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Changelog

Source: NEWS.md

tern 0.9.4.9000

Enhancements

  • Added examples and tests for label_all parameter to extract_survival_biomarkers and extract_survival_subgroups.

Miscellaneous

  • Began deprecation of the unused label_all parameter to tabulate_survival_biomarkers and tabulate_survival_subgroups, with redirection to the same parameter in their associated extract_* functions.

tern 0.9.4

CRAN release: 2024-04-17

New Features

  • Added h_glm_negbin to h_glm_count to enable count data analysis using a negative binomial model.
  • Added argument grade_groups_only to count_occurrences_by_grade to allow users to only display rows for specified grade groups.
  • Added internal function df2gg that converts data.frame objects to ggplot objects.
  • Added functions control_surv_med_annot and control_coxph_annot to configure g_km annotation table sizes/positions.
  • Refactored g_km to output a ggplot object instead of a grob object.
  • Refactored g_forest to output a ggplot object instead of a grob object.

Enhancements

  • Default format for mean p-values (mean_pval) updated from "xx.xx" to "x.xxxx | (<0.0001)".

Bug Fixes

  • Fixed nested column split label overlay issue in rtable2gg to clean up appearance of text labels.
  • Fixed bug in s_ancova causing incorrect difference calculations for arm variables with irregular levels.
  • Fixed bug in format_count_fraction_fixed_dp that did not have the same print when the fraction was 1 (100%).
  • Fixed bug in g_lineplot causing default labels not to update according to specified control settings.
  • Fixed bug causing an error when automatic value formatting was applied to NA values.

Miscellaneous

  • Added function expect_snapshot_ggplot to test setup file to process plot snapshot tests and allow plot dimensions to be set.
  • Adapted to argument renames introduced in ggplot2 3.5.0.
  • Renamed individual_patient_plot.R to g_ipp.R.
  • Removed all instances of deprecated parameters time_unit_input, time_unit_output, na_level and indent_mod.
  • Removed deprecated functions summarize_vars, control_summarize_vars, a_compare, create_afun_summary, create_afun_compare, and summary_custom.
  • Removed vdiffr package from Suggests in DESCRIPTION file.
  • Began deprecation of the named element strat, to be renamed to strata, within the variables argument to h_rsp_to_logistic_variables, h_logistic_mult_cont_df, h_odds_ratio_subgroups_df, h_coxreg_mult_cont_df, h_coxph_subgroups_df, h_tbl_coxph_pairwise, extract_rsp_biomarkers, extract_rsp_subgroups, extract_survival_biomarkers, and extract_survival_subgroups.
  • Began deprecation of the strat argument to s_coxph_pairwise and replaced it with the strata argument.
  • Began deprecation of the forest_grob, forest_dot_line, forest_viewport, vp_forest_table_part, and grid.forest functions.
  • Began deprecation of no longer used Kaplan-Meier helper functions h_ggkm, h_decompose_gg, h_km_layout, h_grob_tbl_at_risk, h_grob_median_surv, h_grob_y_annot, and h_grob_coxph.
  • Began deprecation of grob/grid related functions stack_grobs, arrange_grobs, and draw_grob which are no longer used in tern.

tern 0.9.3

CRAN release: 2023-12-08

New Features

  • Added ref_group_position function to place the reference group facet last, first or at a certain position.
  • Added keep_level_order split function to retain original order of levels in a split.
  • Added level_order split function to reorder manually the levels.
  • Added function get_indents_from_stats to format and return indent modifiers for a given set of statistics.
  • Added internal utility function apply_auto_formatting to check for "auto" formats and replace them with implementation of format_auto in analyze functions.
  • Added utility function labels_use_control to modify labels with control specifications.
  • Added list containing default statistics for each method group, tern_default_stats.
  • Added summarize function version of count_occurrences analyze function, summarize_occurrences.
  • Added referential footnotes to surv_time for censored range observations, controlled via the ref_fn_censor parameter.
  • Added helper function h_adlb_abnormal_by_worst_grade to prepare ADLB data to use as input in count_abnormal_by_worst_grade.
  • Added s_bland_altman function to assess agreement between two numerical vectors.
  • Added function rtable2gg that converts rtable objects to ggplot objects.
  • Added helper function to set default na_str globally with set_default_na_str() and added default_na_str() for all interested functions.

Enhancements

  • Added ref_group_coxph parameter to g_km to specify the reference group used for pairwise Cox-PH calculations when annot_coxph = TRUE.
  • Added annot_coxph_ref_lbls parameter to g_km to enable printing the reference group in table labels when annot_coxph = TRUE.
  • Added x_lab parameter to g_lineplot to customize x-axis label.
  • Remove 25% padding of y-axis in g_lineplot.
  • Added support for creating multiple risk difference columns, each comparing to a single comparison group. Multiple comparison groups can be specified as a vector via the arm_y argument.
  • Allowed numeric vector as count_by input in analyze_num_patients and summarize_num_patients.
  • Aligned plot and table vertically in g_lineplot.

Bug Fixes

  • Fixed bug in decorate_grob preventing text wrapping from accounting for font size.
  • Fixed implementation of na_str argument in all column-wise analysis and tabulation functions.

Miscellaneous

  • Specified minimal version of package dependencies.
  • Upgraded to_string_matrix to take into account widths and other printing parameters.

tern 0.9.2

New Features

  • Added the na_str argument to analyze & summarize_row_groups wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, summarize_occurrences_by_grade, summarize_patients_events_in_cols, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, h_tab_one_biomarker, estimate_incidence_rate, logistic_summary_by_flag, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, summarize_num_patients, analyze_num_patients, summarize_patients_exposure_in_cols, coxph_pairwise, tabulate_survival_subgroups, surv_time, and surv_timepoint.

Enhancements

  • Added formatting function format_count_fraction_lt10 for formatting count_fraction with special consideration when count is less than 10.
  • Updated s_summary.logical output for count_fraction when denominator is zero to display as NA instead of 0 in tables.
  • Updated analyze_vars_in_cols to allow character input to indicate whether nominal time point is post-dose or pre-dose when applying the 1/3 imputation rule.

