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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.tm_t_summary_by to allow NULL input to paramcd argument.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.control argument to tm_t_binary_outcome to control settings for the analysis (methods, confidence intervals, and odds ratios) within the module.na_level argument to tern functions with na_str.strata instead of strat in all tern function calls following the deprecation of this argument/name within tern.formatters from dependencies and replaced the use of its functions relating to variable labels with functions from teal.data.teal_data objects.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_tteteal_data object to teal::init().sort_freq_col to tm_t_events to allow the user to select column to use when sorting by decreasing frequency.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.teal_data object to teal::init().default_total_label and set_default_total_label functions to get and set default total column label (total_label) for modules.tern::default_na_str and tern::set_default_na_str functions to get and set default missing value replacement string (na_level) for modules.tm_g_lineplot forcing module to initialize with a table.aval argument in tm_t_pp_laboratory and tm_g_pp_vitals and replaced it with the aval_var argument.avalu argument in tm_t_pp_laboratory and replaced it with the avalu_var argument.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.summarize_vars function with analyze_vars.tidyr, rlang, magrittr and styler).tm_t_abnormality_by_worst_grade.tm_t_abnormality_by_worst_grade.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.tm_g_forest_tte plot to prevent overlapping text.tm_g_km.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.tm_t_events to maintain indentation after pruning.tm_t_coxreg to drop factor covariate variable levels that are not present to avoid errors when filtering.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.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.tm_g_lineplot to allow user to remove interval from plot.teal_data object to teal::init().tm_t_coxreg preventing table from being displayed when no covariates are selected.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.datanames = "all" parameter with the datasets used internally by the module.chunks with simpler qenv class.datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).synthetic_cdisc_data with refactored synthetic_cdisc_dataset function to speed up dataset loading in tests/examples.tm_a_gee.tm_t_ancova.shinyvalidate::InputValidator for better UI experience. Previously used shiny::validate.tm_a_mmrm to allow for Kenward-Roger adjustments of standard errors and p-values.tm_g_barchart_simple.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.tm_t_coxreg module after refactoring summarize_coxreg in tern to fix indentation.tm_t_exposure module to use new function analyze_patients_exposure_in_cols to fix table structure.tm_g_barchart_simple.svg format.tm_t_summary and tm_t_summary_by preventing users from specifying the numeric_stats argument.scda.2022 rather than scda.2021.param from tm_g_pp_vitals.tm_a_mmrm since we can always use the automatically determined optimizer.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.teal.modules.clinical package instead of scda datasets.testthat 3rd edition and replaced all applicable tests with snapshot testing.lubridate package for date variables in internal data.plot_width in tm_g_forest_rsp to prevent clutter.rcd_2022_02_28.tests/testthat/ to synthetic_cdisc_data("2022_02_28")tm_t_summary (encoding and filtering should be separate).teal.reporter functionality to all modules.tm_t_pp_medical_history module to use the table_with_settings module and return an rtables object.nestcolor in examples, refactored tm_g_barchart_simple to allow use of nestcolor.tm_g_ci.tm_a_mmrm column name when deselecting treatment from “all obs” to “All Patients”, added subtitles and footnotes.tm_t_exposure, cleaned up labels.tm_t_shift_by_grade and tm_t_shift_by_arm_by_worst.tm_t_events_patyear with CI method.tm_g_km.tm_t_binary_outcome.tm_a_mmrm.tm_t_exposure.tm_g_km and tm_t_tte when “Compare Treatments” is off.tm_g_barchart_simple which prevented display of graph.tm_t_abnormality_by_worst_grade.tm_a_mmrm which prevented table headers from displaying.tm_g_forest_rsp when deselecting endpoint.tm_t_binary_outcome that crashed the app when deselecting all paramcd.teal.reporter card names for tm_t_smq.tm_t_shift_by_arm_by_worst by adding validations for choosing different endpoint values.tm_t_coxreg preventing footnotes from displaying for univariate models.nestcolor dependency and replaced deprecated function tern::color_palette with nestcolor::color_palette.tm_g_pp_adverse_eventstm_t_summary_bytm_t_summaryDate, POSIXt).tm_t_binary_outcome to enable an option to apply a continuity correction in the Newcombe method.tm_g_pp_patient_timeline module.Debug Info.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.