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Recent Releases of teal.modules.clinical

teal.modules.clinical - v0.11.1

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

New Contributors

  • @kumamiao made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/1394

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.10.0...v0.11.1

- R
Published by insights-engineering-bot 6 months ago

teal.modules.clinical - v0.10.0

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

  • Workflow propagation by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/1102
  • 1175 fixing validation on col_by_var variable. by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/1178
  • 1149 introduce ylim parameter for tm_g_km module by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1177
  • 1108 {shinytest2} feature branch by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1126
  • 1176 remove Show Warnings from modules by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1180
  • 227 utilize logger::log_shiny_input_change by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1182
  • truetype font support checking PR by @gmbecker in https://github.com/insightsengineering/teal.modules.clinical/pull/1188
  • Bumps {rmarkdown} minimal version by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1186
  • increase rtables dep version by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1195
  • testing for rtables higher level ns PR by @gmbecker in https://github.com/insightsengineering/teal.modules.clinical/pull/1190
  • 553 change level in log_shiny_input_changes and exclude plot sizes in logging by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1191
  • Update DESCRIPTION by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1196
  • Fix documentation of arm_var argument in modules by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1201
  • Add functionality to tm_t_events_patyear to split columns by multiple (nested) variables by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1203
  • Replace use of add_colcounts with the show_colcounts argument by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1207
  • Add option to tm_t_summary to include arm_var labels in table header by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1205
  • Workflow propagations by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/1208
  • Add stats and risk difference parameters to forest plot modules by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1210
  • Fix teal namespace for broken tests by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1213
  • Add options to toggle the "Total deaths" and "Total withdrawals due to AE" rows in tm_t_events_summary by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1216
  • Update DESCRIPTION by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1217
  • Use group_var argument to control_lineplot_vars instead of deprecated strata by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1223
  • update readme by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1218
  • fix: changed the separator in hconcatexpr by @kpagacz in https://github.com/insightsengineering/teal.modules.clinical/pull/1226
  • Workflow propagations by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/1219
  • Update DESCRIPTION tern to 0.9.6 by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1227
  • reset factor level during validate by @donyunardi in https://github.com/insightsengineering/teal.modules.clinical/pull/1229
  • Update scheduled.yaml by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1220
  • use of roxy.shinylive by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1230
  • add rmarkdown to VignetteBuilder by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1237
  • Adds roxy.shinylive to pre-commit configuration by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1238
  • teal.data::datanames() is deprecated in favor of dot-prefix and names() by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1239
  • 1248 Fix shinytest2 tests by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1251
  • Update tm_t_summary_by() column variable text by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1247
  • upversion teal.report, rtables, rtables.officer by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1250
  • update strata var to group_var by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1246
  • Bring back tests for tm_g_pp_therapy by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1271
  • fixes error in adverse events when ASTDY is of difftime type by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1284
  • Fix tmc integration test - Wait for shiny app idle after fit is clicked by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1296
  • add setup-r-dependencies by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1297
  • Fix documentation note about links on r-devel by @llrs-roche in https://github.com/insightsengineering/teal.modules.clinical/pull/1299
  • Stop R process if AppDriver fails in test-examples by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1303
  • 🗃️ Decorators feature branch by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1252
  • 1305 allow delayed data to pass in cs_to_des_select by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/1306
  • upversion dep by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1308
  • Fix logger by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/1312
  • Show only datasets used by @llrs-roche in https://github.com/insightsengineering/teal.modules.clinical/pull/1309
  • Update DESCRIPTION by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1315
  • update packages for the scheduled build by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1314
  • 1441 Introduce transformators parameter in modules by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1313
  • vbump teal.logger by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1319
  • add Remotes to DESCRIPTION by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1321
  • simplify builds dependencies of extra-deps by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1318
  • Update teal.reporter version by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1322
  • vbump teal.code by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1323
  • vbump teal.data by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1326
  • Make sure the code chunks does not break because of warnings by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1327
  • vbump teal.widgets by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1328
  • Duplicated decorators during an edge case of named and unnamed decorators by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1325
  • Add title_text argument to tm_t_mult_events() to control dynamic title by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1334
  • update tmgforest_tte by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1336
  • vbump teal.transform by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1341
  • Add treatment var levels assertion to tm_t_events_summary() by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1345
  • Update DESCRIPTION by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1346
  • Faster check times on CI by @llrs-roche in https://github.com/insightsengineering/teal.modules.clinical/pull/1347
  • Remove default decorator and update docs by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1348
  • Switch to DT::datatable decoration where applicable by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1350
  • fix: make sure the decoration is applied to the forest plots by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1351
  • vbump teal by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1352
  • Add vignettes on decorators by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1353
  • wrap within expr in {} to potentially cheat r cmd check by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/1355
  • Fix "no visible binding for global variable" by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/1354
  • [skip vbump] upversion v0.10.0 by @donyunardi in https://github.com/insightsengineering/teal.modules.clinical/pull/1356