Bug Fixes

  • Fixed bug in g_km causing an error when converting certain annotation width units.

Miscellaneous

  • Began deprecation of na_level argument in s_count_abnormal_by_baseline, a_summary, analyze_vars, analyze_vars_in_cols, compare_vars, h_map_for_count_abnormal, h_stack_by_baskets, summarize_colvars, a_coxreg, and summarize_coxreg and replaced it with the na_str argument.
  • strata and cohort_id parameters renamed to group_var and subject_var respectively in g_lineplot and control_lineplot_vars .

tern 0.9.1

New Features

  • Added imputation_rule function to apply imputation rule to data.
  • Added new format function format_sigfig to allow for numeric value formatting by a specified number of significant figures.
  • Added vectors containing default statistic formats and labels as tern_default_formats and tern_default_labels, respectively.
  • Added function get_stats to return methods from given statistical method groups.
  • Added function get_formats_from_stats to return formats and get_labels_from_stats to return labels for a given set of statistics.
  • Added "auto" option for .formats. It uses format_auto to determine automatically the number of digits.
  • Added title argument to h_grob_tbl_at_risk and annot_at_risk_title argument to g_km and h_km_layout which allows user to add “Patients at Risk” title to Kaplan-Meier at risk annotation table.

Enhancements

  • Refactored tabulate_rsp_subgroups to pass sanitation checks by preventing creation of degenerate subtables.
  • Updated analyze_vars_in_cols to use caching, allow implementation of imputation rule via the imp_rule argument, and allow user to specify cell alignment via the .aligns argument.
  • Updated add_rowcounts to allow addition of row counts from alt_counts_df using the alt_counts argument.
  • Added gp argument to g_forest to control graphical parameters such as font size.

Miscellaneous

  • Grouped functions relating to valid method names and their default formats and labels into new source file utils_defaults_handling.R.
  • Started deprecation of summary_custom() and a_summary() as a S3 method.
  • Renamed statistical method for p-value in the discrete case to pval_counts.
  • Removed a_summary_internal() in favor of only one main a_summary().

tern 0.9.0

CRAN release: 2023-09-01

New Features

  • Added stat_propdiff_ci function to calculate proportion/risk difference and CI.
  • Added risk difference column functionality via the riskdiff argument to functions count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, analyze_num_patients, and summarize_num_patients.

Enhancements

  • Refactored the function a_summary to no longer use the helper function create_afun_summary.
  • Refactored functions summarize_vars and compare_vars to use the refactored a_summary function.
  • Created new internal helper functions ungroup_stats to ungroup statistics calculated for factor variables, and a_summary_internal to perform calculations for a_summary.

Bug Fixes

  • Fixed bug in s_count_occurrences_by_grade so that “missing” grade always appears as the final level.
  • Fixed bug in analyze_vars_in_cols when categorical data was used.
  • Fixed bug in s_count_occurrences_by_grade so that levels are not relabeled when reordering to account for “missing” grades.

Miscellaneous

  • Fixed swapped descriptions for the .N_row and .N_col parameters.
  • Removed internal calls to df_explicit_na. Changes in NA values should happen externally to tern functions, depending on users’ needs.
  • Reinstated correct soft deprecation for create_afun_summary and create_afun_compare.

tern 0.8.5

Enhancements

  • Added ylim argument to g_km to allow the user to set custom limits for the y-axis.
  • Added assertion to g_km which checks whether there is one arm present in the data when annot_coxph is true.
  • Added flag_labels argument to s_count_patients_with_flags to enable more label handling options in count_patients_by_flags.
  • Added the nested argument to analyze wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, estimate_incidence_rate, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, analyze_num_patients, coxph_pairwise, surv_time, and surv_timepoint.

Miscellaneous

  • Started deprecation cycle for summarize_vars and control_summarize_vars. Renamed into analyze_vars and control_analyze_vars to reflect underlying rtables machinery while keeping backward compatibility with aliases.

tern 0.8.4

CRAN release: 2023-06-27

Enhancements

  • Added method for character class to h_coxreg_inter_effect enabling character covariates in summarize_coxreg.

Miscellaneous

  • Began deprecation of time_unit_input and time_unit_output arguments and replaced them with the input_time_unit and num_pt_year, respectively, in control_incidence_rate.
  • Removed deprecated pairwise function.
  • Deprecated a_compare and replaced it with a_summary with argument compare = TRUE.
  • Deprecated helper functions create_afun_summary and create_afun_compare which are no longer used by a_summary and a_compare respectively.

Bug Fixes

  • Fixed long double assertion check in sum(weights) for M1mac installation.

tern 0.8.3

CRAN release: 2023-06-19

Enhancements

  • Added explicit zero counts to g_km plot “at risk” annotation tables.
  • Added a flag for total level split in analyze_patients_exposure_in_cols.
  • Implemented .indent_mods argument in functions h_tab_one_biomarker, h_tab_rsp_one_biomarker, h_tab_surv_one_biomarker, summarize_logistic, logistic_summary_by_flag, tabulate_rsp_biomarkers, a_coxreg, summarize_coxreg, tabulate_survival_biomarkers, surv_time, surv_timepoint, and cfun_by_flag.
  • Updated summarize_coxreg to print covariates in data rows for univariate Cox regression with no interactions and content rows otherwise.
  • Removed “baseline status” text from d_count_abnormal_by_baseline labels.
  • Improved default sizing of annotation tables in g_km and added dynamic scaling of the surv_med and coxph annotation tables, with customization via the width_annots argument.

Bug Fixes

  • Fixed bug in split_text_grob preventing titles and footnotes from being properly formatted and printed by decorate_grob.
  • Fixed bug in g_lineplot preventing the addition of lines to the plot when midpoint statistic calculations result in NA value(s).
  • Fixed tern:::tidy.glm formals to respect broom:::tidy.default formals.

Miscellaneous

  • Updated README to include installation instructions for CRAN.
  • Remove examples for unexported functions.
  • Export functions has_count_in_cols, has_counts_difference, combine_counts, h_tab_rsp_one_biomarker, arrange_grobs, a_count_patients_sum_exposure, a_coxreg, groups_list_to_df, forest_viewport.
  • Updated README to include installation instructions for CRAN.
  • Began deprecation of indent_mod argument and replaced it with the .indent_mods argument in summarize_num_patients and analyze_num_patients.

tern 0.8.2

Breaking Changes

  • Refactored s_coxreg and summarize_coxregto work with new analysis function a_coxreg.

