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Releases: insightsengineering/teal.modules.clinical

v0.13.0

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@insights-engineering-bot insights-engineering-bot released this 03 Jul 13:00
af00f07

Enhancements

  • Added numeric_formats argument to tm_t_summary to customize formatting of numeric statistics.

Bug fixes

  • Fixed tm_g_pp_therapy displaying column names instead of values in the start and end day columns of the therapy table (#1450).

Miscellaneous

  • Multiple decorators can be applied to the same output object (#1465).

What's Changed

New Contributors

Full Changelog: v0.12.0...v0.13.0

v0.13-0-rc1

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@insights-engineering-bot insights-engineering-bot released this 30 Jun 15:32
f590fdd

Enhancements

  • Added numeric_formats argument to tm_t_summary to customize formatting of numeric statistics.

Bug fixes

  • Fixed tm_g_pp_therapy displaying column names instead of values in the start and end day columns of the therapy table (#1450).

Miscellaneous

  • Multiple decorators can be applied to the same output object (#1465).

What's Changed

  • Add copilot-setup-steps workflow by @m7pr in #1453
  • Fix copilot-setup-steps: replace reusable workflow with direct steps by @m7pr in #1454
  • bring back tests by @m7pr in #1441
  • Checking decorators when names don't match what is expected by @llrs-roche in #1458
  • Fix check decorators by @llrs-roche in #1460
  • Refactor on tm_t_abnormaliry: allow treatment flag with all/no values by @osenan in #1462
  • add new argument for numeric formatting in tm_t_summary by @donyunardi in #1464
  • Add new regexp to linter rules for object names by @osenan in #1463
  • Fix variable reference in tm_t_events_summary by @nissinbo in #1466
  • Adds categorical statisticis to summary_by by @averissimo in #1461
  • Fix split_choices for delayed data by @m7pr in #1469
  • Port changes from teal.modules.general that support multiple decorators by @averissimo in #1467
  • use the right variable names by @donyunardi in #1478

New Contributors

Full Changelog: v0.12.0...v0.13-0-rc1

v0.12.0

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@insights-engineering-bot insights-engineering-bot released this 13 Dec 03:11
fb2dbd4

Enhancements

  • Modules return a teal_report object that contains the data, code and report. All the reporter buttons were removed from the modules' UI in favor of the framework level reporter buttons (#1376).
  • Added xticks parameter to tm_g_km module to allow users to specify x-axis tick positions programmatically.
    When xticks is provided, the interactive input field is pre-populated with the specified values as a default.
    Users can then modify these values interactively, and their changes will take precedence over the default.
    When xticks is NULL (default), users can specify this interactively in the module.
  • Updated R version dependency from 4.0 to 4.4.0, as upstream dependency tern requires this.

Bug fixes

  • Modules tm_t_summary and tm_t_summary_by now display and hide missing values (#1437).

v0.12.0-rc1

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@github-actions github-actions released this 03 Dec 17:09
fcde0ec
Commit to trigger the GHA fixed

v0.11.1

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@insights-engineering-bot insights-engineering-bot released this 22 Aug 11:21
512da8b

Enhancements

  • Improved the layout and appearance of the app using bslib components.
  • Added argument conf_type to module tm_g_km to allow users to set a confidence interval type for median survival time estimation.
  • Added denom argument in tm_t_binary_outcome module.
  • Update withr dependency version.

Bug fixes

  • Fixed bug in tm_t_events to return sorted table (#1393).
  • Fixed "Add to Report" failures in tm_g_pp_adverse_events, tm_g_pp_therapy, tm_t_pp_basic_info, tm_t_pp_laboratory and tm_t_pp_prior_medication modules (#1404).

Breaking changes

  • Removed the table object decoration in tm_g_pp_adverse_events, tm_g_pp_therapy (#1404).
  • Deprecated the decorators argument in tm_t_pp_basic_info, tm_t_pp_laboratory and tm_t_pp_prior_medication (#1404).

