Changes in version 1.5.3 (2020-03-09)
+ change tests for rtCorrection, do not use function levels to test for 
if `+`, `.` or `?` is present in the transformation list
+ update vignette that formulas are displayed properly

Changes in version 1.5.2 (2020-01-12)
+ change unit tests for clr and aracne that it doesn't fail in Windows
+ change ppm calculation in structural, use m/z of precursors instead
of m/z differences

Changes in version 1.5.2 (2019-12-11)
+ change unit tests for clr and aracne that it doesn't fail in Windows

Changes in version 1.5.1 (2019-12-05)
+ rename combineStructuralStatistical to combine
+ combine accepts directly the output of createStructuralAdjacency, before the
  function combineStructuralStatistical accepted a numeric matrix (first entry
  of the output of createStatisticalAdjacency)
+ remove the functions consensusAdjacency, createStatisticalAdjacency,
  createStatisticalAdjacencyList
+ add functions statistical, getLinks, topKnet, threshold with improved
  functionality for thresholding the statistical adjacency matrices (based on
  hard thresholds, or top1, top2 or mean consensus matrix calculation according
  to Hase et al.) to replace removed functions
+ rename createStructuralAdjacency to structural
+ change vignette to markdown
+ add parameter directed in structural to allow for directed networks
+ add parameter values to specify if respectively min, max or all values from
  the corresponding feature pairs (in the upper and lower triangle) should be
  taken in statistical

Changes in version 1.3.1 (2019-09-06) 
+ change License to GPL (>= 3)
+ add codecov
+ add Travis-CI for continuous integration
+ add CITATION file 

Changes in version 1.1.2 (2019-04-16)
+ check that MetNet passes all builds without any errors or warnings

Changes in version 1.1.1 (2019-04-03)
+ correct typo in vignette

Changes in version 0.99.24 (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 0.99.23 (2018-10-16)
+ improve createStructuralAdjacency function 

Changes in version 0.99.20 (2018-08-06)
+ replace psych::corr.test by WGCNA::corAndPvalue to improve speed 

Changes in version 0.99.19 (2018-07-26)
+ print message when model calculation in createStatisticalAdjacency is 
  finished 

Changes in version 0.99.18 (2018-07-19)
+ set rfPermute.formula to rfPermute.default in order to use num.cores 

Changes in version 0.99.17 (2018-07-19)
+ set num.cores to 1 in test_statistical for randomForest 

Changes in version 0.99.15 (2018-07-16)
+ do not import stabsel from stabs 

Changes in version 0.99.14 (2018-07-14)
+ use BiocManager instead of BiocLite for installation 

Changes in version 0.99.13 (2018-07-12)
+ do not export functions threeDotsCall and addToList 

Changes in version 0.99.12 (2018-07-12)
+ use BiocStyle package for vignette 
+ remove Makefile
+ use BiocParallel instead of parallel, for instance use bplapply instead
  of mclapply

Changes in version 0.99.11 (2018-07-03)
+ speed up function rtCorrection by vectorizing 

Changes in version 0.99.10 (2018-07-03)
+ speed up function createStructuralAdjacencyMatrix by vectorizing  

Changes in version 0.99.9 (2018-06-26)
+ change 1:... to seq_len() 

Changes in version 0.99.8 (2018-06-26)
+ implement function rtCorrection 

Changes in version 0.99.6 (2018-06-13)
+ use camelCaps for functions 
+ use no spaces between '=' and named arguments

Changes in version 0.99.6 (2018-06-12)
+ fix typo in lasso function 

Changes in version 0.99.5 (2018-06-12)
+ change 1:... to seq_len() 

Changes in version 0.99.4 (2018-06-12)
+ change 1:... to seq_len() 

Changes in version 0.99.3 (2018-06-11)
+ remove sum check for correlation 

Changes in version 0.99.2 (2018-06-11)
+ require R version >= 3.5 

Changes in version 0.99.1 (2018-06-11)
+ remove bugs that there are no WARNINGS and ERRORs when running 
  R CMD check and R CMD BiocCheck 
+ reduce file size of peaklist_example.RData
+ submit to Bioconductor

Changes in version 0.99.0 (2018-05-14)
+ implement functionality to calculate statistical models of correlation 
  (Pearson, Spearman), LASSO, Random Forest, Context likelihood or 
  relatedness network algorithm, algorithm for the reconstruction of 
  accurate cellular networks, constraint-based structure learning 
  algorithm 
+ implement the function create_statistical_network to calcululate the 
  consensus matrix from the different statistically-infered networks
+ implement the function create_structural_network to calculate 
  molecular weight differences and create a network
+ implement the function combine_structural_statistical to combine 
  the structurally-derived and statistically-derived network 
+ implement model partial and semi-partial pearson/spearman correlation
  using the ppcor package 

