v0.7.10

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.

What's Changed

• 683 fix test var labels changes@main by @Melkiades in #684
• 687 fix from formatters na str@main by @Melkiades in #690
• add param 'interacton_y' and 'interaction_item' to get the interactio… by @JiaLiu0001 in #688
• 692 Fix count_abnormal_by_worst_grade PARAM bug by @edelarua in #693
• 694 fix stats ancova old versions@main by @Melkiades in #695
• fix R CMD as-cran by @nikolas-burkoff in #699
• 698 Remove deprecated tern functions by @edelarua in #701
• 588 adding stratified newcombe@main by @Melkiades in #696
• Update check.yaml by @arkadiuszbeer in #685
• 705 Fix nestcolor CRAN check note by @edelarua in #706
• Generalize data handling in tests by @Melkiades in #704
• 707 Fix estimate_proportion tests by @edelarua in #708
• Add tests for prop_strat_wilson and prop_diff_strat_nc by @edelarua in #710
• 711 Add footnotes parameter to g_km by @edelarua in #714
• reintroducing Rdpack by @Melkiades in #715
• 586 Fill empty weights for prop_diff_strat_nc by @edelarua in #718
• Clean NEWS.md by @Melkiades in #721
• new tidyselect friendly by @pawelru in #722
• 723 Fix prop_diff_wald responders bug by @edelarua in #724
• 725 Fix h_ancova bug by @edelarua in #726
• [skip vbump] Release for version 0.7.10 by @insights-engineering-bot in #727

Full Changelog: v0.7.9...v0.7.10