New Contributors

  • @gmbecker made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/1188

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.9.1...v0.10.0

- R
Published by insights-engineering-bot 12 months ago

teal.modules.clinical -

- R
Published by github-actions[bot] 12 months ago

teal.modules.clinical - v0.9.1 cran

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

  • 1077 remove formatters by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/1079
  • Re-add g_forest updates by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/925
  • Allow NULL paramcd value in tm_t_summary_by by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1083
  • Replace instances of deprecated na_level with na_str by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1088
  • Update use of deprecated strat argument from tern by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1081
  • Strict tests by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/985
  • disable total column if not in parallel by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1087
  • Cleanup of # nolint comments by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1091
  • Update snapshots to fix tests by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1093
  • 52 standardise optional notation by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/1094
  • register teal.logger handlers; replace log_info with message by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1010
  • 445 unify html tags by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/1098
  • Update tm_g_km after g_km refactor by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1107
  • Update DESCRIPTION by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1109
  • Replace use of deprecated control_summarize_vars by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1115
  • Rename output IDE to prevent DOM conflicts by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1114
  • run examples using shinytest2 by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/983
  • error=T, purl=F in expected errors in vignettes by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1117
  • checking aligning to the latest versions by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1118
  • remove stop() in test-examples.R by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/1121
  • Update DESCRIPTION by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1123
  • Adds TealAppDriver and skip_if_too_deep for e2e testing by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/1124
  • Expose control argument in tm_t_binary_outcome by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1110
  • Wave 1 - tm_a_gee shinytests by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1127
  • Revert "Wave 1 - tm_a_gee shinytests (#1127)" by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1140
  • [skip vbump] preping for cran release by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1147

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.9.0...v0.9.1

- R
Published by insights-engineering-bot almost 2 years ago

teal.modules.clinical - v0.9.0

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

  • Workflow propagation by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/824
  • Use token in spelling workflow by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/825
  • Refactor tm_t_exposure to remove summary row by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/826
  • Patient Profile Modules only show relevant datanames by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/828
  • Solution for maintaining indent after pruning by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/791
  • Fix bug in tm_t_coxreg when no covariates selected by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/833
  • Fix tm_t_coxreg errors when applying filters by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/831
  • Display Patient ID in relevant templates, clean up data tables in reports by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/834
  • 198 Include user's card labels when generating the report by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/835
  • Add option to remove interval in tm_g_lineplot by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/840
  • chasing deprecations by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/852
  • Update docs to use the newteal_data instead of TealData by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/853
  • fix tm_g_pp_vitals by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/896
  • Update tern version by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/901
  • bump teal.reporter dep version by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/903
  • Fix bug forcing tm_g_lineplot to initialize with a table by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/899
  • Add options to tm_t_events for sorting and overall rows by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/851
  • Remove unused table_names argument from surv_timepoint by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/905
  • tdata to teal_data by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/855
  • fix resolve_delayed by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/909
  • Workflow propagation by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/908
  • 906 update dependency versions by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/907
  • 231 remove get_labels function by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/914
  • Update forest plots following refactor of g_forest by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/911
  • Two arm vars by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/916
  • Fix TMC to work with tern v0.9.3 by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/922
  • 430 use expect_no_error in tests instead of expect_error(, NA) by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/936
  • 919 update vignettes@main by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/927
  • Add default_total_label function by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/942
  • 918 update teal.modules.clinical.R with #' @keywords internal "_PACKAGE" by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/982
  • TMC bug fixes by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/926
  • Replace aval parameter with aval_var by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/939
  • Replace avalu parameter with avalu_var by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/940
  • Adds min package version by @averissimo in https://github.com/insightsengineering/teal.modules.clinical/pull/797
  • Replace base_var parameter with baseline_var by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/941
  • Implement default_na_str by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/984
  • Replace summarize_vars with analyze_vars by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/987
  • Clean up overall argument documentation by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/989
  • update deps of roxygenize hook by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/990
  • Minor improvements to README/vignettes by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/993
  • Clean up documentation for tm_t_shift_by_arm_by_worst by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/997
  • Clean up documentation for tm_t_shift_by_grade by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/998
  • Update DESCRIPTION teal.data (>= 0.4.0) by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1008
  • Consolidate argument_convention file by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1006
  • 618 reduce dependencies of the package by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/981
  • Clean up documentation for tm_t_binary_outcome by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/994
  • Clean up documentation for tm_t_summary_by by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1003
  • Clean up documentation for tm_t_summary by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1004
  • Clean up documentation for tm_t_pp_basic_info by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1024
  • Clean up documentation for tm_g_pp_adverse_events by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1026
  • Clean up documentation for tm_t_pp_prior_medication by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1023
  • Clean up documentation for tm_t_pp_medical_history by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1022
  • Clean up documentation for tm_g_forest_rsp by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1020
  • Clean up documentation for tm_g_pp_therapy by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1025
  • Clean up documentation for tm_t_events_summary by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1015
  • Clean up documentation for tm_t_mult_events by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1019
  • Clean up documentation for tm_t_tte by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1011
  • clean up documentation for tm_t_ancova by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1016
  • Clean up documentation for tm_t_smq by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1018
  • clean up documentation for tmtabnormalitybyworst_grade by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1029
  • clean up tmtabnormality documentation by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1027
  • Clean up documentation for tm_t_shift_by_arm by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1031
  • Clean up tm_g_km documentation by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1030
  • Clean up documentation for tm_t_events_patyear by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1032
  • Clean up documentation for tm_g_forest_tte by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1021
  • Clean up documentation for tm_g_lineplot by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/996
  • Clean up documentation for tm_t_coxreg by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/995
  • Clean up documentation for tm_g_barchart_simple by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1033
  • clean up documentation for tm_t_events_by_grade. by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1039
  • Clean up documentation for tm_t_logistic by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1007
  • Clean up documentation for tm_t_exposure() by @zdz2101 in https://github.com/insightsengineering/teal.modules.clinical/pull/1028
  • Clean up documentation for tm_g_ipp by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1034
  • 944 clean tm a gee@main by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1040
  • tm_t_events review by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/1002
  • Clean up documentation for tm_t_pp_laboratory by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1036
  • Clean up documentation for tm_g_pp_patient_timeline by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1038
  • Clean up documentation for tm_g_ci by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1035
  • Clean up documentation for tm_g_pp_vitals by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1037
  • clean up documentation for tm_a_mmrm by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/1041
  • using library([package]) and getFromNamespace(...) calls. by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/1048
  • 1012 substitute {assertthat} with {checkmate} in a couple of functions by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1046
  • Fix pkgdown redirect by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1049
  • Propagate files from insightsengineering/.github by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/1052
  • [skip actions] Propagate files from insightsengineering/.github by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/1053
  • Update DESCRIPTION teal 0.15.0 by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1054
  • Change r.pkg.template branch to main by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/1055
  • removing internal functions example. by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/1051
  • Append the teal.transform namespace to stay consistent by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1056
  • Check description and vignette by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/1045
  • 1057 fix tm_t_pp_laboratory reshape by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1060
  • Fix assertion on paramcd by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1067
  • Clarify tm_g_pp_patient_timeline error message by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1059
  • final prerelease activities by @donyunardi in https://github.com/insightsengineering/teal.modules.clinical/pull/1065
  • Update DESCRIPTION teal.transform >= 0.5.0 by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1069
  • 1071 prerelease cleanup@main by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/1072
  • Add missing return values by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/1075
  • [Docs] Update module arg docs to only accept choices_selected by @vedhav in https://github.com/insightsengineering/teal.modules.clinical/pull/1078
  • Cran release 0.9.0 [skip vbump] by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/1070

