Changelog

Source: NEWS.md

binneR 2.6.4

• Ensure that duplicated files are not aggregated during spectral binning.

binneR 2.6.3

• Fix the calculation of quartiles in binneR::plotTIC.

• Added the DOI of the methodology article (https://doi.org/10.1007/s11306-022-01923-6) to the package DESCRIPTION and README.

binneR 2.6.2

• Improved themes of all plotting functions.

• Reduced the object size returned by all plotting functions.

binneR 2.6.1

• Fixed performance loss during bin metric calculation caused by the binning width retrieval.

binneR 2.6.0

• Removed the LazyData field from the DESCRIPTION file.

• Removed the Remotes field in the DESCRIPTION file as the metaboData dependency is now available on CRAN.

• The number of decimal places used for spectral binning can now be specified using the binner_dp global option or the BINNER_DP environment variable.

• The vignette example now uses the BdistachyonTechnical data set from metaboData.

• An in-package example data file is now used for documentation examples.

• The vignette chunks that require the metaboData package are no longer executed to avoid GitHub API rate limit issues.

• The file header gathering iostream error is now fixed for large data sets (> 1000 samples).

binneR 2.5.3

• Removed the potential for errors during build of the intensity matrices if identical accurate m/z are retrieved for a bin from multiple samples.

binneR 2.5.2

• Fixed I/O issues for sample sets over ~1200.

• Minor alteration to console output.

binneR 2.5.1

• Performance and memory usage gains through ensuring 0 values are not read from raw files.

• Added console output for processing steps to binneR::binneRlyse() and `binneR::singleSample().

binneR 2.5.0

• S4 class Binalysis now inherits from S4 class BinParameters.

• Fixed retrieval of example data in the usage vignette

• version and creation_date slots added to Binalysis S4 class.

• Added additional accessor methods for the Binalysis S4 class.

• Fixed declaration of generics to ensure they are declared as standard generics.

• Added validators for Binalysis S4 class to ensure that sample information contains the correct fields and that the file names in the specified paths match those in the sample information.

binneR 2.4.2

• Bin measures are now correctly averaged across samples in binneR::plotCentrality() and binneR::plotPurity().

binneR 2.4.1

• Fixed errors in binneR::plotCentrality() and binneR::plotPurity().

binneR 2.4.0

• Added a NEWS.md file to track changes to the package.

• pkgdown site available at https://aberHRML.github.io/binneR/.

• Added binneR::readBinningParameters() for parsing binning parameters from YAML format.

• Accurate mass data and bin measures are now returned (binneR::accurateData()) per sample over per class previously.

• 0.01 amu bins can now be plotted by either averaged across all, by class (cls), or by sample using the type argument in binneR::plotBin().

• The pipe (%>%) from the magrittr package now re-exported.

• Unit test coverage now increased to 100%.

• Updated function documentation examples.

• Parallel processing in binneR is now implemented using the future package. Information on how this can now be used is available in the usage vignette.

• plan() from the future package is now re-exported.