Enhancements

  • Added section_div and na_level arguments to summarize_vars.
  • Added median_range as a numeric variable statistic option for summarize_vars.
  • Corrected ordering of factor levels by d_onco_rsp_label.
  • Added new “Analyze Functions”, “Summarize Functions”, and “Analyze Functions on Columns” overview pages.
  • Consolidated all KM plot documentation within the g_km function.
  • Added a_count_patients_sum_exposure for summarize_patients_exposure_in_cols and new analyze function analyze_patients_exposure_in_cols.
  • Added more informative error when the user selects an invalid method for unstratified analyses in s_proportion_diff.
  • Updated s_summary and s_compare to allow NA values in input variables. For factor variables with NAs, if na.rm = FALSE an explicit NA level will be automatically added. na.rm = TRUE will also consider "<Missing>" values and exclude them.
  • Updated purpose of na_level parameter in s_summary and s_compare to align with other tern functions. Instead of being a string to consider as NA when setting na.rm = TRUE, it now defines a string to print in place of NA values in the output table.

Bug Fixes

  • Fixed missing label for TRTEDTM in tern datasets.
  • Fixed improper implementation of na_level argument in summarize_vars preventing it from having an effect.

Miscellaneous

  • Implemented the lubridate package for date variables in tern datasets.
  • Organized .gitignore and .Rbuildignore files.
  • Removed deprecated footnotes functions and all related files.
  • Started deprecation cycle for pairwise function.
  • Moved count_patients_with_flags functions from count_patients_with_event.R to count_patients_with_flags.R.

tern 0.8.0

Enhancements

  • Added summarize_glm_count function to analyze count data using a linear model.
  • Added legend to g_step.
  • Added formatting functions format_fraction_fixed_dp and format_count_fraction_fixed_dp with fixed single decimal place in percentages.
  • Added na_level and labelstr arguments to summarize_vars_in_cols.
  • Added analyze_num_patients to include summary at the beginning that does not repeat when paginating.
  • Added h_row_first_values function as a more general helper function to retrieve first values from specific rows.
  • Added option to remove "(n)" suffix from unique_count labels for s_num_patients.
  • Added options to g_km to annotate with statistics (annot_stats) and add corresponding vertical lines (annot_stats_lines).

Bug Fixes

  • Fixed bug causing incorrect ordering of numeric grade levels when missing grades are present in s_count_occurrences_by_grade.
  • Refactored summarize_vars_in_cols to work with pagination machinery.
  • Fixed bug to allow passing of conf_level argument to emmeans::contrast() in s_ancova.
  • Fixed bugs in rtables_access.R caused by not checking for specific combinations (also the standard values that were never used) of column indices and names.
  • Fixed single applicable record bug in count_abnormal_by_grade.
  • Fixed bug in add_rowcounts that caused all row count row values to count as zero.
  • Fixed bug in h_col_indices causing an error when pruning with combination columns.
  • Fixed bug in test_proportion_diff missing argument for var_labels.

Documentation and Tests

  • Added more tests to increase code coverage.
  • Created separate documentation files for functions in different sections of pkgdown reference.
  • Created separate .R files for logistic regression and cox regression helper functions.
  • Fixed table tests using analyze_num_patients to generate an initial summary so there is no repetition when paginating.
  • Updated tests to use testthat 3rd edition and replaced applicable tests with snapshot testing.
  • Updated summarize_ancova examples to use iris dataset instead of scda data.
  • Created vignette which saves cached synthetic CDISC dataset files to the data/ folder and generated cached synthetic datasets.
  • Updated all examples/tests to use datasets from the data/ folder instead of scda datasets.
  • Removed all template tests from tern. These tests are in internal repo scda.test.

Miscellaneous

  • Renamed summarize_vars_in_cols to analyze_vars_in_cols to reflect the appropriate analyze logic.
  • Removed redundant summary_in_cols helper functions.
  • Exported function format_xx.
  • Replaced deprecated ggplot2 functions/arguments to fix warnings.
  • Replaced deprecated function forcats::fct_explicit_na with forcats::fct_na_value_to_level.
  • Removed deprecated wrap_text function and related files.
  • Started deprecation cycle for footnotes functions.

tern 0.7.10

New Features

  • Added stratified Newcombe and stratified Wilson statistics to estimate_proportion and estimate_proportion_diff with relative tests.
  • Added stat_mean_pval, a new summary statistic to calculate the p-value of the mean.
  • Added statistic mean_se (mean with standard error) for summarize_variables and related functions.
  • Introduced again Rdpack for references.

Enhancements

  • Redesign of data handling in tests by removing repetitive data loads and library calls.
  • Added DescTools::BinomDiffCI function within tern.
  • Added new parameter to summarize_logistic to specify which pivoted value to use during analysis.
  • Updated s_coxph_pairwise to generate log-rank p-value using original log-rank test instead of Cox Proportional-Hazards Model.
  • Implemented nestcolor in all examples by adapting g_km, g_ipp, g_waterfall, g_step, g_lineplot, and g_forest.
  • Added parameters interaction_y and interaction_item in ANCOVA to make the interaction calculations available.
  • Added new parameter footnotes to add footnotes to g_km.

Migration from assertthat to checkmate

  • Implemented checkmate::assert_vector, checkmate::assert_set_equal, and checkmate::assert_int to check vector type, length, and values.
  • Replaced with standard assertions from checkmate the following functions: all_elements_in_ref, is_df_with_nlevels_factor, is_df_with_no_na_level, is_proportion_vector, is_quantiles_vector, is_character_or_factor, is_nonnegative_count, is_valid_character, assert_character_or_factor, assert_equal_length and has_tabletree_colnames.
  • Modified is_proportion, is_equal_length, is_df_with_no_na_level, is_df_with_nlevels_factor, is_variables, is_df_with_variables, is_df_with_factors, is_valid_factor to use assertion logic.
  • Added more verbose warnings from as_factor_keep_attributes.
  • Made assert_df_with_factors and assert_proportion_value internal functions.
  • Renamed assertthat.R and test-assertthat.R to utils_checkmate.R and test-utils_checkmate.R.

