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parameters to tm_t_events_summary to select/deselect the "Total number of deaths" and "Total number of patients withdrawn from study due to an AE" rows, respectively.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 #1102
• 1175 fixing validation on col_by_var variable. by @kartikeyakirar in #1178
• 1149 introduce ylim parameter for tm_g_km module by @m7pr in #1177
• 1108 {shinytest2} feature branch by @m7pr in #1126
• 1176 remove Show Warnings from modules by @m7pr in #1180
• 227 utilize logger::log_shiny_input_change by @m7pr in #1182
• truetype font support checking PR by @gmbecker in #1188
• Bumps {rmarkdown} minimal version by @averissimo in #1186
• increase rtables dep version by @ayogasekaram in #1195
• testing for rtables higher level ns PR by @gmbecker in #1190
• 553 change level in log_shiny_input_changes and exclude plot sizes in logging by @m7pr in #1191
• Update DESCRIPTION by @shajoezhu in #1196
• Fix documentation of arm_var argument in modules by @edelarua in #1201
• Add functionality to tm_t_events_patyear to split columns by multiple (nested) variables by @edelarua in #1203
• Replace use of add_colcounts with the show_colcounts argument by @edelarua in #1207
• Add option to tm_t_summary to include arm_var labels in table header by @edelarua in #1205
• Workflow propagations by @walkowif in #1208
• Add stats and risk difference parameters to forest plot modules by @edelarua in #1210
• Fix teal namespace for broken tests by @vedhav in #1213
• Add options to toggle the "Total deaths" and "Total withdrawals due to AE" rows in tm_t_events_summary by @edelarua in #1216
• Update DESCRIPTION by @pawelru in #1217
• Use group_var argument to control_lineplot_vars instead of deprecated strata by @edelarua in #1223
• update readme by @pawelru in #1218
• fix: changed the separator in h_concat_expr by @kpagacz in #1226
• Workflow propagations by @walkowif in #1219
• Update DESCRIPTION tern to 0.9.6 by @shajoezhu in #1227
• reset factor level during validate by @donyunardi in #1229
• Update scheduled.yaml by @pawelru in #1220
• use of roxy.shinylive by @pawelru in #1230
• add rmarkdown to VignetteBuilder by @pawelru in #1237
• Adds roxy.shinylive to pre-commit configuration by @averissimo in #1238
• teal.data::datanames() is deprecated in favor of dot-prefix and names() by @averissimo in #1239
• 1248 Fix shinytest2 tests by @m7pr in #1251
• Update tm_t_summary_by() column variable text by @edelarua in #1247
• upversion teal.report, rtables, rtables.officer by @shajoezhu in #1250
• update strata var to group_var by @ayogasekaram in #1246
• Bring back tests for tm_g_pp_therapy by @vedhav in #1271
• fixes error in adverse events when ASTDY is of difftime type by @averissimo in #1284
• Fix tmc integration test - Wait for shiny app idle after fit is clicked by @vedhav in #1296
• add setup-r-dependencies by @vedhav in #1297
• Fix documentation note about links on r-devel by @llrs-roche in #1299
• Stop R process if AppDriver fails in test-examples by @averissimo in #1303
• 🗃️ Decorators feature branch by @averissimo in #1252
• 1305 allow delayed data to pass in cs_to_des_select by @chlebowa in #1306
• upversion dep by @shajoezhu in #1308
• Fix logger by @gogonzo in #1312
• Show only datasets used by @llrs-roche in #1309
• Update DESCRIPTION by @shajoezhu in #1315
• update packages for the scheduled build by @m7pr in #1314
• 1441 Introduce transformators parameter in modules by @m7pr in #1313
• vbump teal.logger by @m7pr in #1319
• add Remotes to DESCRIPTION by @m7pr in #1321
• simplify builds dependencies of extra-deps by @m7pr in #1318
• Update teal.reporter version by @m7pr in #1322
• vbump teal.code by @m7pr in #1323
• vbump teal.data by @m7pr in #1326
• Make sure the code chunks does not break because of warnings by @vedhav in #1327
• vbump teal.widgets by @m7pr in #1328
• Duplicated decorators during an edge case of named and unnamed decorators by @m7pr in #1325
• Add title_text argument to tm_t_mult_events() to control dynamic title by @edelarua in #1334
• update tm_g_forest_tte...

v0.10.0-rc1

Remove platforms that cause dependency installation to get stuck.