New Contributors

  • @zdz2101 made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/1028

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.8.16...v0.9.0

- R
Published by insights-engineering-bot about 2 years ago

teal.modules.clinical - v0.8.16

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

  • Update scda data by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/658
  • Use scda.2022 by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/663
  • Teal refactor by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/598
  • Enable checks for workflow_dispatch event by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/673
  • consistent reactives naming by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/671
  • Fix barchart behaviour by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/683
  • Update staged_dependencies.yaml, adding tern.gee by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/684
  • 423 Add interaction to tm_t_ancova by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/674
  • Update line to produce output. by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/692
  • add gee prototype module with example by @danielinteractive in https://github.com/insightsengineering/teal.modules.clinical/pull/664
  • 696 Add table titles to tm_a_gee report cards by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/697
  • Fix coxreg by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/700
  • Badges and contribution guidelines by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/702
  • tmggpp_vitals: remove param by @mhallal1 in https://github.com/insightsengineering/teal.modules.clinical/pull/713
  • tmc shinyvalidate by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/699
  • Updates tmammrm for new tern.mmrm/mmrm packages by @danielinteractive in https://github.com/insightsengineering/teal.modules.clinical/pull/714
  • remv adsl_key, use USUBJID by default by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/718
  • Check as-cran + default landing page by @arkadiuszbeer in https://github.com/insightsengineering/teal.modules.clinical/pull/719
  • fix faceting in tm_g_km by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/720
  • Update rtables staged dep by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/728
  • Create minimal test data for examples and initialize the substitution by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/721
  • Add TMC example data by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/731
  • Remove remaining scda usage, update to testthat v3.0 by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/732
  • Consistent lowercase dataset names in examples by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/736
  • Remove scda and scda.2022 from staged deps by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/734
  • adding two mo correlation struct, close #716 by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/737
  • Clean up example data modification by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/739
  • add teal.gallery to readme by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/740
  • Fix validate_standard_inputs example by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/743
  • fix barchart by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/744
  • fix svg by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/747
  • Add lubridate for ... date and time by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/749
  • Update AVALC distribution in tmc_ex_adrs by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/751
  • Updating GEE example with interaction term. by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/754
  • 724 improve plot by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/753
  • Workflow updates by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/752
  • Add label option for filtering/selection fields by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/759
  • Update tm_t_coxreg by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/756
  • Fixing tm_g_lineplot for droplevels strata and screening character by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/763
  • Update token name by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/765
  • Update tm_t_exposure to use analyze_patients_exposure_in_cols by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/767
  • Fix R CMD Check note by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/769
  • Remove mentions of STREAM from documentation by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/772
  • Fix numeric_stats bug in tm_t_summary and tm_t_summary_by by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/771
  • Prepare 0.8.15 release [skip vbump] by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/774
  • Update workflows by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/775
  • Improve tm_t_abnormality_by_worst_grade error message by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/778
  • Update control_incidence_rate param names in tm_t_events_patyear by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/785
  • Add option to customize the "All Patients" column label by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/783
  • reduce the amount of spelling issues / WORDLIST by @m7pr in https://github.com/insightsengineering/teal.modules.clinical/pull/782
  • Workflow propagations by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/786
  • Fix snapshot tests by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/789
  • Move TealReportCard to teal by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/793
  • empty by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/796
  • update by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/798
  • propagate argument name change in teal::module by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/801
  • Fix tm_a_mmrm report card text by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/809
  • Increase default width of tm_g_forest_tte plot by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/811
  • 804 deprecation notes in ggplot2 by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/810
  • 799 qenv prints plots to the device when running shiny app by @kartikeyakirar in https://github.com/insightsengineering/teal.modules.clinical/pull/813
  • Can't add reporter in patients timeline module by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/808
  • Improve default annotation table sizing in tm_g_km by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/812
  • 803 page length by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/814
  • update snapshot by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/818
  • update by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/820

