect_peaks_tune_snr(). Changes in version 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). Changes in version 4.1.6 (2023-02-16) - Download improvements: - Progress bar - Detect user interruptions - Sleep 3 seconds between retrying failed downloads Changes in version 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. Changes in version 4.1.4 (2022-11-08) - Disable nested parallelization - Update workaround Biocparallel bpmapply - Revert bpstop to sleep Changes in version 4.1.3 (2022-11-07) - Closer to the fix Changes in version 4.1.2 (2022-11-04) - Try a more robust fix on palomino4 (bpstop() instead sleep) - Use register() in an example to avoid further breakage on palomino - Workaround performance issues on BiocParallel::bpmapply() (https://github.com/Bioconductor/BiocParallel/pull/228) Changes in version 4.1.1 (2022-11-02) - Remove archive dependency - Try fixing build on palomino4, due to race condition in R CMD check Changes in version 3.99.7 (2022-10-27) Minor changes - Fix build issue on palomino4, simplifying helper function Changes in version 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 Changes in version 3.99.5 (2022-10-26) Minor changes - Remove call to deprecated ggplot2::qplot() Changes in version 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 - Remove Bioconductor Build System workaround, since https://github.com/Bioconductor/BBS/issues/220 was fixed. Changes in version 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. Changes in version 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. Changes in version 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 Changes in version 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 Changes in version 3.1.5 - Removed warning about future_options deprecation Changes in version 3.1.4 - bug fix loading bruker files Changes in version 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 Changes in version 3.1.2 (2020-11-04) - Bug fix related with Bioconductor Renviron variable R_CHECK_LENGTH_1_CONDITION Changes in version 3.1.1 (2020-10-30) - Modified order of author list Changes in version 3.1.0 (2020-10-22) - Package accepted in bioconductor Changes in version 2.99.93 (2020-10-22) - Héctor removed as maintainer to ensure a single point of contact Changes in version 2.99.92 (2020-10-22) - Héctor added as maintainer Changes in version 2.99.91 (2020-10-22) - test changed Changes in version 2.99.9 (2020-10-22) - Added Héctor ass author - Bug fix in nmr_read_bruker_fid Changes in version 2.99.8 (2020-10-22) - Deletion of tutorial and download_MTBLS242_demo.R Changes in version 2.99.7 (2020-10-19) - Bugs in import/export functions to SummarizedExperiment solved Changes in version 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 Changes in version 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 Changes in version 2.99.4 (2020-09-28) - Warning in plot_interactive function added - Suppressed other warnings of plot_interactive function Changes in version 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 Changes in version 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 Changes in version 2.99.1 (2020-08-25) - AlpsNMR.Rproj added to gitignore - Modified examples to avoid create files in main package folder Changes in version 2.99.0 (2020-08-24) - Added bootstrap and permutation method and some plots related to it - Minor modifications for bioconductor submision Changes in version 2.5.9002 (2020-05-25) - Changes to pass BiocCheck - Added permutation test and permutation test plot to nmr_data_analysis Changes in version 2.4.9002 (2020-05-13) - Changes to pass checks for R4 Changes in version 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. Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 2.3.1.9000 - Rename package from NIHSnmr to AlpsNMR Changes in version 2.3.1 - Change SNR.Th value from 3 to 4 in pipeline_example.R - Update installation instructions - Last version form Sergio (changes not significant since 2.3.0) Changes in version 2.3.0 - Improve installation instructions under R<3.5 - nmr_peak_detection_tune_snr function added. - Minor bug fixes Changes in version 2.2.0 - Improve installation instructions - Clarify Add metadata vignette - Add normalization diagnostics - Add some data analysis helpers - Enable parallellization for sample loading, peak detection and data analysis helpers - Do not set negative area values to zero, to avoid biasing variances - Add metadata from a single tidy excel function - Add nmr_diagnose to get and set diagnostic information - Add nmr_diagnose support to nmr_normalize - Minor bug fixes Changes in version 2.1.0 - Documentation improvements - nmr_dataset_peak_table object for peak detection results Changes in version 2.0.0 - Too many changes to be listed here. Check the vignette for a summary of all the features. Use browseVignettes("NIHSnmr"). Changes in version 1.2.0 Breaking changes - Rename injection_id to NMRExperiment. - nmr_dataset_load and nmr_dataset_save now use readRDS and saveRDS instead of load and save. This is the right approach to serialize single R objects. If you need a script to convert previously saved datasets (created using nmr_dataset_save) please use NIHSnmr:::nmr_dataset_load_old_and_save("your_old_file.RData", "your_old_file.RDS") to convert the files. Sorry for the inconvenience, but the sooner we fix this the better. - filter to select a subset of samples from an nmr_dataset object has been adapted to dplyr >= 0.7.4. Unless you used the .dots argument in your calls there is no need to change anything. This means we now use a tidy evaluation syntax for filter. - nmr_get_metadata() returns always a data frame / tibble, even when only a single column is requested. It also always includes the "NMRExperiment" column. - nmr_dataset object has two tables metadata and metadata_ext. The metadata_ext table includes all the metadata we add with nmr_add_metadata while metadata has the internal metadata (acquisition parameters, etc). Please use nmr_get_metadata(nmr_dataset) instead of nmr_dataset$metadata. Other changes - Remove workaround to dplyr issue: https://github.com/tidyverse/dplyr/issues/2203 (Sergio Oller reported and fixed the issue, dplyr-0.7.0 is fixed) - The Bruker title file has quite a free format definition. A title file can contain lines like "Field value" or "Field value ;" or simply "value". The heuristics to parse the title file have been improved. - Depend on tidyr 0.8.1. tidyr 0.8.0 had a bug that we reported (and for which we also provided a fix): https://github.com/tidyverse/tidyr/pull/419 - nmr_get_metadata gives a warning if the user asks for metadata columns that are missing. - New nmr_integrate_regions function. - nmr_normalize accepts pqn normalization.