What's Changed

  • Implement bslib and use Bootstrap 5 by @vedhav in #1359
  • Add the conf_type argument to tm_g_km() by @edelarua in #1361
  • Adds denom argument to tm_t_binary_outcome module by @averissimo in #1366
  • 1369 table should be the last object that is returned in tm_t_events by @m7pr in #1372
  • Final UI and bslib changes by @vedhav in #1370
  • Replace switchInput with input_switch by @vedhav in #1385
  • Remove dev_suppress by @gogonzo in #1387
  • Fix minimal versions for scheduled actions by @llrs-roche in #1389
  • Adding new module using summarize_glm_count by @llrs-roche in #1386
  • chore: bump teal.logger dependency to 0.4.0 and remove from Remotes by @m7pr in #1395
  • fix sorting in tm_t_events by @kumamiao in #1394
  • Use the the new add button for adding a card by @vedhav in #1400
  • Final UI/UX changes by @vedhav in #1405
  • Bump version of shiny to support bslib and align with teal's min shiny version by @vedhav in #1410
  • Update modules' code for reproducibility by @llrs-roche in #1399
  • Fixes failing "Add to Report" for modules that have DT table visualization by @averissimo in #1411
  • Update lifecycle badges by @m7pr in #1412
  • chore: bump teal.code dependency to 0.7.0 and remove from Remotes by @m7pr in #1413
  • chore: bump teal.reporter dependency to 0.5.0 and remove from Remotes by @m7pr in #1414
  • [skip vbump] upversion v0.11.0 by @donyunardi in #1415

New Contributors

Full Changelog: v0.10.0...v0.11.1

v0.10.0

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@insights-engineering-bot insights-engineering-bot released this 28 Feb 15:56
1acaa2f

Enhancements

  • Added teal.logger functionality for logging changes in shiny inputs in all modules.
  • Introduced ylim parameter for tm_g_km module that controls width of y-axis.
  • Added functionality to tm_t_events_patyear to split columns by multiple (nested) variables via the arm_var argument.
  • Added arguments arm_var_labels to template_summary and show_arm_var_labels to tm_t_summary to allow user to display arm variable (arm_var) labels in table header.
  • Added argument stats to modules tm_g_forest_rsp and tm_g_forest_tte to allow users to specify statistics to include in the table.
  • Added argument riskdiff to modules tm_g_forest_rsp and tm_g_forest_tte to allow users to add a risk difference table column.
  • Added the count_dth and count_wd parameters to tm_t_events_summary to select/deselect the "Total number of deaths" and "Total number of patients withdrawn from study due to an AE" rows, respectively. These options correspond to the "Count deaths" and "Count withdrawals due to AE" checkboxes available when the module is run.
  • Added the title_text argument to tm_t_mult_events to allow for more customization of the module's dynamic title.
  • Introduced transformators and decorators argument to modules.

Bug fixes

  • Fixed bug in creating modules with delayed_data and teal.transform::all_choices.
  • Fixed bug in tm_g_forest_tte and tm_g_forest_rsp to resolve delayed data loading variables.

Miscellaneous

  • Removed Show Warnings modals from modules.
  • Clarified the documentation specifying whether multiple values can be selected in the arm_var argument for each module.
  • Replaced use of the rtables::add_colcounts() function with the show_colcounts argument to basic_table().
  • Began deprecation cycle for the show_labels argument of template_summary which has no effect on the tm_t_summary module.
  • Replaced instances of deprecated strata argument to tern::control_lineplot_vars() with group_var.
  • Added an assertion to tm_t_events_summary() to check whether all datasets used have the same treatment variable levels.

What's Changed

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v0.10.0-rc1

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@github-actions github-actions released this 28 Feb 15:10
Remove platforms that cause dependency installation to get stuck.

v0.9.1 cran

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@insights-engineering-bot insights-engineering-bot released this 27 Apr 23:51
73902e4

Enhancements

  • Updated tm_g_forest_rsp and tm_g_forest_tte to use refactored version of g_forest. Plots are now displayed as ggplot objects instead of grob objects. Added parameters font_size and rel_width_forest to control font size and width of plot relative to table, respectively.
  • Updated tm_t_summary_by to allow NULL input to paramcd argument.
  • Updated tm_g_km to use refactored version of g_km. Plots are now displayed as ggplot objects instead of grob objects. Added parameters rel_height_plot, font_size, control_annot_surv_med, and control_annot_coxph to control height of plot relative to table, font size, median survival time table size, and Cox-PH table size, respectively.
  • Added the control argument to tm_t_binary_outcome to control settings for the analysis (methods, confidence intervals, and odds ratios) within the module.

