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NEWS

For more fine-grained list of changes or to report a bug, consult

• The issues log
• The commit log

• include local copy of XSD files for validation offline

• Avoid validation failures

• replace deprecated dplyr test behavior #254

• replace deprecated dplyr use #253

• ensure geiger is used conditionally in examples

• minor compatibility fix for CRAN

• CRAN-requested patch for collision with {cli} namespace (#251)
• taxadb -> taxalight for fast resolution of taxon ids

Compatibility with upcoming dplyr release.

• This update fixes a minor bug in a unit test for compatibility with R-devel (4.0.0) as requested by CRAN (#245)

• This update fixes a minor bug in a unit test which was introduced by a recent change to the geiger package.

• Makes various tests more robust, and uses symbolic address for nexml.org (#238)
• Provides a real summary() and improved pretty-print (#237)
• Makes character(0) metadata value behave as empty string (#236)
• Fixes detection of having to split matrix by class (#235)
• Switch over to Additional_repositories for CRAN (#229)
• Do not add ter namespace by default. (#227)
• Replace taxize with taxald (#226)
• Fixes how metadata arguments are passed on to add_basic_meta() (#220)
• Fixes CDAO namespace definition [#219]
• Enables handling of files with rootedge [218]

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

• 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 concordant 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.)

• Fix failing checks on CRAN that require a network connection

• avoid rdf-based tests on solaris architecture, where suggested package rdflib is not available. (CRAN request.)

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

• patch for compatibility with upcoming release of testthat

• Bugfixes following release of new dplyr and new tidyr dependencies

• Migrate Additional_repositories to new address for OmegaHat project.

• get_metadata(), get_taxa() now return much richer data.frames instead of named vectors. This is potentially a non-backwards compatible change if scripts use the output of these functions as lists (#129). See updated metadata vignette. This introduces new dependencies dplyr and lazyeval.
• more robust nexml_read() method for URLs, (#123)
• Avoid assuming the namespace prefix nex for nexml elements (#51, #124, #126). Includes a fix server-side on the NeXML validator as well.
• nexml_validate() points to the new validator. (#126)

• Fix compatibility issue with recent phytools release.

• Upgrade tests to be compatible with newest testthat (0.10.0), bumps testthat dependency version up (#119) thanks @hadley

• Add four new vignettes describing the use of various advanced features in the package: the use of SPARQL queries, advanced use of metadata features, an example of how to extend NeXML with simmap data as the use case, and documentation on the central S4 data structure used in the package.
• Implements the use of Title Case in the package title, as requested (on several occasions) by the CRAN maintainers.

• Update DESCRIPTION to provide a standard install.packages() compatible repository for rrdf, as per request from the CRAN team.

• 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 release this as 2.0.0

Minor bugfix

• Fixes typo that caused validator to fail when nexml.org couldn’t be reached

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
• 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

Initial Release

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