Documentation and NAMESPACE Polishing

  • Added stable badges for:
    • count_abnormal_by_marked (reference to abnormal_by_marked), count_abnormal_lab_worsen_by_baseline and h_adlb_worsen (reference to abnormal_by_worst_grade_worsen_from_baseline), count_abnormal_by_worst_grade (reference to abnormal_by_worst_grade), to_string_matrix, tidy.summary.coxph, tidy.step, surv_timepoint, (reference to survival_timepoint), surv_time (reference to survival_time), coxph_pairwise (reference to survival_coxph_pairwise), extract_survival_subgroups and tabulate_survival_subgroups (reference to survival_duration_subgroups), extract_survival_biomarkers and tabulate_survival_biomarkers (reference to survival_biomarkers_subgroups), control_summarize_vars, s_summary and a_summary (reference to summarize_variables) and kept the S3 method tree.
    • summarize_patients_exposure_in_cols, summarize_num_patients with s_num_patients, s_num_patients_content, summarize_num_patients.
    • count_cumulative, count_missed_doses, count_patients_events_in_cols, summarize_colvars, summarize_change, summarize_ancova,as.rtable, color_palette, add_footnotes.
    • (statistical function controls) control_coxreg, control_coxph, control_incidence_rate, control_lineplot_vars, control_surv_time, control_surv_timepoint, control_logisitic, control_step.
    • stat_mean_ci, stat_median_ci, split_cols_by_groups, explicit_na, sas_na, extract_rsp_subgroups, tabulate_rsp_subgroups, extract_rsp_biomarkers, tabulate_rsp_biomarkers, keep_rows, keep_content_rows, has_count_in_any_col, has_fraction_in_cols, has_fraction_in_any_col, has_fractions_difference, test_proportion_diff, pairwise, logistic_regression, estimate_incidence_rate, control_incidence_rate (reference to incidence_rate), cut_quantile_bins, estimate_multinomial_rsp, decorate_grob_set, extreme_format, fit_rsp_step, fit_survival_step, footnotes, footnotes-set, format_count_fraction, format_fraction_threshold, formatting_functions, format_fraction, combination_function (S4 method), compare_variables (S3 method), kaplan_meier.
  • Internal keywords added, export removed, _pkgdown.yml updated, and tern::: added for tests/examples/vignettes where present for the following functions:
    • (chain functions, reference to abnormal_by_marked) s_count_abnormal_by_marked, a_count_abnormal_by_marked.
    • (chain functions, reference to abnormal_by_worst_grade_worsen_from_baseline) a_count_abnormal_lab_worsen_by_baseline, s_count_abnormal_lab_worsen_by_baseline.
    • (chain functions, reference to abnormal_by_worst_grade) s_count_abnormal_by_worst_grade, a_count_abnormal_by_worst_grade.
    • (chain functions, reference to survival_timepoint) s_surv_timepoint, s_surv_timepoint_diff, a_surv_timepoint, a_surv_timepoint_diff.
    • (chain functions, reference to survival_time) s_surv_time, a_surv_time.
    • (chain functions, reference to survival_coxph_pairwise) s_coxph_pairwise, a_coxph_pairwise.
    • (chain functions, reference to survival_duration_subgroups) a_survival_subgroups.
    • (chain functions, reference to count_cumulative) s_count_cumulative, a_count_cumulative.
    • (chain functions, reference to count_missed_doses) s_count_nonmissing, s_count_missed_doses, a_count_missed_doses.
    • (chain functions, reference to count_patients_events_in_cols) s_count_patients_and_multiple_events, summarize_patients_events_in_cols.
    • (chain functions, reference to incidence_rate) s_incidence_rate, a_incidence_rate.
    • (cox regression helper) cox_regression_inter, decorate_grob_factory, draw_grob, estimate_coef.
    • summary_labels, summary_formats, s_count_patients_sum_exposure, a_change_from_baseline s_change_from_baseline, a_ancova, s_ancova, arrange_grobs, as_factor_keep_attributes, combine_levels, split_text_grob, groups_list_to_df, s_cox_multivariate, is_leaf_table, a_response_subgroups, range_noinf, has_count_in_cols, has_counts_difference, prop_chisq, prop_cmh, prop_schouten, prop_fisher, s_test_proportion_diff, a_test_proportion_diff, fct_discard, fct_explicit_na_if.

Bug Fixes

  • Fixed retrieval method of stats::ancova output due to version inconsistency.
  • Fixed tests to respect the new standard print for NA coming from rtables.
  • Fixed error in tests coming from changes in formatters::var_labels.
  • Fixed prop_diff functions to respect success responses (TRUE values).
  • Fixed error coming from comparing factors vector to characters vector.
  • Fixed empty vector exception for cut_quantile_bins.
  • Fixed exception error when empty strings are present in pivoted columns (rtables split functions)
  • Fixed bug in s_ancova causing an error when the first level of the arm factor is not the control arm.
  • Fixed bug in s_abnormal_by_worst_grade when there is one PARAM level.
  • Fixed bug in prop_diff_wald when selecting all responders, updated tests accordingly.
  • Fixed bug in h_ancova that caused an error when deselecting all covariates.

