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

Versions uploaded to CRAN are marked with [CRAN].

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

[CRAN] v0.91.0 -- 2017/10/06
  - [DOC] Extended 'charge' plot html-documentation (linking to Bittremieux 2017, DOI: 10.1002/mas.21544).
  - [FIX] issue #39 (order of barchart items corrected after changes to ggplot package)
          issue #40 (custom contaminant plot error when not all Raw files are affected)

[CRAN] v0.90.0 -- 2017/08/03
  - [FEATURE] Tables are shown as genuine HTML tables in Html-Output
  
[CRAN] v0.82.6 -- 2017/06/09
  - [FIX] Special Contaminants searched by name in protein ID as well (issue #34)

[CRAN] v0.82.5 -- 2017/05/04
  - [FIX] More robust installation instructions for GitHub package (issue #32)

v0.82.4 -- 2017/04/24
  - [FIX] MS/MS fragment intensity plot fixed for MaxQuant 1.2 results (Basepeak Intensity column was renamed, issue #32)

[CRAN] v0.82.3 -- 2017/04/03
  - [FIX] MS/MS fragment plots can deal with 'Unknown' mass analyzer (e.g. from mzXML input)
  - [FIX] .yaml config file is written completely before actual analysis starts

[CRAN] v0.82.2 -- 2017/02/18
  - [FIX] fix Match-between-runs plotting when data is extremely sparse (issue #30)
  - [DOC] improved description of how to customize YAML config
  - [FEATURE] write out preliminary YAML config upon first invocation, enabling the user to disable metrics on failing runs

v0.82.1 -- 2016/11/03
  -  fixes to new Dependent Peptides (DP) plot (issue #28) (added target sites in percent)

v0.82.0 -- 2016/11/01
  -  [METRIC] new Dependent Peptides (DP) plot (issue #28)
     (if DP were enabled in MaxQuant, the Top5 modifications will be displayed;
      this allows to compare samples, but also hints at overlooked variable modifications)

v0.81.0 -- 2016/10/18
  -  [METRIC] new experimental MS/MS intensity metric 
     (scoring the MS/MS TIC vs. base peak, to look for bad ion transmission or fragmentation)

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

[CRAN] 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  