Changelog

junco 0.1.7

CRAN release: 2026-10-13

Changed

Added "unique_fraction" as a new statistic supported by s_freq_j() and a_freq_j() (#519).
Added lowercase_words argument to string_to_title() to keep specified words lowercase (#524).
Added .cell_footnotes and .row_footnotes arguments to format_stats() (#470).
Removed s_proportion_diff_j() which was a wrapper around tern::s_proportion_diff(). The label and conf_level parameters moved to a_proportion_diff_j() (#442, #467).
Renamed internal functions s_rel_risk_val_j() and s_rel_risk_levii_j() to s_risk_diff_val_j() and s_risk_diff_levii_j() to correctly reflect that they compute risk difference (p1 - p2), not relative risk (p1 / p2) (#442).

Fixed

Fixed get_ref_info() to accept ref_path = NULL (#359).
Fixed junco_get_stats() to inherit any default stats from tern that are not explicitly defined in junco.
Fixed get_ref_info() so that is works in the presence of “overall” column (#332)
CRITICAL: hotfixed tt_to_tlgrtf() lost titles in certain cases (#373)
CRITICAL: hotfixed def_colwidths() when a column label is too long (#281)

Changed

Updated several analysis functions to use h_get_cur_trt_grp() (#295).
Replaced h_get_trtvar_refpath() with h_get_cur_trt_grp() (#295).
Updated get_ref_info() for matching column split paths (#295).
Added the new helper function factor_by_order() (#425).
Renamed in_ref_col() to in_column() and renamed its ref_path argument to col_path.
Updated in_ref_col() to accept ref_path = NULL (#404).
Added the new helper functions cur_col_split_path() and in_column() to support custom analysis functions that depend on the current column split context (#404).
Added a default value for the label argument in c_summary_subset_label().
Updated the documentation of a_summary_subset().
Refactored prepend_label_cell(); Only RowsVerticalSection is now supported.
Removed filter_df_prior_afun(), a_summary_diff_mvars(), a_summary_diff_mvars_label().
Removed formatters exports #317
Deprecate a_coxph_hr for tern:::a_coxph_pairwise() and s_coxph_hr for tern:::s_coxph_pairwise() #158
Reduce sampling of rbmi test to make tests shorter (#323)
Optimize shared tables in test-tt_to_tblfile (#323)
Changed forked h_ancova for the tern one
Add extra statistics to a_eair100_j and introduce scaling factor num_p_year (default = 100) (#361)
Removed ellipsis argument from a_freq_resp_var_j (#236)
Removed dplyr from junco and replaced by base R #201
Replaced assertthat by checkmate for consistency #201
Remove stringi from dependencies #201
Deprecate rbmi_analyse(), make_rbmi_cluster(), par_lapply() for rbmi equivalent functions #367
Deprecate a_kaplan_meier() for tern::a_surv_time()
Changed the label for range_with_cens_info from "Min, max" (junco) to "Min - Max (with censoring)" and the argument from lsmean_diffci to lsmean_diff_with_ci
Deprecate s_coxph_hr() for tern:::a_coxph_pairwise()
Changed stop message in a_freq_j() when label_map option is used in a rowsplit with no data on a character analysis var #386
Use new exported splv_extra and value_expr accessors (insightsengineering#1098)
Update new exported calls from rtables.officer
update documentation to roxygen2 8.0.0
Add extra statistics to a_eair100_j and introduce scaling factor num_p_year (default = 100) (#361)
Updated behavior of formatting functions jjcsformat_count_denom_fraction and jjcsformat_fraction_count_denom and introduce functions jjcsformat_count_denom_fraction_legacy and jjcsformat_fraction_count_denom_legacy for backward compatibility reasons (#450)
Updated insightsengineering urls to pharmaverse
Renamed and refactored postfun_eq5d into stats_in_cols_setup
Added factor assertion on .var in s_freq_j (#453).
Added assertions for the id argument in a_freq_j() and s_freq_j() (#424).