New Contributors

  • @walkowif made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/673
  • @m7pr made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/782
  • @kartikeyakirar made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/813

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.8.14...v0.8.16

- R
Published by insights-engineering-bot over 2 years ago

teal.modules.clinical - v0.8.15

Breaking changes

  • Replaced chunks with simpler qenv class.
  • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI). ### Enhancements
  • Replaced synthetic_cdisc_data with refactored synthetic_cdisc_dataset function to speed up dataset loading in tests/examples.
  • Added new GEE module tm_a_gee.
  • Added interface for selecting an interaction term to tm_t_ancova.
  • Updated encoding input checks to use shinyvalidate::InputValidator for better UI experience. Previously used shiny::validate.
  • Added option to tm_a_mmrm to allow for Kenward-Roger adjustments of standard errors and p-values.
  • Added option to choose facet scale options in tm_g_barchart_simple.
  • Added label parameter to cs_to_select_spec/cs_to_des_select and cs_to_filter_spec/cs_to_des_filter to allow the user to customize the label printed over the selection field.
  • Updated tm_t_coxreg module after refactoring summarize_coxreg in tern to fix indentation.
  • Updated tm_t_exposure module to use new function analyze_patients_exposure_in_cols to fix table structure. ### Bug fixes
  • Fixed bug causing overlapping bars in tm_g_barchart_simple.
  • Fixed bug for figures in svg format.
  • Fixed bug in tm_t_summary and tm_t_summary_by preventing users from specifying the numeric_stats argument. ### Miscellaneous
  • Updated package Suggests to use scda.2022 rather than scda.2021.
  • Removed unused argument param from tm_g_pp_vitals.
  • Removed optimizer choice from tm_a_mmrm since we can always use the automatically determined optimizer.
  • Created datasets to use in examples/tests for adsl, adae, adaette, adcm, adeg, adex, adlb, admh, adqs, adrs, adtte, and advs. These datasets are stored in the data folder and accessible via the tmc_ex_* prefix.
  • Updated all examples and tests to use datasets from the teal.modules.clinical package instead of scda datasets.
  • Updated tests to use testthat 3rd edition and replaced all applicable tests with snapshot testing.
  • Implemented the lubridate package for date variables in internal data.
  • Changed default value of plot_width in tm_g_forest_rsp to prevent clutter.

What's Changed

  • Update scda data by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/658
  • Use scda.2022 by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/663
  • Teal refactor by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/598
  • Enable checks for workflow_dispatch event by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/673
  • consistent reactives naming by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/671
  • Fix barchart behaviour by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/683
  • Update staged_dependencies.yaml, adding tern.gee by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/684
  • 423 Add interaction to tm_t_ancova by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/674
  • Update line to produce output. by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/692
  • add gee prototype module with example by @danielinteractive in https://github.com/insightsengineering/teal.modules.clinical/pull/664
  • 696 Add table titles to tm_a_gee report cards by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/697
  • Fix coxreg by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/700
  • Badges and contribution guidelines by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/702
  • tmggpp_vitals: remove param by @mhallal1 in https://github.com/insightsengineering/teal.modules.clinical/pull/713
  • tmc shinyvalidate by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/699
  • Updates tmammrm for new tern.mmrm/mmrm packages by @danielinteractive in https://github.com/insightsengineering/teal.modules.clinical/pull/714
  • remv adsl_key, use USUBJID by default by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/718
  • Check as-cran + default landing page by @arkadiuszbeer in https://github.com/insightsengineering/teal.modules.clinical/pull/719
  • fix faceting in tm_g_km by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/720
  • Update rtables staged dep by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/728
  • Create minimal test data for examples and initialize the substitution by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/721
  • Add TMC example data by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/731
  • Remove remaining scda usage, update to testthat v3.0 by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/732
  • Consistent lowercase dataset names in examples by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/736
  • Remove scda and scda.2022 from staged deps by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/734
  • adding two mo correlation struct, close #716 by @shajoezhu in https://github.com/insightsengineering/teal.modules.clinical/pull/737
  • Clean up example data modification by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/739
  • add teal.gallery to readme by @pawelru in https://github.com/insightsengineering/teal.modules.clinical/pull/740
  • Fix validate_standard_inputs example by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/743
  • fix barchart by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/744
  • fix svg by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/747
  • Add lubridate for ... date and time by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/749
  • Update AVALC distribution in tmc_ex_adrs by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/751
  • Updating GEE example with interaction term. by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/754
  • 724 improve plot by @chlebowa in https://github.com/insightsengineering/teal.modules.clinical/pull/753
  • Workflow updates by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/752
  • Add label option for filtering/selection fields by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/759
  • Update tm_t_coxreg by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/756
  • Fixing tm_g_lineplot for droplevels strata and screening character by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/763
  • Update token name by @walkowif in https://github.com/insightsengineering/teal.modules.clinical/pull/765
  • Update tm_t_exposure to use analyze_patients_exposure_in_cols by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/767
  • Fix R CMD Check note by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/769
  • Remove mentions of STREAM from documentation by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/772
  • Fix numeric_stats bug in tm_t_summary and tm_t_summary_by by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/771

