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