Miscellaneous

  • Added deprecated badge to g_mmrm.
  • Removed internal function calls in examples (tern:::) and added dontrun to internal function examples.
  • Removed warnings and messages to console occurring in examples and tests.
  • Deprecated functions color_palette and h_set_nest_theme in favor of nestcolor::color_palette and nestcolor::theme_nest, respectively.
  • Removed deprecated functions: color_palette, color_palette_core, h_set_nest_theme, s_cox_univariate.
  • Removed deprecated MMRM functions: fit_mmrm, g_mmrm_diagnostic, g_mmrm_lsmeans, as.rtable.mmrm, h_mmrm_fixed, h_mmrm_cov, h_mmrm_diagnostic, tidy.mmrm, s_mmrm_lsmeans, s_mmrm_lsmeans_single, summarize_lsmeans.
  • Renamed functions arm to study_arm and extract to extract_by_name.
  • Renamed rtables.R to utils_rtables.R.
  • Extracted cox_regression_inter into a separate file from cox_regression.
  • Renamed estimate_incidence_rate.R to incidence_rate.R to match the documentation grouping name.
  • Extracted control_incidence_rate into a separate file because it produces a separate documentation file.
  • Added @md and removed @order from incidence_rate.R. Modified examples accordingly.
  • Removed hyperlink from prop_schouten function documentation.
  • Exported draw_grob function.

tern 0.7.8

Fix

  • h_split_by_subgroups documentation warning fix for wrong placing of example block

Documentation and NAMESPACE polishing

  • Adopting the standard of badges for @description instead of every @descriptionIn function. Corrected accordingly summarize_variables_in_cols
  • Added stable badge for g_lineplot, g_step, g_waterfall, cox_regression, score_occurrences, add_rowcounts, odds_ratio, count_occurrences, count_occurrences_by_grade, explicit_na, df_explicit_na, count_patients_with_event, decorate_grob, combine_groups, append_varlabels, univariate, stack_grobs, count_abnormal (reference to abnormal), count_abnormal_by_baseline (reference to abnormal_by_baseline).
  • Internal keywords added, export removed, _pkgdown.yml polished and tern::: for tests, examples, and vignettes when present for the following functions:
    • (helper functions) h_format_row, h_map_for_count_abnormal
    • (utils functions) make_names, month2day, day2month empty_vector_if_na, aesi_label, n_available, format_xx, arm.
    • count_values_funs, prop_difference, combine_counts.
    • (chain functions) s_count_abnormal, a_count_abnormal.
    • (chain functions) s_count_abnormal_by_baseline, a_count_abnormal_by_baseline, d_count_abnormal_by_baseline.
  • Deprecated s_cox_univariate function has now deprecated badge.

Enhancements

  • Enhanced g_lineplot with table to automatically scale the table height and return a ggplot object.
  • Enhanced g_ipp with caption argument and adjust the position.
  • Enhanced prop_diff, tern function and related functions to be able to apply a continuity correction in the Newcombe method.
  • Enhanced summarize_numeric_in_columns and summarize_variables to allow factor/character summary and to be able to summarize the number of BLQs in AVALC from ADPC dataset.
  • Updated order of summarize variables stats in manual for order consistency.
  • Added a sum option to summarize_variables.
  • Use consistent color palette for plotting (stream by default).
  • Enhanced h_pkparam_sort function with argument key_var to allow data with different column names.

Miscellaneous

  • Updated test-table_aet02.R variant 12.
  • Changed the scda data version to ‘2022-02-28’.
  • Added a template to the pkgdown site.
  • Removed package dependencies of grDevices, stringr, and viridisLite.
  • Renaming summarize_numeric_in_columns to summarize_variables_in_columns.
  • Renaming summarize_vars_numeric_in_cols to summarize_vars_in_cols.
  • Fixed a bug where points on the g_lineplot plot were not connected when missing values.
  • Updated the package authors.

tern 0.7.7

Breaking changes

  • Move MMRM into a separate package tern.mmrm.

New features

  • Added h_pkparam_sort to order PK PARAM value based on the order of the dataset generated by d_pkparam().
  • Added d_pkparam to generate PK parameter map for sorting.

Enhancements

  • Changed the nudge_y argument of h_g_ipp to be dependent on the data, fixing an issue whereby the baseline labels were offset incorrectly.
  • Enhanced stat_mean_ci and s_summary.numeric to calculate the geometric mean with its confidence intervals.

Miscellaneous

  • Updated dependencies and internal adjustments after the rtables package refactor.
  • Removed with_label, var_labels, and var_labels<- to resolve conflict with the formatters package, a new dependency.
  • Added new “Introduction to tern” and “tern tabulation” vignettes.

tern 0.7.6

New features

  • Added h_map_for_count_abnormal to create the map used in trim_levels_to_map split function by calling this helper function. It supports two methods: one with all observed mapping, one with at least low limit above zero and at least one non missing high limit.
  • Added s_summary_numeric_in_cols and summarize_vars_numeric_in_cols functions to generate summary statistics in columns, mainly used for PK datasets.
  • Added five statistics to s_summary.numeric to use in s_summary_numeric_in_cols.

Enhancements

  • Enhanced functions tabulate_survival_subgroups and tabulate_rsp_subgroups (Survival Duration and Best Response analyses) to calculate N-s based on the records considered to create the model.
  • Enhanced the function estimate_proportion and related functions to be able to apply a continuity correction in the Wilson method.
  • Refactored count_abnormal_by_marked and related statistics and formatting functions to use a more efficient layout with .spl_context argument used for determining denominators and with trim_levels_to_map split function under split_rows_by to show the desired levels in the table. This is a breaking change.
  • Refactored count_abnormal_by_worst_grade and related statistics and formatting functions to use a more efficient layout with .spl_context argument used for determining denominators and with trim_levels_to_map split function under split_rows_by to show the desired levels in the table. This is a breaking change.
  • Refactored count_abnormal function and related statistics and formatting functions to use a more efficient layout with trim_levels_to_map split function under split_rows_by to show the desired levels in the table. Also updated abnormal argument to be able to consider more than one level for each direction. This is a breaking change.
  • Enhanced the function estimate_incidence_rate and related functions to consider the week as time unit for data input.

Bug fixes

  • Fixed bug in assertthat functions that output wrong data frame names and limited length of failure message outputs.

Miscellaneous

  • Removed dependency on utils.nest by using the checkmate and purrr packages for validation and moved get_free_cores and skip_if_too_deep functions from utils.nest into tern.

tern 0.7.5

New features

  • Added functions to estimate continuous biomarker effects across subgroups for survival and binary response endpoints, used to produce corresponding forest plots, see survival_biomarkers_subgroups and response_biomarkers_subgroups.
  • Added g_lineplot plot function, including new h_format_row helper function and control_lineplot_vars function. Removed g_summary_by.
  • Added new safety helper function h_stack_by_baskets to stack events in SMQ and/or CQ basket flag in ADAE data set.