New Contributors

  • @walkowif made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/673

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.8.14...v0.8.15

- R
Published by github-actions[bot] over 2 years ago

teal.modules.clinical - v0.8.14

Enhancements

  • Updated all synthetic data for tests to version rcd_2022_02_28.
  • Reverted missing data checkbox in tm_t_summary (encoding and filtering should be separate).
  • Implemented a new widget that allows dragging and dropping to select comparison groups.
  • Added the teal.reporter functionality to all modules.
  • Enhanced the tm_t_pp_medical_history module to use the table_with_settings module and return an rtables object.
  • Implemented nestcolor in examples, refactored tm_g_barchart_simple to allow use of nestcolor.
  • Added more descriptive title/labels and visit name subtitle to tm_g_ci.
  • Updated tm_a_mmrm column name when deselecting treatment from "all obs" to "All Patients", added subtitles and footnotes.
  • Added a title and parameter category subtitle to tm_t_exposure, cleaned up labels.
  • Added titles and worse flag variable subtitles to tm_t_shift_by_grade and tm_t_shift_by_arm_by_worst.
  • Added a footnote to tm_t_events_patyear with CI method.
  • Added a subtitle and footnotes to tm_g_km.
  • Added Stratified Analysis CI method option panel to tm_t_binary_outcome.
  • Added validation for covariate/visit conflicts to tm_a_mmrm.
  • Remove unnecessary brackets from header in tm_t_exposure.
  • Hid footnotes in tm_g_km and tm_t_tte when "Compare Treatments" is off. ### Bug fixes
  • Fixed bug in tm_g_barchart_simple which prevented graph from showing.
  • Fixed broken example for tm_t_abnormality_by_worst_grade.
  • Fixed bug in tm_a_mmrm which prevented table headers from displaying.
  • Fixed bug in tm_g_forest_rsp when deselecting endpoint.
  • Fixed bug in tm_t_binary_outcome that crashed the app when deselecting all paramcd.
  • Fixed teal.reporter card names for tm_t_smq.
  • Fixed bug in tm_t_shift_by_arm_by_worst by adding validations for choosing different endpoint values.
  • Fixed bug in tm_t_coxreg preventing footnotes from displaying for univariate models. ### Miscellaneous
  • Added nestcolor dependency and replaced deprecated function tern::color_palette with nestcolor::color_palette.

What's Changed

  • fix news by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/507
  • Contribution guide updates by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/509
  • implement draggable widget for all modules by @denisovan31415 in https://github.com/insightsengineering/teal.modules.clinical/pull/485
  • 510 revert missing checkbox tm t summary@main by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/513
  • 514 empty string summarize logistic@main by @Melkiades in https://github.com/insightsengineering/teal.modules.clinical/pull/515
  • increase indent teal outputs by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/516
  • docs: replaced github links with the pkgdown links by @kpagacz in https://github.com/insightsengineering/teal.modules.clinical/pull/517
  • fix barchart by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/521
  • Fix barchart by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/524
  • init reporter tmc by @Polkas in https://github.com/insightsengineering/teal.modules.clinical/pull/518
  • fix tmgbarchart by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/529
  • DESC and README by @denisovan31415 in https://github.com/insightsengineering/teal.modules.clinical/pull/531
  • 527 Update to use nestcolor::color_palette by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/530
  • Update Rbuildignore and add auto-updates by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/532
  • slight refactoring for tern.mmrm by @danielinteractive in https://github.com/insightsengineering/teal.modules.clinical/pull/523
  • teal.reporter all modules by @Polkas in https://github.com/insightsengineering/teal.modules.clinical/pull/528
  • 511 Implement nestcolor in TMC by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/534
  • Update pre-commit config to detect _pkgdown.y[a]ml by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/535
  • remove _FILTERED by @gogonzo in https://github.com/insightsengineering/teal.modules.clinical/pull/536
  • reporter cleaning by @mhallal1 in https://github.com/insightsengineering/teal.modules.clinical/pull/537
  • Update documentation workflow by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/539
  • rm inline - css tmc by @Polkas in https://github.com/insightsengineering/teal.modules.clinical/pull/538
  • Updated all test files in tests/testthat/ ("20220228") by @ayogasekaram in https://github.com/insightsengineering/teal.modules.clinical/pull/549
  • 564 Add more descriptive title/labels to tm_g_ci by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/567
  • 578 Fix broken example for tm_t_abnormality_by_worst_grade by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/579
  • Update check.yaml by @arkadiuszbeer in https://github.com/insightsengineering/teal.modules.clinical/pull/570
  • Update tmtbinary_outcome.R by @Polkas in https://github.com/insightsengineering/teal.modules.clinical/pull/582
  • 563 Fix tm_a_mmrm Table Headers by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/583
  • 588 Add "Stratified by" Subtitles by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/594
  • 11 Update tm_a_mmrm column name by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/601
  • 590 Fix typo in tm_t_exposure footnote by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/606
  • 592 Add visit subtitle to tm_g_ci by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/605
  • 593 Fix tm_t_smq card name by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/604
  • 597 Add subtitles and footnotes to tm_a_mmrm by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/610
  • 591 Add tm_t_exposure title/subtitle by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/607
  • 595 Add titles/subtitles for worst flag variable by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/608
  • 561 Add CI Method footnote to tm_t_events_patyear by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/616
  • Turn off auto-styling by @cicdguy in https://github.com/insightsengineering/teal.modules.clinical/pull/617
  • add footnote and update test files by @6iris6 in https://github.com/insightsengineering/teal.modules.clinical/pull/615
  • fix package --as-cran by @donyunardi in https://github.com/insightsengineering/teal.modules.clinical/pull/602
  • 614 Add subtitle/footnotes to tm_g_km by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/620
  • 586 Add Stratified Newcombe to Stratified Analysis CI Method Options for tm_t_binary_oucome by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/624
  • Fix tm_t_tte, tm_t_coxreg footnotes by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/626
  • Removing if condition for by @arkadiuszbeer in https://github.com/insightsengineering/teal.modules.clinical/pull/584
  • 622 Clean up teal.modules.clinical NEWS by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/627
  • update title by @mhallal1 in https://github.com/insightsengineering/teal.modules.clinical/pull/631
  • Fix grammar in NEWS.md by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/632
  • 633 Fix tm_t_abnormality footer by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/646
  • Add validation for tm_a_mmrm covariate/visit conflict by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/649
  • 637 remove unnecessary brackets@main by @JiaLiu0001 in https://github.com/insightsengineering/teal.modules.clinical/pull/645
  • update roxygen for SRC by @nikolas-burkoff in https://github.com/insightsengineering/teal.modules.clinical/pull/651
  • 525: parse cor_struct choices from tern.mmrm package by @danielinteractive in https://github.com/insightsengineering/teal.modules.clinical/pull/647
  • 652 Fix TMC footnotes by @edelarua in https://github.com/insightsengineering/teal.modules.clinical/pull/654
  • [skip vbump] Release for version 0.8.14 by @insights-engineering-bot in https://github.com/insightsengineering/teal.modules.clinical/pull/657

