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).

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.

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.