CRAN-requested patch for collision with {cli} namespace (#251)
taxadb -> taxalight for fast resolution of taxon ids
v2.4.4
Compatibility with upcoming dplyr release.
v2.4.3
This update fixes a minor bug in a unit test for compatibility with
R-devel (4.0.0) as requested by CRAN (#245)
v2.4.2
This update fixes a minor bug in a unit test which was introduced by
a recent change to the geiger package.
v2.4.0
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]
v2.3.0
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
v2.2.0
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.)
v2.1.2
Fix failing checks on CRAN that require a network connection
v2.1.1
avoid rdf-based tests on solaris architecture, where suggested
package rdflib is not available. (CRAN request.)
v2.1.0 2018-05-05
taxize as Suggests only
drop rrdf in favor of rdflib
drop Sxslt in favor of xslt
v2.0.8 2017-11-17
patch for compatibility with upcoming release of
testthat
v2.0.7 2016-06-28
Bugfixes following release of new dplyr and new tidyr
dependencies
v2.0.6 2016-03-07
Migrate Additional_repositories to new address for OmegaHat
project.
v2.0.5 2015-12-31
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)
v2.0.4 2015-10-14
Fix compatibility issue with recent phytools release.
v2.0.3 2015-05-27
Upgrade tests to be compatible with newest testthat (0.10.0), bumps
testthat dependency version up (#119) thanks @hadley
v2.0.2 2015-05-01
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.
v2.0.1 2014-12-26
Update DESCRIPTION to provide a standard
install.packages() compatible repository for
rrdf, as per request from the CRAN team.
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
v1.1.3 2014-08-06
Minor bugfix
Fixes typo that caused validator to fail when nexml.org couldn’t be
reached
v1.1.2 2014-07-19
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
v1.1-0 2014-07-18
Initial Release
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