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NEWS.md
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# dendroNetwork: news {#dendroNetwork}
## dendroNetwork 0.5.5 (development)
### New features
### Minor improvements
### Bug Fixes
### Deprecated and defunct
### Documentation fixes
### 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 \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
## dendroNetwork 0.5.0 (08-02-2024)
### New features
First public release
### Minor improvements
### Bug Fixes
### Deprecated and defunct
### Documentation fixes
### Continuous integration