Changelog

Source: NEWS.md

teal.osprey 0.1.16.9028

• Removed Show Warnings modals from modules.
• Moved teal.data from Suggests to Imports.
• Changed examples from cdisc_data() to teal_data().

Breaking Changes

• Adapted all modules to use teal_data objects.

Enhancements

• Added teal.logger functionality for logging changes in shiny inputs in all modules.

Miscellaneous

• Specified minimal version of package dependencies.

teal.osprey 0.1.16

• Removed scda package dependency from examples.
• Fixed crash in tm_g_heat_bygrade when not plotting Conmed.
• Added validation to tm_g_spiderplot.R that checks if there are duplicates in X and Y facet variables.
• Improved input validation and used the teal::validate_inputs mechanism to send validation messages to the output panel.
• Removed purrr from dependencies.
• Added argument checks to tm_g_patient_profile.
• Modified example apps to use new teal_data and join_keys solutions.

Breaking changes

• Replaced chunks with simpler qenv class.
• In all tm_xyz_srv modules datasets argument containing FilteredData have been replaced with the new argument data (tdata object) and filter_panel_api (FilterPanelAPI).
• Updated arm_var to point to the factor column in ANL. It can’t be a character column anymore.
• Removed redundant formal arguments from tm_g_patient_profile.

teal.osprey 0.1.15

Breaking changes

• Soft deprecate function label_aevar().

Enhancements

• Added teal.reporter to all modules.
• Updated shiny::validate calls to shinyvalidate for better UI overview.
• Implemented nestcolor with slight refactoring to tm_g_swimlane. Added nestcolor in examples.

Miscellaneous

• Added names to the id parameter of teal.code::chunks_push in all modules.
• Updated modules to not use datasets with names with suffix _FILTERED so the package works with the breaking changes in teal.slice.

teal.osprey 0.1.14

Enhancements

• Removed unneeded chunk evaluations in tm_g_patient_profile module.

Miscellaneous

• Added a template to the pkgdown site.
• Updated package authors.

teal.osprey 0.1.13

Enhancements

• Added basic logging to the modules.
• The label of the select input widget to choose the paramcd is no longer hard coded to ADTR in tm_g_spiderplot.

Miscellaneous

• Rewrote module to use moduleServer and updated calls to teal.devel modules which have also been written to use moduleServer.
• Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
• Adjusted package imports to take into account changes to the teal framework.
• Functions from imported packages are now fully specified.

teal.osprey 0.1.12

Breaking changes

• Refactored tm_g_ae_oview to remove the flag variables generated by the module by default and to replace parameter add_flag with flag_var_anl.

Enhancements

• Added the new parameter x_label allowing to change the label of the x axis on the tm_g_swimlane module plot.
• Updated tm_g_ae_sub so that it no longer displays label inputs for group variables with no values selected.

Bug fixes

• Fixed a bug in tm_g_waterfall so that the Tumor Burden Parameter UI element is now respected.

Miscellaneous

• Updated R version requirement to R >= 3.6.
• Removed the function teal::keys in the examples of tm_g_spiderplot and tm_g_waterfall modules.
• Removed dependency on test.nest package.
• Removed dependency on utils.nest package and replaced its functions with equivalents from the checkmate package.

teal.osprey 0.1.11

• Updated LICENCE and README with new package references.
• Updated document and tests with scda synthetic data to replace random.cdisc.data.
• Added error_on_lint: TRUE to .lintr.
• Removed unnecessary importFrom statements.
• Updated tm_g_patient_profile module’s study days range to not accept infinite values.
• Fixed disappearing plots when webpage is zoom in/out.

teal.osprey 0.1.10

Enhancements

• Added a Shiny feature to tm_g_swimlane that will prevent needless re-render of the output when the user has not completely provided inputs to the vertical lines widget.

Miscellaneous

• Altered the Choose Up To 2: inputs widget from the Encoding Panel to be independent of the Filtering Panel in tm_g_butterfly.
• Updated warning message when Tumor Burden Parameter is not selected in tm_g_waterfall.

Bug fixes

• Fixed a bug in tm_g_butterfly that displays the filtering and faceting widgets despite not being provided in the arguments.

teal.osprey 0.1.9

New features

• Added new teal module tm_g_heat_bygrade for a heatmap by grade plot.
• Added new teal module tm_g_ae_sub for an AE by subgroups plot.

Bug fixes

• Fixed misleading validate message in tm_g_ae_oview when either Control or Treatment variable is filtered out.
• Added a validate statement to output a better error message when both the left and right dichotomization values are filtered out of data.

Miscellaneous

• Improved reactivity dependencies across modules.

teal.osprey 0.1.8

• Added validation message if the dataset does not contain subjects from both the control and treatment arms in tm_g_events_term_id.
• Improved validation message if subject has been filtered out of dataset when used with tm_g_patient_profile.
• Fixed modules due to changes to plot_with_settings in latest teal.devel release.
• Updated study day and duration derivation in tm_g_patient_profile.

teal.osprey 0.1.7

Enhancements

• Added additional validation for horizontal and vertical reference lines in tm_g_spider_plot.

Bug Fixes

• Fixed tm_g_patient_profile when adverse event line color variable is not selected.
• Fixed the issue of unknown date format and established minimum number of observation threshold in tm_g_patient_profile.

Miscellaneous

• Retired the following teal modules due to duplication in teal.modules.clinical:
  • Teal module for AE overview summary table - can be replaced with teal.modules.clinical::tm_t_events_summary.
  • Teal module for AE summary table by preferred terms - can be replaced with teal.modules.clinical::tm_t_events.
  • Teal module for AE summary table by highest NCI-CTCAE grade - can be replaced with teal.modules.clinical::tm_t_events_by_grade.
  • Teal module for Disposition table - can be replaced with teal.modules.clinical::tm_t_summary.
• Moved code argument to cdisc_dataset (from cdisc_data) in examples.

teal.osprey 0.1.6

• All graph modules now accept a plot_width argument which specifies the plot width and renders a slider to adjust the width interactively in the module.
• Replaced plot_with_height with plot_with_settings module throughout package.
• Show R Code now produces code generating only the datasets needed for the current module, not all datasets included in the data argument of teal::init.
• Evaluate chunks with chunks_safe_eval rather than chunks_eval.

teal.osprey 0.1.5

• Added new teal modules:
• Teal module for events by term summary plot.
• Teal module for AE overview summary plot.
• Teal module for patient profile plot

teal.osprey 0.1.4

• Minor changes in tests.

teal.osprey 0.1.3

• Technical release with updated dependencies.

teal.osprey 0.1.2

• New waterfall module.
• Refactored due to recent changes in utils.nest.

teal.osprey 0.1.1

• Refactoring package according to the NEST standards:
  • Included test.nest tests.
  • Fixed outdated modules according to current teal functionality.
  • Fixed documentation examples and example_app.R.
  • Simplified dependencies.

teal.osprey 0.1.0

• First versioned release of teal.osprey package, which include the following seven new functions to create teal modules for analysis functions in osprey v0.1.0:
  • Teal module for AE overview summary table.
  • Teal module for AE summary table by preferred terms.
  • Teal module for AE summary table by highest NCI-CTCAE grade.
  • Teal module for Disposition table.
  • Teal module for AE butterfly plot.
  • Teal module for Swimlane plot.
  • Teal module for Spider plot.