NEWS.md

In hubUtils: Core 'hubverse' Utilities

hubUtils 0.1.7

• First submission to CRAN
• Removed hubData dependency

hubUtils 0.1.2

• Bug fix: Corrected bug in v3 config utilities so that configs are detected as v3 if they are v3.0.0 or above, not just v3.0.0. Thanks to @M-7th for reporting.

hubUtils 0.1.1

• Remove hubAdmin Suggests dependency by moving test hub configuration validation to CI (resolved: @annakrystalli, https://github.com/hubverse-org/hubUtils/issues/158)

hubUtils 0.1.0

• Add read_config_file() helper function to read a JSON config file from a file path.
• Add extract_schema_version() helper function to extract the schema version from a schema id or config schema_version property character string.
• Add helpers is_v3_config, is_v3_config_file and is_v3_config_hub to check whether a config object, file or hub is using schema version 3.

hubUtils 0.0.2

• Missing dependency (jsonlite) bug fix.

hubUtils 0.0.1 MAJOR RELEASE

• First major release of hubUtils package containing significant breaking changes. Much of the package has been moved and split across two smaller and more dedicated packages:
• hubData package: contains functions for connecting to and interacting with hub data.
  • Exported functions moved to hubData: connect_hub(), connect_model_output(), expand_model_out_val_grid(), create_model_out_submit_tmpl(), coerce_to_character(), coerce_to_hub_schema() and create_hub_schema().
  • hubUtils functions re-exported to hubData: as_model_out_tbl(), validate_model_out_tbl(), model_id_split() and model_id_merge().
• hubAdmin package: contains functions for administering Hubs, in particular creating and validating hub configuration files. Exported functions moved to hubAdmin:
  • Functions for creating config files: create_config(), create_model_task(), create_model_tasks(), create_output_type(), create_output_type_cdf(), create_output_type_mean(), create_output_type_median(), create_output_type_pmf(), create_output_type_quantile(), create_output_type_sample(), create_round(), create_rounds(), create_target_metadata(), create_target_metadata_item(), create_task_id(), create_task_ids().
  • Functions for validating config files: validate_config(),validate_model_metadata_schema(), validate_hub_config(), view_config_val_errors().

hubUtils 0.0.0.9019

• Minor internal bug fixes and documentation updates.

hubUtils 0.0.0.9018

• Added US and European location datasets. These can be used e.g. when assigning location task ID values for tasks.json config files programmatically (#127).

hubUtils 0.0.0.9017

• connect_hub() and connect_model_output() now identify and report on files that are present and should have been opened but for which a connection was not successful (#124)
• Introduced a number of minor documentation clarifications and bug fixes (#129, #128, #121, #130)

hubUtils 0.0.0.9016

• Added validate_model_metadata_schema() function and included it as part of validate_hub_config() (#110 & #112).

hubUtils 0.0.0.9015

• Added load_model_metadata() function to compile hub model metadata.

hubUtils 0.0.0.9014

• Added coerce_to_character() function for coercing all model output columns to character. This can be much faster than coercing to coerce_to_hub_schema(), especially for dates.
• Added the following parameters to expand_model_out_val_grid():
• all_character: allow for returning all character columns.
• as_arrow_table: allow for returning an arrow data table.
• bind_model_tasks: allow for returning list of model task level grids.
• Bug fix. Handle situation in expand_model_out_val_grid() when required_vals_only = TRUE yet required task ID columns are not consistent across modeling tasks. The function now pads missing task ID column values with NAs.

hubUtils 0.0.0.9013

• Introduced coerce_to_hub_schema() function and applied it to create_model_out_submit_tmpl() & expand_model_out_val_grid() to ensure column data types in returned tibbles are consistent with the hub's schema (#100).
• Fixed bug where optional mean/median output types where being included erroneously when required_vals_only = TRUE.
• Exported function get_round_task_id_names() (#99).
• Memoized function read_config() (#101).

