# 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

- Remove call to deprecated `ggplot2::qplot()`

# 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

- Remove Bioconductor Build System workaround, since 
  https://github.com/Bioconductor/BBS/issues/220 was fixed.

# 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_ppm`function 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

# NIHSnmr 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)

# NIHSnmr 2.3.0

- Improve installation instructions under R<3.5
- nmr_peak_detection_tune_snr function added.
- Minor bug fixes

# NIHSnmr 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

# NIHSnmr 2.1.0

- Documentation improvements
- nmr_dataset_peak_table object for peak detection results

# NIHSnmr 2.0.0

- Too many changes to be listed here. Check the vignette for a summary of all
the features. Use `browseVignettes("NIHSnmr")`.

# NIHSnmr 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.