@title from tm_t_binary_outcome.R that was producing a warning.tm_g_pp_patient_timeline module.pkgdown template to the documentation.Covariates in tm_t_coxreg.R to track user input and reflect the order in the table.tm_t_shift_by_arm_by_worst for the analysis of the laboratory abnormalities with the most severe grade flag.tm_t_events_patyear to include selected parameter in title of the table.tm_t_mult_events to include selected parameter in title of the table.moduleServer and updated calls to teal.devel modules which were also written to use moduleServer.teal.devel. Use ordered = TRUE in cs_to_des_select or cs_to_select_spec to return ordered selection.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.tm_t_abnormality_by_worst_grade when arm_var is not selected.tm_t_binary_outcome to include all responders in the response table by default.tm_g_forest_tte, tm_t_coxreg, and tm_t_binary_outcome listing stratification factors.tm_g_forest_rsp.R causing shiny errors during the runtime.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.rtables::var_labels calls in the documentation examples.tern.mmrm package and change some references after split of tern.teal framework.tm_g_pp_patient_timeline output when switching between absolute and relative days.tm_t_abnormality due to changes in count_abnormal that abnormal argument is taking list as input now.tm_g_pp_patient_timeline parameter, cmtrt, to cmdecod.tm_t_abnormality_by_worst_grade for the analysis of laboratory test results with highest grade post-baseline.tm_t_ancova to include selected parameter(s), visit(s) and the analysis variable in title of the table.tm_g_lineplot for creating line plots.tm_t_logistic to include selected parameter in title of the table.tm_g_forest_rsp to include selected parameter in title of the table.tm_g_forest_tte to include selected parameter in title of the table.tm_g_pp_patient_timeline with bold axes labels and integer values on the axis.tm_g_ipp to allow users not to display AVALU in the title nor in the y axis.logger package and added info level logs upon initialization of a module.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.tm_t_binary_outcome to show selected responses in the output table when selecting “Show All Selected Response Categories”.rsp_table argument to tm_t_binary_outcome to allow the user to initialize the module matching the RSPT01 STREAM template.ggplot2::labs and ggplot2::theme in plot based modules.rtables::basic_table in table based modules.tm_t_binary_outcome to enable an option to apply a continuity correction in the Wilson method.teal.devel::data_extract_input into calls to its replacement teal.devel::data_extract_ui.data_merge_module interface provided by teal.devel and removed usage of the now deprecated function teal.devel::get_input_order.tm_t_binary_outcome module to add a template and removed the now deprecated module tm_t_rsp.utils.nest dependency and replaced calls with checkmate equivalents.tm_g_pp_therapy where if the cmstdy or cmendy argument is of type integer causes the plot to crash.tm_t_smq for the analysis of adverse events by Standardized MedDRA Query.tm_t_shift_by_grade for the analysis of grade laboratory abnormalities.tm_t_exposure for the analysis of duration of exposure for risk management plan.tm_t_shift_by_arm that can display shift table of ECG interval data.tm_a_mmrm to be able to consider the treatment variable in all interactions.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).tm_t_rsp and tm_t_binary_outcome for stratification errors from applied filters.tm_g_km validation check for plot tables font size.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.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.format_count_fraction to fix formatting inconsistency in tm_t_events_summary.count_occurrences vars argument in tm_t_shift_by_grade.tm_t_pp_laboratory to display 4 decimals by default.tm_t_events_by_grade to use the trim_levels_in_group split function instead of the trim_rows function.tm_t_tte.tm_t_rsp and tm_t_binary_outcome.LICENCE and README with new package references.error_on_lint: TRUE to .lintr.insert_rrow and updated usage of count_patients_by_flags in tm_t_events_summary.dplyr package. The functions should be now fully specified (e.g. dplyr::filter).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.numeric_stats to tm_t_summary and tm_t_summary_by to control displayed summary statistics for numeric variables.drop_zero_levels to tm_t_summary_by so that you can drop rows with all zeros from result table.tm_g_patient_profile tabs into 8 separate new modules.tm_g_patient_timeline when the plot is empty.tm_a_mmrm to work without the treatment variable.tm_t_pp_laboratory.tm_g_pp_patient_timeline hiding/showing relative study days on the x-axis.tm_g_forest_tte more informative when deselecting the Endpoint column in the left-hand encoding panel.tm_t_summary.tm_t_coxreg.tm_t_ancova when selected covariate variables contain one level.tm_t_events_patyear when the events variable is empty.tm_g_km to more precisely describe what it controls.tm_t_logistic so that interaction choices depend on the selected covariates.tm_t_rsp so that strata input is visible when comparing treatments.tm_t_pp_laboratory to return identical HTML