New Contributors

  • @ayogasekaram made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/513
  • @Melkiades made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/515
  • @danielinteractive made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/523
  • @donyunardi made their first contribution in https://github.com/insightsengineering/teal.modules.clinical/pull/602

Full Changelog: https://github.com/insightsengineering/teal.modules.clinical/compare/v0.8.13...v0.8.14

- R
Published by github-actions[bot] over 3 years ago

teal.modules.clinical - v0.8.13

Enhancements

tm_g_pp_adverse_events

  • Updated the position of the labels.
  • Updated the plot to render the color legend. #### tm_t_summary_by
  • Enhanced the module to support the geometric mean in the encoding panel. #### tm_t_summary
  • Updated and added a footnote.
  • Enhanced the module to support geometric mean in the encoding panel.
  • Updated the module to display the checkboxes for numeric variables statistics only when numeric variables are part of the selected.
  • Updated validations to warn users when using a dataset with non unique identifiers or when selecting variables with non supported types (i.e. Date, POSIXt).
  • Added a checkbox to remove the column generated by missing values. #### Other modules
  • Updated tm_t_binary_outcome to enable an option to apply a continuity correction in the Newcombe method
  • Simplified the show R code for tm_g_pp_patient_timeline module.
  • Improved the names of the code chunks shown in Debug Info.
  • Improved the validation if treatment variable is not a factor. ### Bug fixes
  • Updated the validation to account for the error when multiple variables are not selected in tm_g_pp_patient_timeline module. ### Miscellaneous
  • Added a pkgdown template to the documentation.
  • Updated package authors.

- R
Published by github-actions[bot] over 3 years ago

teal.modules.clinical - v0.8.11

Breaking changes

  • Updated tm_t_abnormality due to changes in count_abnormal that abnormal argument is taking list as input now.
  • Changed the tm_g_pp_patient_timeline parameter, cmtrt, to cmdecod. ### New features
  • New module tm_t_abnormality_by_worst_grade was added for the analysis of laboratory test results with highest grade post-baseline.
  • Enhanced tm_t_ancova to include selected parameter(s), visit(s) and the analysis variable in title of the table.
  • New module tm_g_lineplot was added for creating line plots.
  • Enhanced tm_t_logistic to include selected parameter in title of the table.
  • Enhanced tm_g_forest_rsp to include selected parameter in title of the table.
  • Enhanced tm_g_forest_tte to include selected parameter in title of the table.
  • Enhanced tm_g_pp_patient_timeline with bold axes labels and integer values on the axis.
  • Enhanced tm_g_ipp to allow users not to display AVALU in the title nor in the y axis. ## Enhancements
  • Added support for logging with the logger package and added info level logs upon initialization of a module.
  • Added default_responses argument to tm_t_binary_outcome and tm_g_forest_rsp to allow the user to specify default selected responses and possible response levels.
  • Updated tm_t_binary_outcome to show only the selected responses in the output table when "Show All Selected Response Categories" is checked.
  • Added rsp_table argument to tm_t_binary_outcome to allow the user to initialize the module matching the RSPT01 STREAM template.
  • Added support for custom arguments for ggplot2::labs and ggplot2::theme in plot based modules.
  • Added support for custom arguments for rtables::basic_table in table based modules.
  • Updated tm_t_binary_outcome to enable an option to apply a continuity correction in the Wilson method. ### Miscellaneous
  • Updated R version requirement to >= 3.6.
  • Refactored calls to the defunct teal.devel::data_extract_input into calls to its replacement teal.devel::data_extract_ui.
  • Updated modules to use new data_merge_module interface provided by teal.devel and removed usage of the now deprecated function teal.devel::get_input_order.
  • Updated tm_t_binary_outcome module to add a template and removed the now deprecated module tm_t_rsp.
  • Removed utils.nest dependency and replaced calls with checkmate equivalents. ### Bug Fixes
  • Fixed bug in tm_g_pp_therapy where if the cmstdy or cmendy argument is of type integer causes the plot to crash.

