Changelog • dendroNetwork

dendroNetwork 0.5.5

CRAN release: 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

dendroNetwork 0.5.4

CRAN release: 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

dendroNetwork 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

dendroNetwork 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

dendroNetwork 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 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

New features

First public release

Minor improvements

Bug Fixes

Deprecated and defunct

Documentation fixes

Continuous integration