Changelog

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parameters to tm_t_events_summary to select/deselect the “Total number of deaths” and “Total number of patients withdrawn from study due to an AE” rows, respectively.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.

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.

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.

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().
• Simplify examples and vignettes code by removing package prefixes where possible.
• 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.
• Fixes partial matching.

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).
• Introduced tests against partial matching.

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.
• Improved default annotation table sizing in tm_g_km.
• Refactored tm_t_exposure to display “total” row as last row in table instead of as a summary row. Added parameters add_total_row to set whether the total row should be displayed and total_row_label to set the total row label.
• Updated tm_t_events to maintain indentation after pruning.
• Updated default reference/comparison arm level selection to work when arm variable levels are filtered out.
• Updated tm_t_coxreg to drop factor covariate variable levels that are not present to avoid errors when filtering.
• Updated tm_t_pp_basic_info, tm_t_pp_medical_history, tm_g_pp_therapy, tm_g_pp_adverse_events, and tm_t_pp_laboratory to print patient ID above table.
• Updated tm_t_pp_basic_info, tm_g_pp_therapy, tm_g_pp_adverse_events, and tm_t_pp_laboratory to use rlistings to print data neatly in reports.
• Updated tm_g_lineplot to allow user to remove interval from plot.
• Updated the documentation and vignettes to demonstrate method to pass teal_data object to teal::init().

Bug fixes

• Fixed bug in tm_t_coxreg preventing table from being displayed when no covariates are selected.

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.
• Hid the datasets that were not being used by the patient profile modules in the filter panel. Replaced the datanames = "all" parameter with the datasets used internally by the module.

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.

Enhancements

• Updated all synthetic data for tests to version rcd_2022_02_28.
• Updated all test files in tests/testthat/ to synthetic_cdisc_data("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 display of graph.
• 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.

Enhancements

Bug fixes

• Fixed summarize_logistic implementation broken by empty string error. upstream. _NA_ is the new standard flag to allow it to pivot over empty entries in data frames.
• Took out @title from tm_t_binary_outcome.R that was producing a warning.
• Updated validation to account for the error when selecting a single variable in tm_g_pp_patient_timeline module.

Miscellaneous

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

Miscellaneous

• Changed the input of Covariates in tm_t_coxreg.R to track user input and reflect the order in the table.

New features

• Added new module tm_t_shift_by_arm_by_worst for the analysis of the laboratory abnormalities with the most severe grade flag.
• Enhanced tm_t_events_patyear to include selected parameter in title of the table.
• Enhanced tm_t_mult_events to include selected parameter in title of the table.

Enhancements

• Rewrote modules to use moduleServer and updated calls to teal.devel modules which were also written to use moduleServer.
• Changed the way of obtaining of selection ordered after changes in teal.devel. Use ordered = TRUE in cs_to_des_select or cs_to_select_spec to return ordered selection.
• Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
• tm_t_events_summary now allows nested arm_var columns matching other outputs such as tm_t_events.
• Added validation in tm_t_abnormality_by_worst_grade when arm_var is not selected.
• Enhanced tm_t_binary_outcome to include all responders in the response table by default.
• Added a subtitle to tm_g_forest_tte, tm_t_coxreg, and tm_t_binary_outcome listing stratification factors.

Bug fixes

• Fixed a bug to prevent processing of empty sets of data by tm_g_forest_rsp.R causing shiny errors during the runtime.
• Fixed a bug where a closed Compare Treatments conditional panel with a marked Combine all comparison groups? option conflicted with adding a column with all patients to tables in tm_t_binary_outcome.R and tm_t_tte.R.

Miscellaneous

• Replaced the deprecated rtables::var_labels calls in the documentation examples.
• Add import of tern.mmrm package and change some references after split of tern.
• Adjusted package imports to take into account changes to the teal framework.
• Ensure consistent vertical order of tm_g_pp_patient_timeline output when switching between absolute and relative days.

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

• Added new module tm_t_abnormality_by_worst_grade 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.
• Added new module tm_g_lineplot 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 selected responses in the output table when selecting “Show All Selected Response Categories”.
• 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 required R version 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.