- R
Published by github-actions[bot] about 4 years ago

teal.modules.clinical - v0.8.10

New features

  • New module tm_t_smq was added for the analysis of adverse events by Standardized MedDRA Query.
  • New module tm_t_shift_by_grade was added for the analysis of grade laboratory abnormalities.
  • New module tm_t_exposure was added for the analysis of duration of exposure for risk management plan.
  • New module tm_t_shift_by_arm that can display shift table of ECG interval data.

Bug fixes

  • Corrected tm_a_mmrm to be able to consider the treatment variable in additional interactions.
  • Fixed tm_t_binary_outcome and tm_t_rsp so that correct CI estimation method is chosen for Proportions Difference in Stratified Analysis (i.e. Wald-type confidence interval with CMH weights).

Enhancements

  • Added validation checks to tm_t_rsp and tm_t_binary_outcome for stratification errors when filters are applied.
  • Added tm_g_km validation check for plot tables font size.
  • Enhanced tm_g_km to add the selected paramcd in the plot title.
  • tm_t_events now can display layouts with two nested column as treatment variables. The same pruning and sorting options can be applied.
  • Previously package helper functions were never exported. These functions have now been exported so they can be utilized.
  • tm_t_events_by_grade now can display grading groups in nested columns with col_by_grade option. In addition, module now supports pruning and sorting options similar to tm_t_events.
  • Used format_count_fraction to fix formatting inconsistency in tm_t_events_summary.
  • Updated count_occurrences vars argument in tm_t_shift_by_grade.
  • Updated tm_t_pp_laboratory to display 4 decimals by default.

Miscellaneous

  • Updated LICENCE and README with new package references.
  • Added error_on_lint: TRUE to .lintr.
  • Removed insert_rrow and updated usage of count_patients_by_flags in tm_t_events_summary.
  • Changed how the package calls functions from the dplyr package. The functions should be now fully specified (e.g. dplyr::filter).

- R
Published by insights-engineering-bot over 4 years ago

teal.modules.clinical - v0.8.9

  • Added a capability to remember the order of user input to some encoding UI elements. The inputs with tracking enabled are marked with a double arrow icon. The affected modules are: tm_t_summary, tm_t_summary_by, tm_g_forest_rsp, tm_g_forest_tte, tm_t_events_summary, tm_t_abnormality, tm_t_mult_events.
  • Added a new argument numeric_stats to tm_t_summary and tm_t_summary_by to control displayed summary statistics for numeric variables.
  • Added a new argument drop_zero_levels to tm_t_summary_by so that rows with all zeros can be dropped from result table.
  • Split tm_g_patient_profile tabs into 8 separate new modules.
  • Added the option to select patient ID from the filter panel for all the modules of patient profile.
  • Added an additional validation for tm_g_patient_timeline when the plot is empty.
  • Enhanced tm_a_mmrm to work without the treatment variable.
  • Added the option to choose the number of decimal places for rounding in tm_t_pp_laboratory.
  • Added a check box to tm_g_pp_patient_timeline hiding/showing relative study days on the x-axis.
  • Added a title with patient's id to plots in patient profile modules.
  • Made the grey error message in tm_g_forest_tte more informative when the Endpoint column was deselected in the left-hand encoding panel.
  • Added the twenty-fifth and seventy-fifth quantile to summary statistics in tm_t_summary.
  • Added an interaction p-value column for tm_t_coxreg.
  • Added an additional validation for tm_t_ancova when selected covariate variables contain just one level.
  • Added an additional validation for tm_t_events_patyear when the events variable is empty.
  • Changed the description of the font size input in Additional plot settings (tm_g_km) to more precisely represent what it controls.
  • Enhanced tm_t_logistic so that interaction choices depend on the selected covariates.
  • Enhanced tm_t_rsp so that strata input is only visible when treatments are compared.
  • Fixed Get R Code output of tm_t_pp_laboratory to return identical HTML formatted table as displayed in the app.
  • Added an additional validation for tm_t_coxreg to ensure treatment, strata and covariate variables do not overlap.
  • Limited the label repel feature in tm_g_pp_patient_timeline to X-axis for a more consistent look.
  • Updated tm_t_summary_by so that paramcd is not required when analyzing ADSL variables.
  • Updated tm_t_coxreg so that it can work when there is no covariate selected.
  • Updated tm_a_mmrm so that it can work when treatment variable is not selected.
  • Updated tm_g_forest_tte so that total number of events are also shown in the table.
  • Updated tm_t_events_summary to work with pooled studies.
  • Updated tm_t_coxreg to validate the at level.
  • Updated tm_t_logistic to validate the at level.
  • Added an additional validation for tm_t_binary_outcome and tm_t_rsp to ensure strata variable contains more than one level when just one strata variable is selected.
  • Updated the warning message when all statistics are deselected in tm_t_summary and tm_t_summary_by explaining at least one statistic has to be selected.

