Changes in version 1.29.2 (2023-04-18)
+ replace the error message in shinyCircos test


Changes in version 1.29.1 (2022-11-23)
+ replace aes_string by aes since aes_string is deprecated in newest ggplot2 
  version

Changes in version 1.27.2 (2022-10-19)
+ use Spectra from Spectra for spectral representation instead of MSpectra
  from MSnbase
+ remove compare_Spectra and normalizeddotproduct functions and use 
  compareSpectra from Spectra package
+ change vignette from Rnw to Rmd 

Changes in version 1.27.1 (2022-10-12)
+ add ShinyApps in biocViews

Changes in version 1.19.0 (2020-07-02)
+ adapt to changes in MSnbase (renaming of Spectra to MSpectra)

Changes in version 1.17.0 (2020-01-14)
+ change unit tests to testthat
+ change color 1:4 to colour character vector 

Changes in version 1.15.2 (2019-09-09) 
+ add codecov
+ add Travis-CI for continuous integration
+ add CITATION file

Changes in version 1.15.1 (2019-08-29)
+ add ggplot2 in dependencies
+ change GPL-2 to GPL-3 license

Changes in version 1.15.0 (2019-04-23)
+ implement the MSnbase Spectra/Spectrum2 as the container for MS2 
  spectra, change all functions that they accept Spectra objects
+ write function convertMsp2Spectra that converts MSP files to 
  Spectra files
+ change data files: change convertMSP2MSP.RData to convertMsp2Spectra, 
  create spectra.RData, update similarityMat.RData
+ remove data files: binnedMSP.RData, idMSMStoMSP.RData

Changes in version 1.13.1 (2019-04-04)
+ check if package passes R CMD build and R CMD check without
  any error messages and vignette can be run without any errors

Changes in version 1.11.1 (2018-10-22)
+ adjust NEWS file to new format according to ?news: 
  o entries are grouped according to version, with version header 
    'Changes in version' at the beginning of a line, followed by a version 
    number, optionally followed by an ISO 8601 format date, possibly 
    parenthesized
  o entries may be grouped according to category, with a category header 
    (different from a version header) starting at the beginning of a line
  o entries are written as itemize-type lists, using one of o, *, - or + as 
    item tag. Entries must be indented, and ideally use a common indentation 
    for the item texts

Changes in version 1.11.0 (2018-10-15)
+ remove Makefile from directory vignettes/
+ check if package passes R CMD build and R CMD check without
  any error messages and vignette can be run without any errors

Changes in version 1.9.0 (2018-04-16)
+ no changes, check if package passes R CMD build and R CMD check without
  any error messages and vignette can be run without any errors
   
Changes in version 1.7.0 (2017-11-14)
+ implement calculation for parameter m = 0 in NDP 

Changes in version 1.5.0 (2017-10-20)
+ no changes, check if package passes R CMD build and R CMD check without
  any error messages and vignette can be run without any errors

Changes in version 1.1.6 (2017-06-05)
+ correct bug fix for msp binning when there is only one entry for msp entry 
+ improve function binning when there is only one fragment 

Changes in version 1.1.5 (2017-04-03)
+ extend unit tests for shinyApp, plottingFunctions and convert2MSP 

Changes in version 1.1.4 (2017-01-28)
+ change MSP class, create slots mz, rt, names, classes, information and adduct
+ add tabPanels in shinyCircos (Main, Appearance) 
+ rearrange position of legend, implement option to show/not show legend
+ rescale plot when changing window size, allow for further scaling/descaling 
  of the plot
+ adjust convertMSP2MSP to new class MSP, create unit tests 
+ include msp2msp matrix, a test data set for convertMSP2MSP
+ set methods for names, classes, adduct and information
+ change the interactive shinyCircos such that the user can update the annotation 
  data of an MSP object (name, class, information and adduct ion information) 
   
Changes in version 1.1.3 (2016-12-05)
+ use new email adress 
+ use option to calculate MSP-object from msp-file directly 

Changes in version 1.1.2 (2016-11-17)
+ use absolute masses when calculating similarities in 
  createSimilarityMatrix (bug fix) 
+ add option links in highlight, i.e. should links be plotted or not? 

Changes in version 1.1.1 (2016-11-04)
+ change slider input as such that one is able to select a lower 
  and lower bound instead of only a lower bound 

Changes in version 0.99.6 (2016-10-10)
+ improve allocation of clicked features in shinyCircos 
+ change line width and colour in plotCircos 

Changes in version 0.99.5 (2016-09-15)
+ add arguments colour and transparency for functions plotCircos and highlight

Changes in version 0.99.4 (2016-08-17)
+ add arguments splitIndMZ and splitIndRT in function convert2MSP and
  fix bug (colnames classes instead of class) in convert2MSP 
+ update vignette, unit tests and manuals [2016-08-17 Wed]

Changes in version 0.99.3 (2016-08-01)
+ remove verbatim Textouput(help) in shinyApp 
+ change function createSimilarityMatrix in order that it does not
  change ordering of row names 
+ update unit tests and manuals 

Changes in version 0.99.2 (2016-07-26)
+ do not reorder again in createOrderedSimMat function 
+ change allocatePrecursor2mz function such, that it is compatible with 
  all sd01 and sd02 objects 

Changes in version 0.99.1 (2016-06-14)
+ rewrite functions that they do not require the argument dfNameGroup (data.frame
  containing group and unique identifier) any longer 
+ the function binning uses now the function cut to create bins
  binning has two methods implemented to calculate from these bins 
  median and mean m/z values from the fragment m/z values
+ documentation about data sets is extended
+ include 'Suggests: BiocGenerics' in the DESCRIPTION file

Changes in version 0.99.0 (2016-05-14)
+ submit package to Bioconductor file tracker 

Changes in version 0.98.0 (2016-04-16)
+ add information of hovered objects in shinyCircos 
+ allow for subsetting of MSP objects (2016-04-12)
+ add unit tests for exported functions (2016-04-12)