Added

Added jjcsformat_percentage() for formatting percentage values (#519).
Added a new analysis function a_combo_prop_diff_pval_mf() for proportions, risk differences, and risk difference tests with adaptive Mantel-Fleiss-based method selection (#517).
Added s_test_proportion_diff_mf() and a_test_proportion_diff_mf() adaptive test of stratified response-proportion differences using the Mantel–Fleiss criterion (#457).
Added s_proportion_diff_mf() and a_proportion_diff_mf() adaptive estimation of stratified response-proportion differences using the Mantel–Fleiss criterion (#456).
Added a_cond_proportion_j() which implements conditional method selection between Wald and Clopper-Pearson confidence intervals based on the number of responses and the denominator (and the method selection can either be done on cell level or on row level).
Added a_sum_ratio_j() analysis function for computing sum, unique-row sum, and their ratios against a denominator column.
Added strict_match() for uniquely matching a value in the odd or even positions of a character vector.
Added categorize_pval() for assigning p-values to validated, user-defined categories.
Added pool_rubin_scalar() and pool_z_stat() for pooling scalar estimates and z statistics across imputations.
Added resp_multiple_imputation() to impute missing binary responses across scenarios and pool CMH risk-difference and p-value results.
Updated documentation and examples for label_map in a_freq_j (#235)
Added tern methods for difference in proportions in a_freq_j and a_freq_resp_var_j : cmh_sato, cmh_mn, uncond_exact_diff (#389)
Added a_summary_j_with_exclude() to allow tern::a_summary() analyses to be skipped for selected row split levels.
Added a_summarize_mmrm_with_exclude() to allow MMRM summaries to be skipped for selected row split levels.
Added rightside() to extract the right-hand side of a formula as a scalar character value.
Added a_three_tier() as extension to a_two_tier().
Added formatting function format_sigfig_j() as alternative to tern::format_sigfig(). (#436)
Added new standard column structure functions: make_multicomp_splfun(), grouped_cols_w_diffs(), grouped_cols_w_subgrps(), shift_tbl_col_struct(), and some_v_all_col_struct().
Added varying decimal precision utility functions fmt_spec_single_d, fmt_spec_df_d, fmt_spec_var_d. (#474)
Added utility functions get_fmt_details and compare_fmt_specs for reviewing format specification objects.

0.1.6 - 2026-05-05 (CRAN release)

Fixed

Fixed s_kaplan_meier() range censoring indicator handling to no longer produce NA values in the output when either all subjects are censored or none are censored.
Aligned a_freq_resp_var_j() with a_freq_j() by adding .formats and na_str parameters to allow user customization of output formatting and NA string representation (#67).
Fixed the hanging indent in the first column of the body of the table (#138)
Export leftside(), postfun_eq5d ac_blank_line and tt_to_tblfile
Minor bugfix in DOCX exporter when calculating the number of pages (#188)
Fixed tt_to_flextable_j() to have correct left-indentation in header col 1 (#171) and footer first line starting with newline (#171)
Fixed relative risk difference derivations for combined column facets in a_freq_j(), a_freq_resp_var_j() and a_eair100_j() (#195)
Fixed calculation of ‘reduce_first_col_indentation’ and section break positions in insert_keepNext_vertical_pagination() (#218)
Fixed the little gaps in neighboring spanning headers in the docx exporter (#216)
Fixed blank pages happening at the end of the docx (#177)
DOCX exporter fixed watermark location in case of listings
DOCX exporter updated table border width from 0.75 to 0.875 inches
DOCX exporter when having vertical pagination in tables or listings, fixed the rows misalignment from page 2 and below compared to RTF
Fixed bug in s_summarize_desc_j() when applied to almost constant data due to behavior from t.test.default() (#257)
tt_to_tlgrtf() now is passing vectorized colwidths when exporting ‘allparts’ to match the colwidths of the individual parts (#225)

