Changes in version 1.27.4 (2025-10-24)
+ adjust unit tests for aracne 

Changes in version 1.27.3 (2025-10-23)
+ add 1 as diagonal values in adj in vignette

Changes in version 1.27.2 (2025-10-10)
+ extend unit test to larger data table in test_methods.R

Changes in version 1.27.1 (2025-10-02)
+ adjust unit tests after ggplot2 changes

Changes in version 1.17.2 (2023-02-03)
+ improve structural function to work with transformation tables that are
  tibble objects (contribution by Elva Maria Novoa-del-Toro)
+ added unit tests for the transformation tibble case (contribution by Elva
  Maria Novoa-del-Toro)

Changes in version 1.17.1 (2022-11-23)
+ replace aes_string by aes since aes_string is deprecated in newest ggplot2
  version

Changes in version 1.15.2 (2022-05-18)
+ improve documentation for function correlation and statistical and
  include information that also ggm can be used

Changes in version 1.15.1 (2022-04-27)
+ set ci in corr.test to FALSE to speed up calculation of correlation values
  (function correlation)

Changes in version 1.13.2 (2022-03-04)
+ add function addSpectralSimilarity and allow to add a MS2 similarity
  matrix (contribution by Liesa Salzer)
+ adjust the functions threshold and combine to be able to deal with
  MS2 similarities  (contribution by Liesa Salzer)
+ adjust the vignette to the changes imposed by the new function
  addSpectralSimilarity (contribution by Liesa Salzer)

Changes in version 1.13.1 (2022-02-11)
+ update unit tests, e.g. remove ggm for as.data.frame, set R=1000 for bayes

Changes in version 1.11.6 (2021-11-24)
+ add ggm method in statistical and implement dealing with NA
  values for partial correlation and ggm
+ add (optional) calculation of ranked absolute coefficients in
  threshold for the top1, top2, and mean types to take into account
  negative coefficients (e.g. from pearson or spearman correlation)
+ remove ppcor package and use psych::partial.r for partial correlation,
  calculate the t-values/p-values based on the partial correlation
  coefficients
+ use knnmi.all from parmigene to calculate MI scores, remove mpmi::cmi
  dependency

Changes in version 1.11.5 (2021-10-12)
+ add assays in structural based on columns in transformations that are
  defined by the var argument in structural, adjacency matrices of type
  will be stored in the AdjacencyMatrix object defined in the columns of
  transformation
+ implement structural that it can also calculate mass differences of 0 for
  undirected networks

Changes in version 1.11.4 (2021-09-09)
+ shift calculation of as.data.frame(am) in mz_summary
+ several fixes of typos in the comments and vignette
+ fix rtCorrection function

Changes in version 1.11.3 (2021-08-30)
+ change calculation of mass differences, use the differences between
  (M_2+ppm)-(M_1-ppm) and (M_2-ppm)-(M_1+ppm) instead of (M_1-ppm)-(M_1) and
  (M_2+ppm)-(M_1) for querying against the list of transformations

Changes in version 1.11.2 (2021-08-30)
+ change error message in test_combine

Changes in version 1.9.6 (2021-08-27)
+ change error message in test_combine

Changes in version 1.9.6 (2021-05-05)
+ reduce dependencies, remove the sna package

Changes in version 1.9.5 (2021-05-04)
+ add functionality to adjust for multiple testing in correlation
+ return symmetric matrices when returning ppm ranges in structural

Changes in version 1.9.4 (2021-04-30)
+ add font in mz_vis to mono
+ split the example on how to use filter in mz_summary from the visualisation

Changes in version 1.9.3 (2021-04-28)
+ introduce AdjacencyMatrix S4 class, derived from SummarizedExperiment, to
  store the adjacency matrices. AdjacencyMatrix objects can be of type
  structural, statistical, and combine
+ adjust the documentation and tests for AdjacencyMatrix objects
+ add the functions mz_summary and mz_vis (contribution of Liesa Salzer)

Changes in version 1.9.2 (2021-03-24)
+ add section on structual matrix generation for directed=FALSE

Changes in version 1.9.1 (2021-02-20)
+ fix typos in the vignette

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

