Changes in version 0.5.5 (2025-07-25)                  

New features

Minor improvements

  - dendronetwork: it is now possible to choose which correlation to use
    for creating network(s): using the correlation after the
    Hollstein(1980) transformation r_hol or the correlation without any
    transformation (r). The default is now r_hol.

Bug Fixes

Deprecated and defunct

  - moved folder with paper to separate repository:
    https://github.com/RonaldVisser/dendroNetwork_paper

Documentation fixes

  - improved the documentation of the CPM en GN functions

  - corrected minor typos in the documentation.

Continuous integration

                 Changes in version 0.5.4 (2024-04-30)                  

New features

  - replaced magrittr-pipe %>% by native R pipe |>
    
      - dependency of magrittr was removed
    
      - dependency on R-version changed to >= 4.1.0

  - transferred to ROpenSci: https://github.com/ropensci/dendroNetwork

Minor improvements

  - Tested with latest version of Cytoscape: 3.10.2
    (https://cytoscape.org/download.html) and all works fine

Bug Fixes

  - added global variables to prevent notes

  - added various files to build ignore

Deprecated and defunct

Documentation fixes

  - updated all links to https://github.com/ropensci/dendroNetwork or
    https://docs.ropensci.org/dendroNetwork/
  - updated installation instruction
  - minor language corrections
  - description corrections
  - corrected links
  - updated DESCRIPTION file for CRAN
  - donttest{} was added to RING_Visser_2021.R because testing takes to
    long for CRAN.

Continuous integration

  - removed pkgdown deployment, and now relying on ROpenSci:
    https://devguide.ropensci.org/pkg_ci.html

                        Changes in version 0.5.3                        

New features

Minor improvements

Bug Fixes

Deprecated and defunct

Documentation fixes

  - added descriptions of Cytoscape in the readme and vignettes
  - added vignette: dendrochronological_data which describes the data to
    be used.
  - minor corrections

Continuous integration

                        Changes in version 0.5.2                        

New features

Minor improvements

  - added a CONTRIBUTING.md file for contribution guidelines
  - added check to determine if input graph is an igraph object for all
    functions that need an igraph as input
  - added check to determine if input tree-ring dataset is rwl object
    for sim_table

Bug Fixes

  - corrected bug in cyto_clean_styles()
  - corrected error in wuchwerte(). It is not using the anos1 dataset
    from dplR anymore
  - corrected error in cyto_create_gn_style and cyto_create_cpm_style
  - updated cyto_create_cpm_style because it was not working properly.

Deprecated and defunct

  - dev-folder removed, since this was not needed (created by biocthis)

Documentation fixes

  - update acknowledgements in readme and paper
  - corrected text of documentation in cor_mat_overlap()
  - added pkgdown site: https://ronaldvisser.github.io/dendroNetwork/
  - moved some images to man/figures
  - added Vignette on Cytoscape use
  - moved information for using big dataset to separate vignette
  - updated README: added more installation instructions
  - corrected examples in cyto_create_gn_style and cyto_create_cpm_style

Continuous integration

                        Changes in version 0.5.1                        

New features

Minor improvements

  - replaced igraph::graph.data.frame() with
    igraph::graph_from_data_frame(), since the former is deprecated in
    igraph 2.0.0
  - replaced igraph::is.simple with igraph::is_simple
  - replaced igraph::decompose.graph with igraph::decompose
  - correction to calls to functions grDevices::colorRampPalette and
    stats::pnorm

Bug Fixes

Deprecated and defunct

Documentation fixes

  - minor corrections to README
  - added codemeta.json using codemetar::write_codemeta()
  - added .github/CONTRIBUTING.md using usethis::use_tidy_contributing()
  - DESCRIPTION: added URL and BugReports to DESCRIPTION + package
    checks
  - correction in clique_community_names(_par) functions, due to [k]
    seen as link
  - added \dontrun{} to cytoscape functions

Continuous integration

  - added GitHub Action for BiocMananager
    (https://lcolladotor.github.io/biocthis/index.html)
  - added more tests
  - excluded Cytoscape-functions from testing

                        Changes in version 0.5.0                        

New features

First public release

Minor improvements

Bug Fixes

Deprecated and defunct

Documentation fixes

Continuous integration