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

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

v0.9.0 cran

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 #824
• Use token in spelling workflow by @walkowif in #825
• Refactor tm_t_exposure to remove summary row by @edelarua in #826
• Patient Profile Modules only show relevant datanames by @averissimo in #828
• Solution for maintaining indent after pruning by @ayogasekaram in #791
• Fix bug in tm_t_coxreg when no covariates selected by @edelarua in #833
• Fix tm_t_coxreg errors when applying filters by @edelarua in #831
• Display Patient ID in relevant templates, clean up data tables in reports by @edelarua in #834
• 198 Include user's card labels when generating the report by @m7pr in #835
• Add option to remove interval in tm_g_lineplot by @edelarua in #840
• chasing deprecations by @chlebowa in #852
• Update docs to use the new teal_data instead of TealData by @kartikeyakirar in #853
• fix tm_g_pp_vitals by @gogonzo in #896
• Update tern version by @m7pr in #901
• bump teal.reporter dep version by @chlebowa in #903
• Fix bug forcing tm_g_lineplot to initialize with a table by @edelarua in #899
• Add options to tm_t_events for sorting and overall rows by @edelarua in #851
• Remove unused table_names argument from surv_timepoint by @edelarua in #905
• tdata to teal_data by @chlebowa in #855
• fix resolve_delayed by @gogonzo in #909
• Workflow propagation by @walkowif in #908
• 906 update dependency versions by @chlebowa in #907
• 231 remove get_labels function by @kartikeyakirar in #914
• Update forest plots following refactor of g_forest by @edelarua in #911
• Two arm vars by @gogonzo in #916
• Fix TMC to work with tern v0.9.3 by @edelarua in #922
• 430 use expect_no_error in tests instead of expect_error(, NA) by @m7pr in #936
• 919 update vignettes@main by @ayogasekaram in #927
• Add default_total_label function by @edelarua in #942
• 918 update teal.modules.clinical.R with #' @keywords internal "_PACKAGE" by @m7pr in #982
• TMC bug fixes by @gogonzo in #926
• Replace aval parameter with aval_var by @edelarua in #939
• Replace avalu parameter with avalu_var by @edelarua in #940
• Adds min package version by @averissimo in #797
• Replace base_var parameter with baseline_var by @edelarua in #941
• Implement default_na_str by @edelarua in #984
• Replace summarize_vars with analyze_vars by @edelarua in #987
• Clean up overall argument documentation by @edelarua in #989
• update deps of roxygenize hook by @pawelru in #990
• Minor improvements to README/vignettes by @edelarua in #993
• Clean up documentation for tm_t_shift_by_arm_by_worst by @edelarua in #997
• Clean up documentation for tm_t_shift_by_grade by @edelarua in #998
• Update DESCRIPTION teal.data (>= 0.4.0) by @shajoezhu in #1008
• Consolidate argument_convention file by @edelarua in #1006
• 618 reduce dependencies of the package by @m7pr in #981
• Clean up documentation for tm_t_binary_outcome by @edelarua in #994
• Clean up documentation for tm_t_summary_by by @edelarua in #1003
• Clean up documentation for tm_t_summary by @edelarua in #1004
• Clean up documentation for tm_t_pp_basic_info by @edelarua in #1024
• Clean up documentation for tm_g_pp_adverse_events by @edelarua in #1026
• Clean up documentation for tm_t_pp_prior_medication by @edelarua in #1023
• Clean up documentation for tm_t_pp_medical_history by @edelarua in #1022
• Clean up documentation for tm_g_forest_rsp by @edelarua in #1020
• Clean up documentation for tm_g_pp_therapy by @edelarua in #1025
• Clean up documentation for tm_t_events_summary by @edelarua in #1015
• Clean up documentation for tm_t_mult_events by @edelarua in #1019
• Clean up documentation for tm_t_tte by @edelarua in https://github.com/insightsengineering/teal.mod...