New features

• Added new module tm_t_smq for the analysis of adverse events by Standardized MedDRA Query.
• Added new module tm_t_shift_by_grade for the analysis of grade laboratory abnormalities.
• Added new module tm_t_exposure for the analysis of duration of exposure for risk management plan.
• Added 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 all interactions.
• Fixed tm_t_binary_outcome and tm_t_rsp to choose the correct CI estimation method 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 from applied filters.
• 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 options for pruning and sorting are available.
• Exported package helper functions.
• Updated tm_t_events_by_grade to display grading groups in nested columns with col_by_grade option and support pruning and sorting options like 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.
• Updated tm_t_events_by_grade to use the trim_levels_in_group split function instead of the trim_rows function.
• Added a table title to tm_t_tte.
• Added table titles to tm_t_rsp and tm_t_binary_outcome.

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).

New features

• Added capability to remember the order of user input to some encoding UI elements. Inputs marked with a double arrow icon have tracking enabled. 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 you can drop rows with all zeros from result table.

Enhancements

• 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 a 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 gray error message in tm_g_forest_tte more informative when deselecting the Endpoint column 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 a validation for tm_t_ancova when selected covariate variables contain one level.
• Added a validation for tm_t_events_patyear when the events variable is empty.
• Changed the font size input description for tm_g_km to more precisely describe 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 visible when comparing treatments.

Bug fixes

• Fixed Get R Code output of tm_t_pp_laboratory to return identical HTML formatted table as displayed in the app.
• Added a 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 validation for the at level of tm_t_coxreg.
• Updated validation for the at level of tm_t_logistic.
• Added a validation for tm_t_binary_outcome and tm_t_rsp to ensure strata variable contains more than one level when selecting one strata variable.
• Updated the warning message when deselecting all statistics in tm_t_summary and tm_t_summary_by to explain need to select at least one statistic.

Enhancements

• Added the option to download and expand tables.
• In tm_g_km added support for downloading images and updated x-axis label to show 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 selecting two columns for arm_var, the second variable will nest under the first one.
  • Added argument show_labels to template_summary to show the label for a single summary variable in the table.
• Added a new parameter conf_arg to tm_t_rsp to be consistent with other efficacy modules.
• Added validation statement in tm_g_ipp module to print message when deselecting Timepoint Variable drop-down.
• Removed header definition in tm_g_forest_rsp and tm_g_forest_tte as there is now a default header in g_forest.
• Fixed validation 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 show when the parent dataset and analysis dataset are different.

Miscellaneous

• 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 labeling related to regression type in the encoding panel from tm_t_coxreg.

Bug fixes

• Added a validation for the case when filtering out all rows 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.
• Updated tm_t_coxreg to take at values into account.
• Added a check in tm_t_coxreg to have interactions in univariate models but not in multivariate models.
• Updated tm_t_events_summary to work with pooled studies.

New Module

• Added new module tm_g_patient_profile to profile patients based on predefined categories.
• Added new module tm_g_ipp for individual patient plots.

Enhancements

• Added the argument drop_arm_levels to all safety modules. This allows removal of columns based on factor levels not found in filtered data.
• Updated tm_g_km 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).
• Added the argument time_unit_var to template_g_km to add the time unit to the x-axis label.

Miscellaneous

• Removed redundant Analysis Data: label from Encodings Panel.
• Removed limit requiring 15 or fewer columns for tabulation modules. New upper threshold is 100 columns.
• Decreased the lower limit for number of observations required by modules. Safety tables require at least one record. Requirements for efficacy outputs 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 lower 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.

New Features

• Added new module tm_g_ci for confidence interval plots.
• Added new module tm_t_ancova for analysis of variance summary tables.
• Added new module tm_t_mult_events for multi-event tables.

Enhancements

• 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.

Miscellaneous

• Added vignette about substitute which can be helpful when developing analysis template functions for teal modules.

Bug fixes

• Updated tm_t_events module to use user’s non-default choices for prune_freq and prune_diff.