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Changelog

Source: NEWS.md

teal.modules.clinical 0.8.14

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

teal.modules.clinical 0.8.13

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 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

  • 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.

teal.modules.clinical 0.8.12

Miscellaneous

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

teal.modules.clinical 0.8.12

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.

teal.modules.clinical 0.8.11

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

  • 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.

teal.modules.clinical 0.8.10

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).

teal.modules.clinical 0.8.9

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 grey 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.

teal.modules.clinical 0.8.8

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.

teal.modules.clinical 0.8.7

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.

teal.modules.clinical 0.8.6

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.

teal.modules.clinical 0.8.5

  • All graph modules now accept a plot_width argument which specifies the plot width and renders a slider to adjust the width interactively in the module.
  • FilteredData object is now passed to arm_ref_comp_observer and modules now support nested lists containing delayed_data objects.
  • Replace plot_with_height module with new plot_with_settings module.
  • Update examples to use code argument inside cdisc_dataset.

teal.modules.clinical 0.8.4

  • Extend tm_t_coxreg to optionally produce univariate Cox regressions.
  • Updated tm_t_binary_outcome to display Odds Ratio estimates, include new methods for CIs and p-values and display a summary for individual response categories.
  • Updated tm_t_tte to optionally compare between arms, removed conf_level argument.
  • Updated tm_g_km to optionally compare between arms.
  • Extend tm_g_km to optionally scale X axis range in case of more than one plot.
  • New tm_a_mmrm for MMRM analysis.
  • Deprecated tm_t_mmrm (superseded by tm_a_mmrm).

teal.modules.clinical 0.8.3

  • New tm_t_coxreg module for multi-variable Cox regressions.
  • New tm_t_binary_outcome module.
  • New tm_t_events_patyear module: events rate adjusted for patient-year at risk table.
  • Remove grade_levels argument from tm_t_events_by_grade.
  • Updated response table for single arm.
  • New tm_t_abnormality module.
  • Removed get_relabel_call and get_relabel_call2 in favor of teal.devel::get_relabel_call and teal.devel::get_anl_relabel_call.

teal.modules.clinical 0.8.2

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

teal.modules.clinical 0.8.1

  • New tm_t_events and tm_t_events_by_grade modules.

teal.modules.clinical 0.8.0

  • Optionally show KM and CoxPH table in tm_g_km.

teal.modules.clinical 0.7.0

  • Use teal.devel.

teal.modules.clinical 0.6.0

  • Package renamed to teal.modules.clinical.
  • Rename tm_t_summarize_variables to tm_t_summary.
  • Usage of teal::choices_selected() function instead of *_var and *_var_choices arguments.