- R
Published by insights-engineering-bot over 4 years ago

teal.modules.clinical - v0.8.2

  • add confidence level for survfit, coxph, ztest; add confidence type, ties, percentiles to tm_t_tte
  • optionally use only single term in tm_t_events and tm_t_events_by_grade modules
  • new tm_t_logistic module
  • new tm_t_mmrm module
  • new modules tm_t_summary_by and tm_t_events_summary
  • add stratified analysis to tm_g_forest_tte and tm_g_forest_rsp
  • add confidence level and plotting symbol size options to tm_g_forest_rsp and tm_g_forest_tte

- R
Published by insights-engineering-bot over 4 years ago

teal.modules.clinical - v0.8.5

  • 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.
  • FilteredData object is now passed to arm_ref_comp_observer and modules now support nested lists containing delayed_data objects.
  • Replace plot_with_height module with new plot_with_settings module.
  • Update examples to use code argument inside cdisc_dataset.

- R
Published by insights-engineering-bot over 4 years ago

teal.modules.clinical - v0.8.6

  • New module tm_g_ci was added for confidence interval plots.
  • New module tm_t_ancova was added for analysis of variance summary tables.
  • Refactored all modules using the redesigned rtables and tern packages.
  • Enhanced modules. They now take advantage of data_extract_spec and data_merge_module functionality from teal.
  • Reduced clutter from repeated datasets in the encodings panels.
  • Updated all modules to use OptionalSelectInput for conf_level.
  • Added vignette about substitute which can be helpful when developing analysis template functions for teal modules.

- R
Published by insights-engineering-bot over 4 years ago

teal.modules.clinical - v0.8.7

  • New module tm_g_patient_profile was added to profile patients based on predefined categories.
  • New module tm_g_ipp was added for individual patient plots.
  • The argument drop_arm_levels was added to all safety modules. This allows removal of columns based on factor levels not found in filtered data.
  • tm_g_km updated to allow plot of failure probability on y-axis, tick interval selection on x-axis and option to create plot without confidence interval ribbon (new default).
  • The argument time_unit_var was added to template_g_km to add the time unit to the x-axis label.
  • Removed redundant Analysis Data: label from Encodings Panel.
  • Removed limit requiring 15 or fewer columns for tabulation modules. New maximum threshold is 100 columns.
  • Lowered limit for minimum number of observations required by modules. Safety tables require at least one record. For efficacy outputs the requirement is per treatment group: tm_a_mmrm requires five records, tm_t_logistic and tm_t_coxreg require two records and the remaining modules require at least one record per treatment group. For graphs, the minimum threshold is two records.
  • Removed argument cnsr_val from tm_t_events_patyear and added new argument events_var.
  • arm_ref_comp_observer to include parentname argument.
  • Show R code to include datasets retrieved from data_extract_spec objects.
  • Refactored out the stringr dependency from the patient profile module.
  • Added missing table calls in chunks for tm_t_events and tm_t_events_by_grade.

- R
Published by insights-engineering-bot over 4 years ago

teal.modules.clinical - v0.8.8

  • Added the option to download and expand tables.
  • In tm_g_km added support for downloading images and updated x-axis label to be shown in title case.
  • For tm_g_patient_profile:
    • Added a slider for the font size in plots.
    • Added persistence for selected table lengths.
    • The timeline plot now supports more edge cases.
    • In vitals tab, removed unused label text legend, updated plot to display stable colors per levels, cleared x-axis limit and fixed legend to update when filtering. Also added a note to clarify the supported horizontal lines cases.
    • Updated adverse events tab to show a warning message instead of an empty plot when data is empty.
    • Fixed PARAMCD selected levels for current patient.
  • For tm_t_tte:
    • Updated the pre-processing code inside template_tte so that a dataset without any events still produces a table.
    • Updated code to use correct denominator for duration of response endpoints.
  • For tm_t_summary:
    • Modified the parameter arm_var to accept more than one column. When two columns are selected for arm_var, then the second variable will be nested under the first one.
    • Added argument show_labels to template_summary so that the label for a single summary variable is shown in the table.
  • Added a new parameter conf_arg to tm_t_rsp to be consistent with other efficacy modules.
  • Added validate statement in tm_g_ipp module to print message when Timepoint Variable drop down is deselected.
  • Removed header definition in tm_g_forest_rsp and tm_g_forest_tte as there is now a default header in g_forest.
  • Fixed validate statement in tm_t_coxreg so that models without strata and using likelihood tests return a result.
  • Clarified functionality of drop_arm_levels for tm_t_summary and tm_t_summary_by. In the encodings panel, the checkbox will only be shown when the parent dataset and analysis dataset are different.
  • Replaced the remaining two observe function calls with observeEvent to optimize performance.
  • Fixed grammar in the "Select a patient's id" error message in the tm_g_patient_profile.
  • Fixed the font_size default of the templates to be 12L instead of a vector of 3 integers and cleaned associated unnecessary code.
  • Fixed deprecated function warning in tm_g_barchart_simple.
  • Fixed subgroup_var definition truncation in tm_g_forest_rsp and tm_g_forest_tte.
  • Clarified "Type of Regression" related labeling in the encoding panel from tm_t_coxreg.
  • Added a validation for the case when all rows are filtered out in the therapy tab of tm_g_patient_profile.
  • Updated the internals of the modules to read data from the correct field of the filter_spec objects.
  • Fixed the reactivity between the filter panel and the PARAMCD variable levels input in tm_g_patient_profile vitals tab so that the plot does not get reset when filtering.
  • Updated the vitals plot tab in tm_g_patient_profile to drop NA entries in the plot.

- R
Published by insights-engineering-bot over 4 years ago