teal

Breaking changes

• Changed the HTML identifiers of teal modules - now each nested module receives its own shiny namespace.
• Deprecated all functions related to connectors that have been moved to their own separate packages.
• Removed raw_dataset, raw_dataset_connector, named_dataset, named_dataset_file, named_dataset_connector, relational_dataset, relational_dataset_file, relational_dataset_connector, key, as_cdisc, as_cdisc_relational.
• Removed rcd_connection and rcd_data; scda_dataset_connectors can be passed into cdisc_data and teal_data directly.
• Replaced rcd_dataset_connector and rcd_cdisc_dataset_connector with scda_dataset_connector and scda_cdisc_dataset_connector respectively.
• Renamed teal_show_js_log option into teal.show_js_log to match options naming convention.
• Removed %is_in% and stop_shiny internal utility functions.

New features

Logging

• Added support for logging using the logger package.
• Added a new function register_logger, which registers a logger in a given namespace.
• Added trace and info levels log messages to the teal framework.
• Added pid and shiny session token into footnote so app developers can identify logs for apps.

Other

• Added print methods to the DatasetConnector, RelationalData, RelationalDataconnector and JoinKeys classes and added input validation to the implementation of the print method that was already in the Dataset object.

• Added public facing constructor functions for CDISCDataConnector, RelationalDataConnector, and DataConnection classes.

• Modified data_extract_spec to allow both the filter and select parameters to be NULL, which results in the data_extract_ui acting as if a filter_spec with all variables as possible choices had been supplied as the filter argument and a select_spec with the multiple parameter set to TRUE had been supplied as the select argument.

• Added support of the full screen for a module when the filters argument is equal NULL.

• Added support for shiny::moduleServer passed to the server parameter of teal::module.

• Added teal.threshold_slider_vs_checkboxgroup as an R option: if a categorical variable has more than this number of unique values, the filter panel uses a drop-down select input instead of a checkbox group.

• Extended the FilteredData API to allow managing filter states programmatically and not only from the UI of a teal application.

• Hid the buttons to remove filters from all datasets and each dataset when there are no active filters.

• Updated init to accept RelationalData, data.frame, MultiAssayExperiment, Dataset, DatasetConnector, list or a function returning a named list as data input.

Bug fixes

• choices_selected now correctly removes duplicates from the array passed to its choices parameter.
• Fixed call returned by FilterState in case of using MultiAssayExperiment::subsetByColData. Now single condition for variable containing NA values is !is.na(var) & var == <condition>.
• Fixed data loading of DatasetConnector being dependent on other Dataset or DatasetConnector objects.
• Fixed restoring a bookmarked filter state of teal application.
• Refactored module_nested_tabs to fix the issue with the filter panel not reacting to an input change in a nested module.
• updateOptionalSelectInput no longer sets input to NULL when logical value is passed to selected.
• Fixed setting JoinKeys when key name between two Dataset object differs.
• Fixed printing of the JavaScript console logs to the R console when teal.show_js_log = TRUE.

Miscellaneous

• Soft-deprecate mae_dataset() in favor of more general dataset() constructor.
• Added a vignette describing the modifications to teal applications users can apply using R options.
• Added default values to the label argument of select_spec and filter_spec.
• Added validation to FilteredDataset::get_data to accept logical input only.
• Changed references to outdated functions of teal.devel in the documentation.
• Introduced a Teal prefix to all public R6 classes to avoid name collisions with other packages.
• Removed dependency on utils.nest and replaced its functionality in teal with equivalents from the checkmate package and base R.
• Replaced the old shiny server functions of DataConnection, RelationalDataConnector, DatasetConnector, and RelationalData with the shiny::moduleServer equivalents.
• Running a teal application via ui_teal_with_splash and srv_teal_with_splash is now no longer recommended because it doesn't support new features (e.g. logging, bookmarking). Use init instead.
• Updated the R version requirement to >= 4.0.
• Updated the "filter panel collapse" icon to remove warnings when using shiny version >= 1.7.
• Removed some of the non-exported, debugging modules.
• Updated the footer tag style to be less visible.