dendroNetwork 0.5.5
CRAN release: 2025-07-25
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.
Deprecated and defunct
- moved folder with paper to separate repository: https://github.com/RonaldVisser/dendroNetwork_paper
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
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
dendroNetwork 0.5.2
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 theanos1
dataset from dplR anymore - corrected error in
cyto_create_gn_style
andcyto_create_cpm_style
- updated
cyto_create_cpm_style
because it was not working properly.
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
andcyto_create_cpm_style
dendroNetwork 0.5.1
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
withigraph::is_simple
- replaced
igraph::decompose.graph
withigraph::decompose
- correction to calls to functions
grDevices::colorRampPalette
andstats::pnorm
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