Enhancements

  • Added a couple of new statistics to s_summary.numeric. Added names attribute to each element of the final list returned by the s_summary.numeric function. Added summary_formats and summary_labels helper functions.
  • Added option to also convert logical variables to factor variables in df_explicit_na.
  • Refactored h_append_grade_groups to improve its flexibility, robustness and clearness, and to make sure the result is ordering according to the order of grade_groups. Also, added remove_single argument which controls whether the elements of one-element grade groups are in the output or removed.
  • Added var_labels and show_labels arguments to count_occurrences and count_patients_with_flags to allow for creation of a title row.
  • Added na_level argument to count_abnormal_by_baseline.
  • Updated h_append_grade_groups to no longer fill-in empty grade groups with zeros.

Bug Fixes

  • Fixed prop_diff_cmh to handle edge case of no FALSE (or TRUE) responses.
  • Enhanced g_mmrm_diagnostic to improve error handling when data is not amenable to the Locally Weighted Scatterplot Smoothing.
  • Fixes in g_km:
    • Plot can now display any combination of the annotation tables for number of patients at risk, median survival time, and Cox-PH summary.
    • Function will return a warning instead of an error if the arm variable includes a single level and annot_coxph = TRUE.
    • Lines in the plot now start at time 0 and probability 1.
    • Category labels can include the equals sign.

Miscellaneous

  • Fixed day2month and month2day to work with NA data.
  • Added parameters for stat_mean_ci and stat_median_ci so that they may return different outputs.
  • Added functionality in h_row_counts to handle analysis rows with NULL cells.
  • Updated LICENCE and README with new package references.
  • Added error_on_lint: TRUE to .lintr.

tern 0.7.4

New features

  • Added new safety layout functions:
    • count_abnormal_by_marked tabulates marked laboratory abnormalities.
    • summarize_patients_exposure_in_cols tabulates patient counts and sum of exposure across all patients.

Enhancements

  • Enhanced MMRM-related functions for fitting models without arm variable.
  • Updated cox_regression to work without covariates. Also in case of interaction model summary, p-values for main effect coefficients are no longer displayed.
  • Descriptive statistics returned by summarize_vars now include quantiles. summarize_vars now accepts the control function control_summarize_vars to specify details about confidence level for mean and median and quantile details. The control argument replaces conf_level.
  • Added var_labels and show_labels arguments to count_occurrences_by_grade.
  • Changed indent argument in append_varlabels to accept non-negative integer to represent the indent space defined by user. Previous calls with Boolean indent will do an integer conversion and produce a warning.

Bug Fixes

  • Corrected tabulate_survival_subgroups and related survival forest plot functions to use total number of events, instead of observations, as default for scaling the symbol sizes in the plot. (The user might still use total number of observations manually if they wish to do so.)
  • Helper function h_adsl_adlb_merge_using_worst_flag will now impute BTOXGR for missing visits.

Miscellaneous

  • Deleted count_abnormal_by_worst_grade_by_baseline and its related statistic and analysis functions as a simpler design will create lab abnormality tables.
  • Switched data in examples to use scda instead of random.cdisc.data package.

tern 0.7.3

New Features

  • Added Subgroup Treatment Effect Pattern (STEP) model fitting functions fit_rsp_step and fit_survival_step, the corresponding tidy method tidy.step as well as the graph function g_step.
  • Added new layout function compare_vars which compares variables of different types between columns and produces a p-value for the comparison to the reference column. Function built on top of the summarize_vars functionality.
  • Added utility functions:
    • cut_quantile_bins cuts a numeric vector into quantile bins.
    • fct_collapse_only collapses levels of a factor and keeps those in the order provided.
    • fct_explicit_na_if inserts explicit missings in a factor based on a condition.
    • range_noinf is a kind of a wrapper function of base::range. It returns c(NA, NA) instead of c(-Inf, Inf) for zero-length data.

Enhancements

  • Cox regression via fit_coxreg_univar and fit_coxreg_multivar is now also possible without treatment arm. In the univariate case this means that it fits separate univariate models for the provided covariates and tabulation of corresponding effect estimates can later occur.
  • Added fraction in result returned by s_count_occurrences. It contains a list of numerators and denominators with one element per occurrence.
  • Updated sum_num_patients and count_occurrences for the result unique and count_fraction to return (0, 0) when input is empty.
  • Added a new argument groups_lists to extract_survival_subgroups, extract_rsp_subgroups and associated helper functions which allows to group factor levels of subgroup variables into manually defined groups, enhancing the flexibility of the resulting forest graphs.
  • Forest graph function g_forest now extracts default arguments from attributes of the input table produced by tabulate_rsp_subgroups and tabulate_survival_subgroups so that the user does not have to do this manually anymore.
  • In g_km:
    • Remove arm variable name from arm labels in plot legend and annotation tables.
    • Show symbol used to mark censored cases and match order of arm variable factor levels in the legend.
    • Display hazard ratio and its confidence interval to two decimal places.
    • Updated default position of hazard ratio table to stay on the left bottom corner but above x-axis.
    • Use arm value as strata name in when treatment arm variable has a single level.
  • Updated s_surv_time function to use a newly created function range_noinf instead of base::range.
  • New argument no_fillin_visits added to h_adsl_adlb_merge_using_worst_flag to specify excluded visits from the post-baseline worst toxicity grade output. Improved h_adsl_adlb_merge_using_worst_flag to include variables shared between adsl and adlb, along with PARAM, PARAMCD, ATOXGR, BTOXGR and optionally AVISIT, AVISITN when by_visit = TRUE. Prior output contained USUBJID, ARMCD, PARAMCD, ATOXGR, and BTOXGR.

Bug Fixes

  • Fix bug in s_surv_timepoint for cases when there are zero patients at risk.
  • Modified stat_median_ci function so that when passing empty var with empty name, no row names contain missing values error would show.

