Refactor a_summary

DESCRIPTION

@@ -146,6 +146,7 @@ Collate:
     'summarize_glm_count.R'
     'summarize_num_patients.R'
     'summarize_patients_exposure_in_cols.R'
+    'summary_stats.R'
     'survival_biomarkers_subgroups.R'
     'survival_coxph_pairwise.R'
     'survival_duration_subgroups.R'

NAMESPACE

@@ -1,12 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(a_compare,character)
-S3method(a_compare,factor)
-S3method(a_compare,logical)
-S3method(a_compare,numeric)
-S3method(a_summary,character)
-S3method(a_summary,factor)
-S3method(a_summary,logical)
+S3method(a_summary,default)
 S3method(a_summary,numeric)
 S3method(as.rtable,data.frame)
 S3method(h_coxreg_inter_effect,character)
@@ -270,7 +264,9 @@ export(summarize_num_patients)
 export(summarize_occurrences_by_grade)
 export(summarize_patients_events_in_cols)
 export(summarize_patients_exposure_in_cols)
-export(summarize_vars)
+export(summary_custom)
+export(summary_formats)
+export(summary_labels)
 export(surv_time)
 export(surv_timepoint)
 export(tabulate_rsp_biomarkers)

NEWS.md

@@ -5,6 +5,14 @@
 * Fix bug in `analyze_vars_in_cols` when categorical data was used.
 * Removal of internal calls to `df_explicit_na`. Changes in `NA` values should happen externally to `tern` functions, depending on users' needs.
 
+### Enhancements
+* Refactored `a_summary` to no longer use helper function `create_afun_summary`. 
+* Refactored `summarize_vars` and `compare_vars` to use refactored `a_summary`.
+* Created new internal helper functions `ungroup_stats` to ungroup statistics calculated for factor variables, and `a_summary_internal` to perform calculations for `a_summary`.
+
+### 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 0.8.5
 
 ### Enhancements
@@ -13,9 +21,6 @@
 * 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
 
 ### Enhancements
@@ -24,6 +29,8 @@
 ### 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.

R/analyze_functions.R

@@ -32,7 +32,7 @@
 #'   leverage `analyze_colvars` to have the context split in rows and the analysis
 #'   methods in columns.
 #' * [summarize_change()]
-#' * [analyze_vars()]: formerly known as [summarize_vars()], it was renamed to reflect
+#' * [analyze_vars()]: formerly known as `summarize_vars()`, it was renamed to reflect
 #'   core function [rtables::analyze()].
 #' * [surv_time()]
 #' * [surv_timepoint()]