Reorganize and group defaults for stats and their default formats/lab…

…els -> addition of auto for DMT01 (#1051)

Fixes #994 (for now)

Still todo:

- [x] tests for filtering
- [x] Examples
- [x] Evaluate the effect of having a list instead of a character vector
(it was the second, I am more inclined towards first)
- [x] start deprecation of `summary_formats`, `summary_labels`
- [x] discuss: consider changes in `summary_custom` (to discuss with
@edelarua)
- [x] wontdo: replace it within `count_occurences` and
`summarize_num_patients` (once reworked, wont do for now)
- [x] wontdo: consider using automatic function name getter for calling
function (related to previous. Not necessary until reworked)
- [x] wontdo: start deprecating other defaults (not related for now)

---------

Signed-off-by: Davide Garolini <dgarolini@gmail.com>
Signed-off-by: Davide Garolini <davide.garolini@roche.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

DESCRIPTION

@@ -148,14 +148,14 @@ 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'
     'survival_time.R'
     'survival_timepoint.R'
     'utils.R'
     'utils_checkmate.R'
+    'utils_default_stats_formats_labels.R'
     'utils_factor.R'
     'utils_grid.R'
     'utils_rtables.R'

NAMESPACE

@@ -1,7 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(a_summary,default)
-S3method(a_summary,numeric)
 S3method(as.rtable,data.frame)
 S3method(h_coxreg_inter_effect,character)
 S3method(h_coxreg_inter_effect,factor)
@@ -113,6 +111,7 @@ export(fit_logistic)
 export(fit_rsp_step)
 export(fit_survival_step)
 export(forest_viewport)
+export(format_auto)
 export(format_count_fraction)
 export(format_count_fraction_fixed_dp)
 export(format_extreme_values)
@@ -128,7 +127,10 @@ export(g_km)
 export(g_lineplot)
 export(g_step)
 export(g_waterfall)
+export(get_formats_from_stats)
+export(get_labels_from_stats)
 export(get_smooths)
+export(get_stats)
 export(groups_list_to_df)
 export(h_adlb_worsen)
 export(h_adsl_adlb_merge_using_worst_flag)
@@ -278,6 +280,8 @@ export(tabulate_rsp_biomarkers)
 export(tabulate_rsp_subgroups)
 export(tabulate_survival_biomarkers)
 export(tabulate_survival_subgroups)
+export(tern_default_formats)
+export(tern_default_labels)
 export(test_proportion_diff)
 export(to_n)
 export(to_string_matrix)
@@ -300,6 +304,7 @@ importFrom(magrittr,"%>%")
 importFrom(methods,new)
 importFrom(rlang,.data)
 importFrom(stats,pchisq)
+importFrom(stats,setNames)
 importFrom(survival,Surv)
 importFrom(survival,coxph)
 importFrom(survival,strata)

NEWS.md

@@ -2,12 +2,22 @@
 ### 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.
 
 ### 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.
 
+### 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
 ### New Features
 * Added `stat_propdiff_ci` function to calculate proportion/risk difference and CI.