RNeXML - RNeXML

- R
Published by cboettig over 6 years ago

RNeXML - RNeXML v2.3.0

An extensive and rapidly growing collection of richly annotated phylogenetics data is now available in the NeXML format. NeXML relies on state-of-the-art data exchange technology to provide a format that can be both validated and extended, providing a data quality assurance and adaptability to the future that is lacking in other formats. See Vos et al 2012 for further details on the NeXML format.

Release Notes

This release addresses several aspects improving the handling of metadata:

• add_meta() now works for trees and characters (#213, PR #217)
• Handles nested meta elements properly (#196, PR #197)

Misc fixes:

• enable handling of rootEdge (#207, PR #218)
• Replaces taxize backend with faster alternative taxadb method. (#224, PR #226). This remains only a suggested package and has much lighter dependencies as well.
  
• add hex

- R
Published by cboettig about 7 years ago

RNeXML - RNeXML v2.2.0

An extensive and rapidly growing collection of richly annotated phylogenetics data is now available in the NeXML format. NeXML relies on state-of-the-art data exchange technology to provide a format that can be both validated and extended, providing a data quality assurance and adaptability to the future that is lacking in other formats. See Vos et al 2012 for further details on the NeXML format.

Release Notes

• Fixes various (previously broken) aspects of handling polymorphic and uncertain states for discrete (non-molecular) and continuous characters, including obtaining a character matrix (#174), ensuring proper column types (#188), and serializing to NeXML (#192).
• Adds the optional ability to, in addition to the character matrix, obtain a concordantly formatted matrix of state types (standard, polymorphic, uncertain).
• Fixes loss of certain literal-valued metadata when serializing to NeXML. #193
• Drops package phylobase as dependency. (Also removes circular dependency chain, because phylobase depends on RNeXML.)

- R
Published by cboettig over 7 years ago

RNeXML - RNeXML: The next-generation phylogenetics format comes to R

An extensive and rapidly growing collection of richly annotated phylogenetics data is now available in the NeXML format. NeXML relies on state-of-the-art data exchange technology to provide a format that can be both validated and extended, providing a data quality assurance and adaptability to the future that is lacking in other formats. See Vos et al 2012 for further details on the NeXML format.

Release Notes

- R
Published by cboettig over 7 years ago

RNeXML - RNeXML

Streamlines some dependencies:

• taxize as Suggests only
• drop rrdf in favor of rdflib
• drop Sxslt in favor of xslt

- R
Published by cboettig almost 8 years ago

RNeXML - RNeXML 2.0.8

- R
Published by cboettig over 8 years ago

RNeXML - RNeXML v2.0.7 released to CRAN

- R
Published by cboettig about 9 years ago

RNeXML -

NEWS

For more fine-grained list of changes or to report a bug, consult - The issues log - The commit log

Versioning

Releases will be numbered with the following semantic versioning format:

..

And constructed with the following guidelines: - Breaking backward compatibility bumps the major (and resets the minor and patch) - New additions without breaking backward compatibility bumps the minor (and resets the patch) - Bug fixes and misc changes bumps the patch - Following the RStudio convention, a .99 is appended after the patch number to indicate the development version on Github. Any version Coming from Github will now use the .99 extension, which will never appear in a version number for the package on CRAN.

For more information on SemVer, please visit http://semver.org/.

v2.0.0

• add URL and BugReports to Description. #103
• for consistency with other add_ methods, the nexml object is now the last, not the first, argument to add_basic_meta. As this changes the function API, it could break code that does not explicitly name the arguments, so we should consider releasing this as 2.0.0

v1.1.3

Minor bugfix - Fixes typo that caused validator to fail when nexml.org couldn't be reached

v1.1.2

Less aggressive unit-tests - nexml_validate now returns NULL if the validation cannot be performed. Unit tests now consider either TRUE or NULL as acceptable.
- Just skips the uuid unit test if uuid package is not available - Documented versioning practice in NEWS

v1.1.1

Documentation and less agressive unit tests - Unit tests relying on the Figshare API are not run (without failing) if authentication to figshare server fails - Documentation updated to include examples for all functions

v1.1-0

Initial Release

- R
Published by cboettig over 11 years ago