hubUtils 0.0.0.9012

• Fixed bug (#95 & #97) which was causing connect_hub() to error when "csv" was an accepted hub file format but there were no CSV in the model output directory. Now connect_hub() checks for the presence of files of each accepted file format and only opens datasets for file formats of which files exists. If there are no files of any accepted file_format in the model output directory, the S3 hub_connection object returned consists of an empty list.
• Fixed bug (#96) which was required hubUtils to be loaded for std_colnames to be internally available.

hubUtils 0.0.0.9011

• Changed default behavior of create_model_out_submit_tmpl(). Function now, by default, returns rows of complete cases only and the behavior is controlled by argument complete_cases_only. Argument remove_empty_cols was also removed.

hubUtils 0.0.0.9010

• Support for Hubs using schema earlier than v2.0.0 deprecated. Currently a warning is issued when interacting with such Hubs. Support will eventually be retired completely and errors will be produced with Hubs using older config schema.
• Added create_model_out_submit_tmpl() for generating round specific model output template tibbles (#82).
• Added lower level utilities:
  • expand_model_out_val_grid() for creating an expanded grid of valid task ID and output type ID across round modeling tasks and output types.
  • get_round_idx(): for getting an integer index of the element in config_tasks$rounds that a character round identifier maps to.
  • get_round_ids(): for getting a list or character vector of Hub round IDs.
• Added additional tasks.json validation checks via validate_config():
  • Check that all task_id and output_type_id values are unique across required and optional properties.
  • In rounds where round_id_from_variable is TRUE, check that the specification of the task_id set as round_id is consistent across modeling tasks.
  • Check that round_id values are unique across rounds.
• Exported object std_colnames which contains standard column names used in hubverse model output data files, for use in other hubverse packages (#88).

hubUtils 0.0.0.9009

• Added as_model_out_tbl() function to standardize model output data by converting to a model_out_tbl S3 class object. (#32, #33, #63, #64, #66)
• To support back-compatibility with model output data in older hubs, added functions model_id_merge() and model_id_split() to create model_id column from separate team_abbr and model_abbr columns and vice versa (#63).

hubUtils 0.0.0.9008

• Added argument output_type_id_datatype to connect_hub() to allow overriding default behavior of automatically detecting the output_type_id column data type from the tasks.json config file (#70).
• Exposed create_hub_schema() argument partitions to connect_hub() function to accommodate custom hub partitioning.
• Added argument partition_names to connect_model_output() to accommodate custom hub partitioning.
• Added argument schema to connect_model_output() to allow for overriding default arrow schema auto-detection.
• Moved jsonvalidate package to Imports so Hub administrator functionality accessible through standard installation.
• Removed argument format from create_hub_schema() which now creates the same schema from a tasks.json config file, regardless of the data file format (#80).

hubUtils 0.0.0.9007

• New function validate_hub_config() allows maintainers to check the validity of hub config files in a single call. Function view_config_val_errors() also modified to create combined report for hub config files from output of validate_hub_config().
• Breaking change: All model-output data are expected to have output_type & output_type_id instead of type & type_id respectively.

hubUtils 0.0.0.9006

• connect_hub() now automatically determines the output_type_id column data type from the tasks.json config file coercing to the highest possible data type, "character" being the lowest denominator.
• Introduced function create_hub_schema() for determining the schema for data in a hub's model-output directory from a tasks.json config file.
• connect_hub() now allows establishing connections to hubs with multiple file type formats.
• create_output_type_categorical() function was renamed to create_output_type_pmf().
• When extracting data via a hub connection, the column containing model identification information, inferred from model-output data directory partitions, was renamed from "model" to "model_id".

hubUtils 0.0.0.9005

• Re-implemented connect_hub() function to open connection to model-output data implemented through an arrow FileSystemDataset object. This allows users to create custom dplyr queries to access model output data.

hubUtils 0.0.0.9004

• Added functionality to help create JSON configuration files.

hubUtils 0.0.0.9003

• Added validate_config() function to validate JSON configuration files against Hub schema as well as function view_config_val_errors() for viewing a concise and easier to navigate table of validation errors.
• Added a NEWS.md file to track changes to the package.

hubUtils documentation built on Sept. 18, 2024, 5:09 p.m.