Miscellaneous

  • Replaced instances of deprecated na_level argument to tern functions with na_str.
  • Replaced argument/list element name strata instead of strat in all tern function calls following the deprecation of this argument/name within tern.
  • Removed formatters from dependencies and replaced the use of its functions relating to variable labels with functions from teal.data.

What's Changed

Full Changelog: v0.9.0...v0.9.1

v0.9.0 cran

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@insights-engineering-bot insights-engineering-bot released this 26 Feb 01:36
c2db189

Breaking Changes

  • Adapted all modules to use teal_data objects.
  • Module arguments that previously accepted inputs from teal.transform::choices_selected() or teal.transform::data_extract_spec() now only accept input from teal.transform::choices_selected(). The affected modules are: tm_a_gee, tm_a_mmrm, tm_g_ci, tm_g_forest_rsp, tm_g_forest_tte, tm_g_ipp, tm_g_km, tm_g_lineplot, tm_g_pp_adverse_events, tm_g_pp_patient_timeline, tm_g_pp_therapy, tm_g_pp_vitals, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_ancova, tm_t_binary_outcome, tm_t_coxreg, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_logistic, tm_t_mult_events, tm_t_pp_basic_info, tm_t_pp_laboratory, tm_t_pp_medical_history, tm_t_pp_prior_medication, tm_t_shift_by_arm, tm_t_shift_by_arm_by_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, and tm_t_tte

Enhancements

  • Updated the documentation and vignettes to demonstrate method to pass teal_data object to teal::init().
  • Added parameter sort_freq_col to tm_t_events to allow the user to select column to use when sorting by decreasing frequency.
  • Added parameter incl_overall_sum to tm_t_events to allow the user to choose whether overall summary rows are included at the top of the table.
  • Updated the documentation and vignettes to demonstrate method to pass teal_data object to teal::init().
  • Added default_total_label and set_default_total_label functions to get and set default total column label (total_label) for modules.
  • Implemented tern::default_na_str and tern::set_default_na_str functions to get and set default missing value replacement string (na_level) for modules.

Bug fixes

  • Fixed bug in tm_g_lineplot forcing module to initialize with a table.

Miscellaneous

  • Deprecated the aval argument in tm_t_pp_laboratory and tm_g_pp_vitals and replaced it with the aval_var argument.
  • Deprecated the avalu argument in tm_t_pp_laboratory and replaced it with the avalu_var argument.
  • Deprecated the base_var argument in tm_g_ipp, tm_t_shift_by_arm, and template_shift_by_arm_by_worst and replaced it with the baseline_var argument.
  • Specified minimal version of package dependencies.
  • Replaced usage of deprecated summarize_vars function with analyze_vars.
  • Reduced package dependencies (removed tidyr, rlang, magrittr and styler).

What's Changed

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v0.8.16

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@insights-engineering-bot insights-engineering-bot released this 14 Aug 14:36
1fd76e0

Enhancements

  • Added more informative error message when grade mapping error occurs in tm_t_abnormality_by_worst_grade.
  • Fixed label indentation in tm_t_abnormality_by_worst_grade.
  • Added total_label argument to enable customization of the "All Patients" column/row label in the following modules: tm_a_mmrm, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_binary_outcome, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_mult_events, tm_t_shift_by_arm, tm_t_shift_by_arm_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, and tm_t_tte.
  • Increased default width of tm_g_forest_tte plot to prevent overlapping text.
  • Improve default annotation table sizing in tm_g_km.

Miscellaneous

  • Updated control_incidence_rate parameter names in tm_t_events_patyear from time_unit_input and time_unit_output to input_time_unit and num_pt_year, respectively, after parameter names were changed in tern.

What's Changed

New Contributors

Full Changelog: v0.8.14...v0.8.16