phylobase - phylobase v0.8.12

• CRAN maintenance release. The phylobase vignette is now written in Rmarkdown.

Full Changelog: https://github.com/fmichonneau/phylobase/compare/v0.8.10...v0.8.12

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Published by fmichonneau over 2 years ago

phylobase - phylobase v0.8.10

CHANGES IN phylobase VERSION 0.8.10

• CRAN maintenance release in prepartion for R 4.0.0 with stringsAsFactors=FALSE as default. For backwards compatibility, stringsAsFactors is set to TRUE internally to mimic the previous default behavior. For the time being, conversion to non-factors data types will need to be handled manually.

- R
Published by fmichonneau over 6 years ago

phylobase - phylobase v0.8.8

CHANGES in phylobase VERSION 0.8.8

• CRAN maintenance release. Updated documentation of the ancestors() function to remove unused ....

- R
Published by fmichonneau over 6 years ago

phylobase - phylobase 0.8.6

• Maintenance release

- R
Published by fmichonneau over 7 years ago

phylobase - phylobase 0.8.4

• CRAN maintenance release

- R
Published by fmichonneau about 9 years ago

phylobase - phylobase 0.8.2

• Fix typo in example of phylo4d methods

- R
Published by fmichonneau over 10 years ago

phylobase - phylobase 0.8.0

CHANGES IN phylobase VERSION 0.8.0

New features

• Initial basic support for converting RNeXML objects in phylo4 and phylo4d format.
• New methods: internalEdges(), terminalEdges()
• descendants() has now a "ALL" argument to include self in results
• New method: nodeHeight() provides a consistent and comprehensive way of calculating the distance between a node and either the root or the tips. (fix #3)
• The replacement methods for labels, tipLabels, nodeLabels, edgeLabels now accept NA or NULL to remove labels (fix #2)

Major changes

• readNexus and readNewick now internally use the package rncl to parse files. They also use a different approach to reconstruct the edge matrix. These changes make file parsing faster. Objects created with this new approach may not exactly be identical to those created in previous versions as node numbering might differ, they should however be fully compatible with each others.
• readNexus and readNewick can now parse tree files with trees containing a subset of the taxa listed in the TAXA Block.
• Source code for the package is hosted on GitHub at https://github.com/fmichonneau/phylobase

Minor changes

• All tests done with testthat
• rootNode returns the rootNode using the same format as getNode().
• All documentation is in Roxygen format
• hasPoly, hasRetic, hasSingle are now methods instead of functions.

Deprecated functions

• nodeDepth and depthTips are now deprecated and are replaced by nodeHeight

Bug fixes

• Fix bug: NA in labels were considered duplicated by checkPhylo4().
• Fix bug #605 (R-forge) -- treePlot subsets numeric data for plotting.
• Fix bug #4: descendants() behave like ancestors() when provided with a vector of nodes and is consistent across all arguments.

- R
Published by fmichonneau almost 11 years ago