formatted table as displayed in the app.tm_t_coxreg to ensure treatment, strata and covariate variables do not overlap.tm_g_pp_patient_timeline to X-axis for a more consistent look.tm_t_summary_by so that paramcd is not required when analyzing ADSL variables.tm_t_coxreg so that it can work when there is no covariate selected.tm_a_mmrm so that it can work when treatment variable is not selected.tm_g_forest_tte so that total number of events are also shown in the table.tm_t_events_summary to work with pooled studies.at level of tm_t_coxreg.at level of tm_t_logistic.tm_t_binary_outcome and tm_t_rsp to ensure strata variable contains more than one level when selecting one strata variable.tm_t_summary and tm_t_summary_by to explain need to select at least one statistic.tm_g_km added support for downloading images and updated x-axis label to show in title case.tm_g_patient_profile:
PARAMCD selected levels for current patient.tm_t_tte:
template_tte so that a dataset without any events still produces a table.tm_t_summary:
arm_var to accept more than one column. When selecting two columns for arm_var, the second variable will nest under the first one.show_labels to template_summary to show the label for a single summary variable in the table.conf_arg to tm_t_rsp to be consistent with other efficacy modules.tm_g_ipp module to print message when deselecting Timepoint Variable drop-down.tm_g_forest_rsp and tm_g_forest_tte as there is now a default header in g_forest.tm_t_coxreg so that models without strata and using likelihood tests return a result.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.observe function calls with observeEvent to optimize performance.tm_g_patient_profile.font_size default of the templates to be 12L instead of a vector of 3 integers and cleaned associated unnecessary code.tm_g_barchart_simple.subgroup_var definition truncation in tm_g_forest_rsp and tm_g_forest_tte.tm_t_coxreg.tm_g_patient_profile.filter_spec objects.PARAMCD variable levels input in tm_g_patient_profile vitals tab so that the plot does not get reset when filtering.tm_g_patient_profile to drop NA entries in the plot.tm_t_coxreg to take at values into account.tm_t_coxreg to have interactions in univariate models but not in multivariate models.tm_t_events_summary to work with pooled studies.tm_g_patient_profile to profile patients based on predefined categories.tm_g_ipp for individual patient plots.drop_arm_levels to all safety modules. This allows removal of columns based on factor levels not found in filtered data.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).time_unit_var to template_g_km to add the time unit to the x-axis label.Analysis Data: label from Encodings Panel.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.cnsr_val from tm_t_events_patyear and added new argument events_var.arm_ref_comp_observer to include parentname argument.data_extract_spec objects.stringr dependency from the patient profile module.tm_t_events and tm_t_events_by_grade.tm_g_ci for confidence interval plots.tm_t_ancova for analysis of variance summary tables.tm_t_mult_events for multi-event tables.rtables and tern packages.data_extract_spec and data_merge_module functionality from teal.OptionalSelectInput for conf_level.substitute which can be helpful when developing analysis template functions for teal modules.tm_t_events module to use user’s non-default choices for prune_freq and prune_diff.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.plot_with_height module with new plot_with_settings module.code argument inside cdisc_dataset.tm_t_coxreg to optionally produce univariate Cox regressions.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.tm_t_tte to optionally compare between arms, removed conf_level argument.tm_g_km to optionally compare between arms.tm_g_km to optionally scale X axis range in case of more than one plot.tm_a_mmrm for MMRM analysis.tm_t_mmrm (superseded by tm_a_mmrm).tm_t_coxreg module for multi-variable Cox regressions.tm_t_binary_outcome module.tm_t_events_patyear module: events rate adjusted for patient-year at risk table.grade_levels argument from tm_t_events_by_grade.tm_t_abnormality module.get_relabel_call and get_relabel_call2 in favor of teal.devel::get_relabel_call and teal.devel::get_anl_relabel_call.survfit, coxph, ztest; add confidence type, ties, percentiles to tm_t_tte.tm_t_events and tm_t_events_by_grade modules.tm_t_logistic module.tm_t_mmrm module.tm_t_summary_by and tm_t_events_summary.tm_g_forest_tte and tm_g_forest_rsp.tm_g_forest_rsp and tm_g_forest_tte.tm_t_events and tm_t_events_by_grade modules.CoxPH table in tm_g_km.teal.devel.teal.modules.clinical.tm_t_summarize_variables to tm_t_summary.teal::choices_selected() function instead of *_var and *_var_choices arguments.teal.tern.tern prefixed with an tm_.teal.oncology into two packages: tern and teal.oncology where tern contains all the analysis code and teal.oncology contains the teal modules that make the analysis function interactive with encodings and filtering. Find the tern package here: https://github.com/insightsengineering/tern.atezo SREPs.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.