Rphenoscape release v0.3.0

This is a major new release with a renamed, restructured, and better streamlined API.

Note that this release is not backwards compatible with previous ones. Many function calls from the v0.2.x series remain available with deprecation warnings, and are slated for removal in 0.4.x.

Major changes include the following:

• a02c294 State symbol to label translation is now polymorphic state-capable
• 37d6354 Upgrades to using KB API v2, including
  • f1c6464 Replaces taxa corpus with annotated-taxa/taxon-variation (#254)
  • 41db43d Adds corpus=states to corpus_size/term_freqs
  • 8f58e1b Switches to named corpus kb phenoscape api
• Overhauls term category determination and use, including
  • 4083c01 Allows "entity" or "phenotype" for term_freqs() as
  • 58936f2 Removes subclass recursion and other fixes for term category
  • 629c814 Improves algorithm and documentation for term category
  • e01258f Removes term_freqs taxon_annotations corpus
  • 1a0390c Removes term IRI decoding logic
• 7589303 Adds mutual excusivity functions
• fc03aba Adds Owl class for use with get_ontotrace_data()
• 47f6c71 Adds terminfo class
• Streamlined and restructured function API and naming, including
  • 3759ab3 Combines NeXML char matrix functions
  • 527c3c5 Renames pk_get_IRI.R to get_IRI.R
  • 97a84bf Removes pk_ prefix from term.R functions
  • 4e353e0 Removes pk prefix from pk_is_descendant/pk_is_ancestor
  • 6dd42e4 Renames pk_get_study_xml to get_study_data
  • d38f801 Renames pk_get_ontotrace_xml to get_ontotrace_data
  • e7f5106 Replaces pk_*_class with term_classification
  • 52b6fca Renames pk_get_study_list to get_studies (#126)
  • 81eb0b9 Renames pk_get_iri to get_term_iri (#125)
• b535e62 Moved CI testing from GitHub action to CircleCI
• Various improvements to documentation and examples

RPhenoscape release v0.2.16

This is primarily a bug fix release. Changes since the last release include the following:

• ba60b7c Fixes RNeXML links in documentation
• 217b373 Support for PHENOSCAPE_API environment to control KB endpoint URL
• 57c5f16 Filters out label-less terms from flagged ontologies
• 26d6eab Fixes handling of term freqs that are missing or zero
• c3024d9 Handles HTTP 404 returned for no matches
• 8479be3 Fixes HTTP error reporting
• 862be7e Migrates from Travis-CI to GitHub Actions (#150)
• 788230e Forces use of GET for phenotype info queries

RPhenoscape release v0.2.15

Changes since the last release include the following:

• 9b736b0 Implements profile similarity
• ff5adae Improves recovery of labels for pregenerated post-comps
• 4d5f04c Adds Resnik (MICA) similarity
• 73b2857 Improves term frequency calculation for taxon annotations
• 09d4a8b Improves success rate of auto-determining term type
• 330fc7d Adds ability to obtain or calculate term frequencies
• 35eae42 Adds function for auto-determining category of terms
• 291f183 Adds ability to retrieve taxa when creating phenotype obj

RPhenoscape release v0.2.14

Includes the following changes since the last release:

• 03931e0 Adds ability for charstates to accumulate over list
• 8645f28 Adds pretty-printing for phenotype objects
• 0b02473 Adds phenotype class and methods

RPhenoscape release v0.2.13

Changes since the last release include the following:

• badf246 Fixes install instructions for different versions of remotes
• 8730595 Fixes typo in get_phenotypes() description
• 76c00e9 Adds function to test which phenotypes are in studies
• 418ce51 Adds ability to query studies by phenotype ID
• 4e5f500 Adds custom set user-agent to request headers

RPhenoscape release v0.2.12

Changes since previous release include the following:

• 3d2de68 Fixes documentation
• 447650c Allows controlling ontotrace behavior if names fail to resolve
• 4f0c355 Adapts obtaining term labels to recent change in KB API
• 466773a Switch to POST also for JSON-returning queries when query is long

RPhenoscape release v0.2.11

Changes since previous release include the following:

• dd3f0e4 Fixes get_phenotypes failure if called from apply() and friends
• a051002 Initial KB annotation summary and metadata retrieval method get_KBinfo()

RPhenoscape release v0.2.10

Changes since the previous version include the following:

• 3698827 Adds check for content-length header
• b4d1a2a Adds ability to request (phenotype,taxon) tuples (#105)

RPhenoscape release v0.2.9

Changes since previous version include the following:

• a784fd1 Vectorizes pk_taxon_detail and pk_is_extinct (#103)
• bdfaf05 Handles API endpoints returning zero content if no match
• d422947 Adds documentation for internal get_XXX_data functions
• a90b30d Allows ensuring certain names are present in the result

RPhenoscape v0.2.8

Changes since previous version include the following:

• e7c690c DESCRIPTION more accurate and comprehensive
• f3e9c57 Adds function for adding provenance records to nexml object
• 9545c2b Adds the ability to drop OTUs and characters from nexml
• 8e08d4f Fixes various small documentation formatting issues