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