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monarchr 1.5.1

Bug fixes

  • Improved the URL try order for the Monarch Neo4j API.

monarchr 1.5.0

New features

  • Exporting to cytoscape() for visualization.
  • Added caching for neo4j_engine queries (enabled by default, length of R session only)

Bug fixes

  • Fixed a method signature inconsistency for summary().

monarchr 1.4.0

New features

  • example_graph() function for engines
  • Engine summary() now returns named lists of available node categories and edge predicates for convenient auto-completion

monarchr 1.3.0

New features

  • summary() function for engines

Bugfixs

  • fix backend bug in Neo4j table queries not handling default params properly
  • add batch queries for Neo4j backend engine
  • added summary() for KG engines to summarize total node and edge count information

monarchr 1.2.2

Bugfixs

  • Add fallback URLs for monarch_engine()

monarchr 1.2.1

New features

  • New save_kgx() and load_kgx() for saving/loading graphs.

Bugfixes

  • Reduced size of package with smaller example data
  • Fixed a bug in expand() where the engine was not carried through for file-engine backed graphs
  • Unit tests dependent on live-hosted Monarch KG now allow for minor changes in result counts

monarchr 1.1.0

New features

  • New kg_join() function

Bug fixes

  • Fix expand() to include new edges when multiple nodes with the same id are part of the query.

1.0.1: Fix missing self loops in plot

monarchr 1.0.0

1.0.0 is a major update to monarchr functionality and APIs.

  • Engines
    • monarchr now supports the Monarch cloud-hosted KG, other Neo4j-hosted KGs, and file-based KG access from kghub.org
    • Queries to hosted databases are now paged for efficiency
  • API updates and new features
    • fetch_edges() is now expand()
    • fetch_nodes() now supports bulk fetching by provided ID list or node properties
    • limit parameter added to expand() and fetch_nodes() for exploratory queries
    • monarch_semsim() provides semantic-similarity matching via the Monarch cloud-hosted API
    • Basic plot() added based on ggraph
    • Improved display of graphs as node and edge tables in R markdown docs

monarchr 0.2.2

New features

  • README:
    • Create to README.Rmd to enable autofilling.
    • Add badges
    • Add link to docs site
  • DESCRIPTION:
    • Add URL/BugReports fields
  • vignettes
    • Change Basics.Rmd --> monarchr.Rmd to match conventions.
    • Name chunks in vignette
    • Add session info to end of vignette

monarchr 0.2.1

  • Add rworkflows GHA for automated checking, site building, and Docker container creation.
  • Update .Rbuildignore.
  • Add NEWS file.
  • Add Title, Description, and Authors to DESCRIPTION.
    • Hope you don't mind me adding our names here @oneilsh, I anticipate making lots of contributions!
  • Add tidyr Import to DESCRIPTION.
  • Add vignettes header info.
  • Fix edges docs by adding title.
  • Add VignetteBuilder: knitr to DESCRIPTION.
  • Fix cypher_query example by adding ids
  • Fix cypher_query_df example by adding ids
  • Export cypher_query_df
  • Get monarchR closer to passing rcmdcheck (methods for edges/nodes not yet being recognized)