Miscellaneous

  • Deprecated s_cox_univariate function, use fit_coxreg_univar function instead.
  • Updated default formats of hr and hr_ci in a_coxph_pairwise and median in s_surv_time to align with STREAM.
  • Updated the pre-processing code in the files test-table_ttet01.R and test-table_dort01.R to make sure the analysis variable EVNT1 has both levels of the factor defined.
  • Improved error message when number of levels in a factor variable in a data frame is not as expected.

tern 0.7.2

  • Fixed column label internal test errors.

tern 0.7.1

  • New argument position_surv_med added to g_km to move position of the annotation table with median survival times.
  • Fixed bug in g_km related to the ignored arguments pch and size which were not passed on to helper function h_ggkm.
  • Updated xticks and max_time arguments in g_km for greater functionality. max_time added as an argument in h_xticks to allow this.
  • Fixed bug in prop_diff_cmh that led to NaN weighted proportion difference estimates and missing confidence intervals. Before this change, when including no patients from one treatment arm for at least one stratum the estimation did not lead to numeric results.
  • Fixed bug in prop_cmh giving an error in case of at least one stratum containing less than two observations.
  • New argument n_events added to estimate_incidence_rate.
  • New argument denom added to count_occurrences.
  • New arguments yval and ci_ribbon added to g_km.
  • Add new individual patient plot function g_ipp along with helpers h_g_ipp and h_set_nest_theme.
  • Fixed bug in count_patients_with_events, now shows zero counts without percentage.
  • Fixed bug in get_mmrm_lsmeans which did not allow MMRM analysis of more than 3000 observations.
  • Updated stat_mean_ci and stat_median_ci to handle edge cases with number of elements in input series equal to 1. For such cases, NA_real_ is now returned, instead of NA or +/-Inf for confidence interval (CI) estimates.
  • Rename n_lim argument of stat_mean_ci to n_min to better reflect its desired meaning.

tern 0.7.0

This version of tern introduces a major rewriting of tern due to the change to layout based tabulation in rtables. tern now does not build tables directly anymore, instead it provides analysis functions to build tables, see the examples. * Counting patients with abnormal values post-baseline with count_abnormal. * Counting patients with graded abnormal values with count_abnormal_by_worst_grade. * Counting patients with abnormal values by baseline status with count_abnormal_by_baseline. * Counting patients with missed doses with s_count_missed_doses and count_missed_doses. * Counting patients with event flags with count_patients_with_event and count_patients_with_flags. * Summarizing variables with summarize_vars (supports numeric, factor, character and logical variables). Note that factors need to have NAs converted to na_level before use. * Summarizing change from baseline with summarize_change. * Summarizing variables in columns with summarize_colvars. * Estimating difference for responder proportions with estimate_proportion_diff. * Estimating difference for Odds Ratio with estimate_odds_ratio. * Testing the difference in responder proportions with test_proportion_diff. * Estimating the responder proportion for the level of a factor with estimate_multinomial_response. * Fitting and tabulating the results of Cox regressions with fit_coxreg_univar, fit_coxreg_multivar and summarize_coxreg, respectively. * Pruning occurrence tables (or tables with counts and fractions) with flexible rules, see ?prune_occurrences for details. * Sorting occurrence tables using different options, see ?score_occurrences for details. * Fitting and tabulating MMRM models with fit_mmrm and as.rtable and summarize_lsmeans, see ?tabulate_mmrm for details. * Counting the number of unique and non-unique patients with summarize_num_patients. * Counting occurrences with count_occurrences. * Counting occurrences by grade with summarize_occurrences_by_grade and count_occurrences_by_grade. * Counting patients and events in columns with summarize_patients_events_in_cols. * Tabulating the binary outcome response by subgroup with extract_rsp_subgroups and tabulate_rsp_subgroups. * Tabulating the survival duration by subgroup with extract_survival_subgroups and tabulate_survival_subgroups.

tern 0.6.9

  • Removing not used imports.

tern 0.6.8

  • Improved handling of missing data in aggregation functions: a_mean_sd, a_median, a_n_true_and_freq, a_count, a_q1q3, a_iqr, a_range.
  • New default p-value method in s_test_proportion_diff: Chi-Squared Test with Schouten Correction.
  • Add new function t_contingency for contingency tables.
  • Renamed the class splitText to dynamicSplitText to resolve the name conflict with the package ggpubr.
  • Add rreplace_format for tabulation post-processing.
  • Add new tern function t_ancova to create ANCOVA tables, as well as corresponding elementary table function t_el_ancova and summary function s_ancova.
  • Add new tern function s_odds_ratio to estimate Odds Ratio of response between categories, as well as the corresponding elementary table function t_el_odds_ratio.
  • Added new CI methods (agresti-coull, jeffreys) for s_proportion.
  • Added new CI methods anderson-hauck and newcombe to s_proportion_diff.
  • Added new p-value methods (Fisher’s Exact, Chi-Squared Test with Schouten Correction) for s_test_proportion_diff.
  • The binary summary table function t_binary_outcome takes now lists (instead of character vectors) specified by the helper function control_binary_comparison as the arguments strat_analysis and unstrat_analysis. Odds Ratio estimates and CIs are now removable and included by default, similarly to the other subsections of the arm comparison analyses. Also added argument rsp_multinomial.
  • Add new table function t_el_multinomial_proportion.
  • Add new table function t_abn_shift.
  • Add new MMRM analysis function s_mmrm, as well as corresponding table functions t_mmrm_lsmeans, t_mmrm_cov, t_mmrm_diagnostic, t_mmrm_fixed, and plot functions g_mmrm_lsmeans, g_mmrm_diagnostic. The results of these match SAS results (up to numeric precision).
  • Deprecated old MMRM functions a_mmrm and t_mmrm (they give a deprecation warning but still work) to remove in the next release. The reason is that the results of these functions don’t match SAS results.
  • Fix bug in g_km related to numbers in patients at risk table to correct numbers for integer time-to-event variable inputs.

