R Library Release Notes

R Library Release Notes#

Version 2.0.0: June 5, 2026#

Deprecation and Removal:

  • Completely removed read_alignment, write_alignment, and AlignmentSchema. Removed “Alignment” from the valid definitions list and AIRRSchema.

Tabular Data and Parsing:

  • Updated read_tabular to initially treat logical columns as character data to prevent silent NA conversions during parsing, then explicitly casting valid logical character values.

  • Updated validate_tabular to support character strings representing logical values (e.g., “TRUE”, “T”, “False”, “F”) when validating logical fields.

Validation:

  • Enhanced validate_entry to support comprehensive validation of arrays without reference schemas, including item type checking (string, integer, number, boolean) and enum constraints.

  • Added rigorous type and enum validation for individual fields within validate_entry, providing explicit warnings for unrecognized types.

  • Added an ontology validation check in validate_entry to ensure that an ontology field is structured as a list before performing recursive validation.

Data Model and Schema:

  • Updated AIRRSchema to replace the Acknowledgement schema with the new Contributor schema.

  • Added a safety check in extract_field_content to handle fields with null properties safely.

Version 1.6.1: February 12, 2026#

  • Sync version with release of python airr package.

Version 1.6.0: July 7, 2025#

  • Updated schema set.

Version 1.5.0: August 29, 2023#

  • Updated schema set and examples to v1.5.

Version 1.4.1: August 27, 2022#

Significant internal refactoring to improve schema generalizability, harmonize behavior between the python and R libraries, and prepare for AIRR Standards v2.0.

Rearrangement:

  • Added the aux_types argument to read_tabular, read_rearrangement, and read_alignment to allow explicit declaration of the type for fields that are not defined in the schema.

  • Renamed read_airr, write_airr, and validate_airr to read_tabular, validate_tabular, and validate_tabular, respectively.

Data Model and Schema:

  • Defined new read_airr, write_airr, and validate_airr functions that support AIRR Data Model files that store arrays of objects in JSON or YAML.

  • Added support for the AIRR Model Data File and associated schema (DataFile, Info). The Data File data format holds AIRR object of multiple types and is backwards compatible with Repertoire metadata.

  • Added support for the new germline and genotyping schema (GermlineSet, GenotypeSet) and associated schema.

Version 1.3.0: May 26, 2020#

  • Updated schema set to v1.3.

  • Added info slot to Schema object containing general schema information.

Version 1.2.0: August 17, 2018#

  • Updated schema set to v1.2.

  • Changed defaults to base="1" for read and write functions.

  • Updated example TSV file with coordinate changes, addition of germline_alignment data and simplification of sequence_id values.

Version 1.1.0: May 1, 2018#

Initial release.