Changes in version 1.1                         

Changes in version 1.1.3

  - update tests after update of OBO file / rmzqc

Changes in version 1.1.2

  - Fix implementation of mzAquisitionRange
  - add numberEmptyScans in qualityMetrics function
  - add unit tests for export in rmzqc format
  - add interpretation aid of metrics in vignette

Changes in version 1.1.1

  - move msdata from Suggests to Imports
  - rename function rtDuration to chromatographyDuration
  - rename function rtOverTicQuantiles to ticQuartersRtFraction
  - create function numberEmptyScans
  - add attributes (MS QC terms) to the output of the Spectra metrics
    functions if the output matches the described term
  - add rmzqc to IMPORTS
  - add functionality to export quality metrics as in rmzqc format
  - adjust documentation to newest version of PSI MS CV obo file
  - add to the vignette information on how the metrics are calculated
  - add argument filterEmptySpectra to remove entries of length 0 or
    that have intensity 0, implement the argument in the functions
    calculateMetricsFromOneSampleSpectra, calculateMetricsFromSpectra,
    calculateMetricsFromMsExperiment, and calculateMetrics

                        Changes in version 0.99                         

Changes in version 0.99.9 (2023-04-18)

  - enable parallel processing in calculateMetricsFromSpectra
  - rename ticQuantileToQuantileLogRatio to
    ticQuartileToQuartileLogRatio
  - rename rtOverTicQuantile to rtOverTicQuantiles
  - return quartiles instead of quantiles in precursorIntensityQuartiles
  - add mzR to Suggests in DESCRIPTION

Changes in version 0.99.8 (2023-09-02)

  - adjust behaviour of metrics function when Spectra object of length 0
    is presented, return NA values instead of raising an error

Changes in version 0.99.7 (2023-06-02)

  - adjust ticQuantileToQuantileLogRatio that it adheres to Quameter
    calculation

Changes in version 0.99.6 (2022-11-29):

  - extend section Description in DESCRIPTION
  - add sections BugReports and URL in DESCRIPTION
  - update dependency to R version 4.2.0
  - transfer source code in R/Lee2019-data.R to
    inst/sources/Lee2019-data-source.R
  - use partial_bundle to reduce the file size of plotly graphics

Changes in version 0.99.5 (2022-10-12):

  - add section on alternative software in vignette
  - simplify the vignette with regard to dealing with the RPLC and HILIC
    example data set and adjust the Lee2019-data.R accordingly to keep
    the RPLC/HILIC information in the dataOrigin slot of the Spectra
    object

Changes in version 0.99.4 (2022-10-11):

  - add missing comma in DESCRIPTION

Changes in version 0.99.3 (2022-10-11):

  - delete Maintainer field in DESCRIPTION
  - add instructions to install MsQuality in vignette and README.md via
    remotes/BiocManager instead of devtools

Changes in version 0.99.2 (2022-09-20):

  - create branch msexperiment to store infrastructure and functions for
    MsExperiment objects
  - remove MsExperiment objects since this is still in BioC review and
    solely rely on Spectra objects
  - adjust documentation for the implemented changes (removal of
    MsExperiment)

Changes in version 0.99.1 (2021-11-23)

  - simplify calculateMetricsFromSpectra:
      - the function does not any longer match the arguments by the
        formal arguments of the metric functions
      - the function does not any longer combine the parameters
      - the additional arguments do not take longer the parameter list
        of arguments but comma-separated arguments given to ...
      - for all metric functions the ... parameter is added
      - adjust the vignette and help pages
  - rename functions to camel case

Changes in version 0.99.0 (2021-09-10)

  - add quality metrics/functions (metrics based on HUPO-mzQC):
      - rtDuration (QC:4000053),
      - rtOverTICquantile (QC:4000054),
      - rtOverMsQuarters (rtOverMSQuarters),
      - ticQuantileToQuantileLogRatio (QC:4000057, QC:4000058),
      - numberSpectra (QC:4000059, QC:4000060),
      - medianPrecursorMz (QC:4000065),
      - rtIQR (QC:4000072),
      - rtIQRrate (QC:4000073),
      - areaUnderTIC (QC:4000077),
      - areaUnderTICRTquantiles (QC:4000078),
      - extentIdentifiedPrecursorIntensity (QC:4000125),
      - medianTICRTIQR (QC:4000130),
      - medianTICofRTRange (QC:4000132),
      - mzAcquisitionRange (QC:4000138),
      - rtAcquisitionRange (QC:4000139),
      - precursorIntensityRange (QC:4000144),
      - precursorIntensityQuartiles ((QC:4000167, QC:4000228,
        QC:4000233),
      - precursorIntensityMean (QC:4000168, QC:4000229, QC:4000234),
      - precursorIntensitySD (QC:4000169, QC:4000230, QC:4000235),
      - msSignal10XChange (QC:4000172, QC:4000173),
      - ratioCharge1over2 (QC:4000174, QC:4000179),
      - ratioCharge3over2 (QC:4000175, QC:4000180),
      - ratioCharge4over2 (QC:4000176, QC:4000181),
      - meanCharge (QC:4000177, QC:4000182),
      - medianCharge (QC:4000178, QC:4000183)
      - .rt_order_spectra (helper function)
  - add the functions calculateMetricsFromSpectra,
    calculateMetricsFromMsExperiment to calculate the metrics based on
    Spectra and MsExperiment objects
  - add functions plotMetric, plotMetric_tibble to visualize the metrics
  - add shiny application shinyMsQuality to interactively visualize the
    metrics