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dendroNetwork: news

dendroNetwork 0.5.5

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

dendroNetwork: news

dendroNetwork 0.5.4

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

dendroNetwork 0.5.3 (05-04-2024)

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

dendroNetwork 0.5.2 (29-03-2024)

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

dendroNetwork 0.5.1 (10-02-2024)

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 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

dendroNetwork 0.5.0 (08-02-2024)

New features

First public release

Minor improvements

Bug Fixes

Deprecated and defunct

Documentation fixes

Continuous integration

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.