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

New Contributors

• @walkowif made their first contribution in #673
• @m7pr made their first contribution in #782
• @kartikeyakirar made their first contribution in #813

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

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

New Contributors

• @walkowif made their first contribution in #673

Full Changelog: v0.8.14...v0.8.15

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 #507
• Contribution guide updates by @insights-engineering-bot in #509
• implement draggable widget for all modules by @denisovan31415 in #485
• 510 revert missing checkbox tm t summary@main by @ayogasekaram in #513
• 514 empty string summarize logistic@main by @Melkiades in #515
• increase indent teal outputs by @ayogasekaram in #516
• docs: replaced github links with the pkgdown links by @kpagacz in #517
• fix barchart by @nikolas-burkoff in #521
• Fix barchart by @nikolas-burkoff in #524
• init reporter tmc by @Polkas in #518
• fix tm_g_barchart by @gogonzo in #529
• DESC and README by @denisovan31415 in #531
• 527 Update to use nestcolor::color_palette by @edelarua in #530
• Update Rbuildignore and add auto-updates by @insights-engineering-bot in #532
• slight refactoring for tern.mmrm by @danielinteractive in #523
• teal.reporter all modules by @Polkas in #528
• 511 Implement nestcolor in TMC by @edelarua in #534
• Update pre-commit config to detect _pkgdown.y[a]ml by @insights-engineering-bot in #535
• remove _FILTERED by @gogonzo in #536
• reporter cleaning by @mhallal1 in #537
• Update documentation workflow by @insights-engineering-bot in #539
• rm inline - css tmc by @Polkas in #538
• Updated all test files in tests/testthat/ ("2022_02_28") by @ayogasekaram in #549
• 564 Add more descriptive title/labels to tm_g_ci by @edelarua in #567
• 578 Fix broken example for tm_t_abnormality_by_worst_grade by @edelarua in #579
• Update check.yaml by @arkadiuszbeer in #570
• Update tm_t_binary_outcome.R by @Polkas in #582
• 563 Fix tm_a_mmrm Table Headers by @edelarua in #583
• 588 Add "Stratified by" Subtitles by @edelarua in #594
• 11 Update tm_a_mmrm column name by @edelarua in #601
• 590 Fix typo in tm_t_exposure footnote by @edelarua in #606
• 592 Add visit subtitle to tm_g_ci by @edelarua in #605
• 593 Fix tm_t_smq card name by @edelarua in #604
• 597 Add subtitles and footnotes to tm_a_mmrm by @edelarua in #610
• 591 Add tm_t_exposure title/subtitle by @edelarua in #607
• 595 Add titles/subtitles for worst flag variable by @edelarua in #608
• 561 Add CI Method footnote to tm_t_events_patyear by @edelarua in #616
• Turn off auto-styling by @cicdguy in #617
• add footnote and update test files by @6iris6 in #615
• fix package --as-cran by @donyunardi in #602
• 614 Add subtitle/footnotes to tm_g_km by @edelarua in #620
• 586 Add Stratified Newcombe to Stratified Analysis CI Method Options for tm_t_binary_oucome by @edelarua in #624
• Fix tm_t_tte, tm_t_coxreg footnotes by @edelarua in #626
• Removing if condition for by @arkadiuszbeer in #584
• 622 Clean up teal.modules.clinical NEWS by @edelarua in #627
• update title by @mhallal1 in #631
• Fix grammar in NEWS.md by @edelarua in #632
• 633 Fix tm_t_abnormality footer by @edelarua in #646
• Add validation for tm_a_mmrm covariate/visit conflict by @edelarua in #649
• 637 remove unnecessary brackets@main by @JiaLiu0001 in #645
• update roxygen for SRC by @nikolas-burkoff in #651
• 525: parse cor_struct choices from tern.mmrm package by @danielinteractive in #647
• 652 Fix TMC footnotes by @edelarua in #654
• [skip vbump] Release for version 0.8.14 by @insights-engineering-bot in #657

New Contributors

• @ayogasekaram made their first contribution in #513
• @Melkiades made their first contribution in #515
• @danielinteractive made their first contribution in #523
• @donyunardi made their first contribution in #602

Full Changelog: v0.8.13...v0.8.14

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.

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.

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).