Changes in version 4.0.4 (2023-02-16)
- Backport fixes from AlpsNMR 4.1.6
- Retry failed downloads automatically up to three times
- Sleep 3 seconds between download attempt retries.
Changes in version 4.0.3 (2023-02-10)
- Backport fixes from AlpsNMR 4.1.5
- Replace deprecated dplyr::select() calls.
- Fix and simplify implementation for determining number of latent
variables in plsda (same results).
- Bump dplyr dependency requirement
Changes in version 4.0.2 (2022-11-10)
- Backport fixes from AlpsNMR 4.1.4
- Disable nested parallelization to increase stability
- Add workaround to BiocParallel bug in bpmapply memory usage
- Add workaround to R CMD check race condition when checking
examples
- Fix download_MTBLS242() (simplify code and avoid setwd() issues)
Changes in version 4.0.1 (2022-11-02)
- Attempt fix build issue on palomino4 by adding one last example that
waits two seconds
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.