This NEWS file mainly serves as a changelog file,
i.e. a list of new features / bugfixes by version number.

#################################
#########   CHANGELOG  ##########
#################################

v0.80.14 -- 2016/10/13
  -  CRAN test fix (make PANDOC optional -- prevents Html reports and Vignettes)

v0.80.13 -- 2016/10/07
  -  minor documentation changes prior to CRAN submission
  
v0.80.12 -- 2016/09/28
  -  bug fixes
      - fix error during in 'PG: Ratio Density' plot when all ratio data is empty (e.g. for blank samples)

v0.80.11 -- 2016/08/11
  -  bug fixes
      - augment fix from v0.80.9 since MaxQuant for finding a MBR reference Raw file

v0.80.10 -- 2016/08/04
  -  automatic detection which txt files are present [only these are used]

v0.80.9 -- 2016/08/02
  - bug fixes
     - MBR-Metric: if more than one RT-reference is found (which can happen for a VERY stable LC), the first is picked
       https://github.com/cbielow/PTXQC/issues/25
  - minor doc improvements     

v0.80.8 -- 2016/07/13
  - bug fixes
     - avoid crash in pre-calibration metric when there is only a single peptide identified in (any) Raw file

v0.80.7 -- 2016/06/09
  - features
     - support for 32bit R for Drag'n'Drop batch file
  - bug fixes
     - fix missing score distribution plots for custom contaminants
     - small documentation improvements
          
v0.80.6 -- 2016/06/06
  - bug fixes
     - fix NA's (empty bars) in MBR ID transfer plot for very sparse Raw files
     - fix crash when plotting EVD aux-plots for Raw files with NO ID's (0% id rate)
      
v0.80.5 -- 2016/04/15
  - bug fixes
      https://github.com/cbielow/PTXQC/issues/23  (EVD: MS/MS Oversampling bug)

v0.80.4 -- 2016/04/11
  - bug fixes
      https://github.com/cbielow/PTXQC/issues/22  (Drag'n'drop of folders with space character)
  
v0.80.3 -- 2016/04/08
  - bug fixes
      https://github.com/cbielow/PTXQC/issues/21
  - Html report will be created prior to PDF file (if both are requested [default])
  - minor doc improvments (Metric help texts in Html report)

v0.80.2 -- 2016/04/04
  - reduce memory footprint (~50% reduction; replacing ddply() with data.table[])

v0.80.1 -- 2016/03/15
  - experimental missing value metric (on peptide level)
    - density plots (showing what intensities are usually missing)
      - includes simple inter-Raw file normalization scheme
    - percentage of missing values (lower is better) -- used for scoring in heatmap
    
v0.80.0 -- 2016/02
  - Report format is by default now Html and PDF (you get two identical reports)
  - Html report includes help texts describing each metric and scoring
  - order of metrics is now matching the wet-lab workflow (roughly), but can be customized (i.e. user-defined) using the YAML config
  - removed Bioconductor dependency (for easier installation)
  - bugfixes / minor improvements

v0.70.3
  - internal restructuring

v0.70.2
  - faster loading of txt files / better consistency checking
  - support for Chinese "NA" entries in Txt files
  
v0.70.1
  - fix empty parameter page (bug in 0.70.0)
  
v0.70.0
  - support for data containing MS3 scans  