tern 0.6.7

  • For functions with row_by argument, inputs no longer require use of nested_by.
  • Add stat_mean_ci and stat_median_ci for error bars in ggplot2.
  • Add new tern function t_coxreg as single interface for diverse cox regression types.
  • Add compound table for binary endpoint: t_binary_endpoint and elementary functions: t_el_proportion, t_el_proportion_diff and t_el_test_proportion_diff. The supporting summary functions added are: s_proportion, s_adj_proportion_diff, s_proportion_diff and s_test_proportion_diff.
  • Added new tern function t_events_patyear to create event table adjusted person-years.
  • Added new tern function t_abnormality and the elementary table function t_el_abnormality.
  • Removed grade_levels argument from t_events_term_grade_id functions. Post-processing by reordering the leaves of the table tree creates a different ordering of rows if required. Creating a helper function will occur at a later time.
  • Added prune_zero_rows argument to t_events_per_term_grade_id and t_max_grade_per_id to not show rows of all zeros as they can clutter the visualization in the Shiny app and make it slower.
  • Fixed position of (N=xx) in t_summary_by output when summarizing numeric columns in parallel with compare_in_header.
  • Rename t_coxph to t_coxph_pairwise to reflect the model process, add details in documentation.
  • Remove test.nest dependency.
  • Keep column labels when splitting data into tree.

tern 0.6.6

  • Remove test.nest dependency.

tern 0.6.5

  • Change default option for denominator to be N in t_summary.
  • Fix IQR bug: IQR as Q3 minus Q1.
  • Add new function t_logistic for multi-variable logistic regression table.
  • Add new function df_explicit_na to replace NA by explicit values.
  • Added possibility in t_tte to specify confidence level independent for survfit, coxph, and ztest, see the manual.
  • Fixed bug in t_rsp of not showing p-value, odds ratio and CIs when strata_data is not NULL.
  • Added stratified analysis for t_forest_rsp and t_forest_tte, with footnotes in g_forest.
  • Added footnotes, footnotes<- and add_footnotes<- functions to deal with footnotes.
  • Added argument conf_int for confidence interval level to t_el_forest_rps, t_forest_rsp, t_el_forest_tte, t_forest_tte.
  • Added argument col_symbol_size to g_forest to control the relative size of symbols used in the plot.
  • Added s_coxph_pairwise function to perform pairwise testing, used by t_tte and t_coxph.
  • Added methods for t_count_true replacing t_summary_true.
  • Updated t_count_unique to create analysis subsets, added t_el_count_unique for vectors.
  • Fixed bug in t_events_term_id so that table sort order is by decreasing frequency instead of alphabetical.
  • Added function color_palette and a new nest color palette.

tern 0.6.4

  • Refactored after renaming functions in utils.nest.
  • Added event_type argument to t_events_per_term_grade_id.
  • Added one/two-arm t-test functions.
  • Improvements in t_summary_by.
  • Internal code refactoring.

tern 0.6.3

  • Added node S4 class to create trees:
    • For all related tree functions see the reference under trees.
  • Removed functions:
    • Moved all the label functions to rtables.
    • Deleted keys and keys<- functions.
  • New helper functions:
    • Exported tabulate_pairwise.
    • get_N, col_N_add_total, check_id.
    • na_as_level.
    • as_factor_keep_attributes.
    • r_by.
  • New TLGs:
    • Disposition elementary table t_el_disposition.
    • t_el_forest_tte, t_el_forest_rsp.
  • Changed Arguments:
    • All compound tables:
      • Added table_tree argument which returns a node object.
    • t_summary.numeric:
      • Added f_numeric to choose which statistics to calculate.
    • t_summary.factor:
      • denominator now also allows for omit if wanting to omit percentages.
    • t_summary_by:
      • Renamed by to row_by.
    • t_forest_rsp, t_forest_tte:
      • Changed functionality of group_data using row_by_list.
      • Removed na_omit_group.
    • t_count_unique:
      • Removed indent argument, use the indent function in rtables. instead

tern 0.6.2

  • Use cached data from random.cdisc.data to speed up testing.
  • Added t_summary.Date method.
  • Added save_join.

tern 0.6.1

  • Fixed colors in Kaplan-Meier Plot
  • Refactor of all functions to pass test.nest tests:
    • Changed width_row.names argument of g_forest function into width_row_names.
    • Changed censor.show argument of g_km function into censor_show.
    • Changed col.legend.title argument of g_waterfall function into col_legend_title.
    • Changed na.rm argument of t_count_unique function into na_rm.
    • Changed row.name argument of t_count_unique function into row_name.
    • Changed na.omit.group argument of t_forest_rsp function into na_omit_group.
    • Changed na.omit.group argument of t_forest_tte function into na_omit_group.
    • Changed row.name.TRUE and row.name.FALSE arguments of t_summary.logical into row_name_true and row_name_false respectively.
    • Rename splotTextGrob into split_text_grob.
    • Fix examples.
    • Refactor of internal functions code.

tern 0.6.0

  • Removed functions addTable, t_summarize_by_visit, t_summarize_variables.
  • Added t_summary_by function.
  • Refactor of g_km function, renamed kmGrob into kmCurveGrob.
  • Refactor t_events_* family of functions.
  • Updated examples.

tern 0.5.0.3

New TLGs
  • t_summary and methods for data.frame, numeric, logical, character, factor, and Date objects.
  • t_events_per_term_id, t_events_per_term_grade_id: Adverse Events & Concomitant Treatment Tables.
  • t_max_grade_per_id, t_count_unique, t_events_summary elementary tables used for the Adverse Events & Concomitant Treatment Tables.
  • g_waterfall: Horizontal Waterfall Plot.
New Helper Functions
  • decorate_grob, decorate_grob_set, decorate_grob_factory, splitTextGrob.
  • stack_grobs, arrange_grobs, draw_grob.
TLG changes
  • t_tte now shows two rows with ranges for event and censored times, respectively.
  • g_km works with one arm survfit objects.
  • In forest plot functions, added formatting to display extreme values to “>999.9”.
  • t_summarise_variables uses now n instead of N as a denominator for calculating percentages for factors by default.
  • t_rsp now works when all response values are TRUE or FALSE.
Deprecated Functions
  • Deprecated t_summarize_variables as t_summary is more powerful.
  • Replacing t_summarize_by_visit with t_summary_by will occur in an upcoming release.

tern 0.5.0

  • First version with harmonized analysis functions names and arguments.