NEWS.md

In AlpsNMR: Automated spectraL Processing System for NMR

AlpsNMR 3.0.5 (2021-1-20)

• Bug fix loading bruker files

AlpsNMR 3.0.4 (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 3.0.3 (2020-11-04)

• Bug fix related with Bioconductor Renviron variable R_CHECK_LENGTH_1_CONDITION

AlpsNMR 3.0.2 (2020-10-30)

• Solved malformed autor field

AlpsNMR 3.0.1 (2020-10-30)

• Release branch 3_12 updated

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

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.

AlpsNMR documentation built on April 1, 2021, 6:02 p.m.