Release v0.9.8 · insightsengineering/tern

Refactored 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(), coxph_pairwise(), estimate_multinomial_rsp(), estimate_proportion(), estimate_proportion_diff(), estimate_odds_ratio(), summarize_ancova(), summarize_glm_count(), summarize_num_patients(), surv_timepoint(), and test_proportion_diff() to work without make_afun().
Refactored afun_riskdiff(), count_occurrences(), count_occurrences_by_grade(), count_patients_with_event(), count_patients_with_flags(), count_values(), estimate_incidence_rate(), h_tab_one_biomarker(), summarize_change(), summarize_colvars(), summarize_patients_exposure_in_cols(), survival_time(), tabulate_rsp_subgroups(), tabulate_survival_subgroups(), tabulate_rsp_biomarkers(), and tabulate_survival_biomarkers() to align with new analysis function style.
Added geom_sd and geom_mean_sd to s_summary() as default available statistics.
Added denom parameter to estimate_proportion().
Added weights_emmeans argument to summarize_ancova().

Fixed bug in a_count_patients_with_flags() preventing select custom label/indentation formats from being applied.
Fixed bug in tabulate_rsp_subgroups() and tabulate_survival_subgroups() preventing the pct option from having an effect when adding a risk difference column.
Fixed bug with the order of .stats when adding custom statistical functions.
Fixed bug with multiple custom functions not being represented correctly as a list of output stats.

Began deprecation of the unused table_names argument to count_abnormal_lab_worsen_by_baseline().
Began deprecation of the unused h_split_param() function.
Began deprecation of the unused label_all parameter to tabulate_rsp_subgroups(), with redirection to the same parameter in extract_rsp_subgroups().
Began deprecation of the no longer used helper functions h_tab_one_biomarker(), h_tab_rsp_one_biomarker(), and h_tab_surv_one_biomarker().
Updated documentation to remove suggestions to use make_afun().
Added warnings for geom_mean statistical output.
Moved helper functions h_tab_rsp_one_biomarker() and h_tab_surv_one_biomarker() into h_biomarkers_subgroups.R.
Reorganized the utility documentation related to factors (utils_factor.R) into a single file.
Converted as_factor_keep_attributes() to an exported function.
Removed internal function ungroup_stats() and replaced its usage with the get_*_from_stats() functions.
Removed s_count_nonmissing() as it is a non-repeated small and internal function.

What's Changed

Fix label and indentation processors by @edelarua in #1379
Remove the ungroup_stats() function by @edelarua in #1385
Fix pct bug in tabulate_rsp_subgroups when risk difference column is added by @edelarua in #1387
Retire make_afun() - Batch 3 by @edelarua in #1389
Remove lookup-refs by @m7pr in #1395
Fix failed scheduled test by @shajoezhu in #1396
refactor geom sd and fix custom stat order by @Melkiades in #1393
Retire make_afun() - Batch 2 by @edelarua in #1392
Add in missing analysis function option for custom statistics by @edelarua in #1400
Retire make_afun() - Batch 4 by @edelarua in #1394
Refactor tabulate_*() functions and deprecate their helper functions by @edelarua in #1398
Refactor remaining analysis functions by @edelarua in #1401
Batch 1 by @Melkiades in #1403
Fix analysis function refactor bugs by @edelarua in #1406
upversion r min version, and survial depednecies by @shajoezhu in #1408
feature: denom addition to estimate_proportions() by @Melkiades in #1404
Update .revdeprefs.yaml by @shajoezhu in #1410
[821] Feature Request: Add weights option to ancova by @yurovska in #1412
v0.9.8 Release [skip vbump] by @edelarua in #1413

Full Changelog: v0.9.7...v0.9.8