Changed

Updated c_summary_subset_label(): removed .spl_context argument and renamed subset_expr to filter_expr.
Renamed a_summary_j() to a_summary_subset() and updated its purpose, implementation, and arguments.
Added new stats/labels/formats/indents to junco_utils_default_stats_formats_labels.r file.
Renamed s_diff_mean_ci() to s_diff_means(), and added new statistics to s_diff_means().
Moved safe_t_test() from a_summarize_aval_chg_diff.R to a new file safe_t_test.R,
Moved add_blank_line_rcells() from s_functions.R to blank_line.R.
changed return value n for s_ancova_j into n_fit, to differentiate between these two statistics for combined function s_summarize_ancova_j() (#117)
added default label for median_range “Median (min, max)” in junco_default_labels_start
changed label from “experimental” to “stable” for default_stats_formats_labels
refactored functions tt_to_flextable_j() and export_as_docx_j()
created generic wrapper function export_TLG_as_docx(), which now calls export_as_docx_j() and export_graph_as_docx() (#173)
Functions export_as_docx_j() and export_graph_as_docx() still exist but are now internal, i.e. not exported
updated vignette to explain correctly how to insert newlines in the headers of Tables and Listings (#179)
“watermark” argument in the docx exporter is now a String instead of a Boolean (#181)
faster docx unit tests (#197)
LS means tabulation uses very slightly updated column header (no blanks around the hyphen in “Testing-Reference”)
Bump flextable and remove the skip() units tests (#193)
Update colwidths tests to derive values
Fix old TODOs in tests
docx exporter added missing defaults (#186)
Changed all snapshot tests to cran = TRUE
Footnotes in docx and RTF outputs are now 1 table row/cell (#285)
removed label “experimental” for theme_docx_default_j, tt_to_flextable_j and export_TLG_as_docx

Added

Added a_diff_means(), which is based on the existing s_diff_means().
Added multi-comparator functionality (#271)
Hotfix: Added several new functions for creating the Vital Sign tables for core and clinpharm: a_summary_diff_mvars(), a_summary_j(), c_summary_subset_label(), filter_df_prior_afun(), prepend_label_cell(), s_diff_mean_ci(), s_summary_diff(), safe_t_test() (#304).
Added option to perform a_summarize_ancova_j in a layout with a combined column facet (#117) + slight change in return value for s_ancova_j(), now we have n_fit instead of n returned
Added option to switch on/off the export of the csv in both tt_to_tlgrtf() and export_as_docx_j()
Added option to specify the output folder for the csv
Added argument ‘validate’ to export_TLG_as_docx() and tt_to_flextable_j() (#213)
Added “watermark” argument in the docx exporter for Figures (#181)
Added argument mult_adj_emmeans in fit_mmrm_j() to enable (single-step or step-down) Dunnett multiplicity adjustment for LS means contrasts (p-values and confidence intervals) for more than one experimental arm within visits.
Added option for subgroup variable in the vars argument of fit_mmrm_j() to enable fitting an overall MMRM with subgroup interaction terms.
Export helpers for LS means tabulation: lsmeans_wide_cfun, lsmeans_wide_first_split_fun_fct, lsmeans_wide_second_split_fun_fct
Added lifecycle to suggests

0.1.5 - 2026-03-03 (minor hotfix release)

Added and Removed

Added new behavior for nested countsource in h_a_freq_dataprep altdf_subset (#200)

0.1.4 - 2026-02-02 (minor hotfix release)

Fixed

“caption” paragraph style in the docx exporter is now handled by flextable (#182)
Fixed tt_to_tlgrtf(), when exporting an empty listing do not lose Title and Footers
Fixed tt_to_tlgrtf() argument label_width_ins which was not applying the change in the row label column width (#166).

Changed

Reinstate rbmi as dependency

0.1.3 - 2026-01-12 (minor hotfix release)

Changed

Address CRAN NOTES.

0.1.2 - 2025-12-10

Added and Removed

Add a_two_tier() analysis function
Add a_maxlev() to be able to calculate count and percentage of the maximum level of an ordered factor per subject
Remove brackets_to_rtf()
Export rbmi_pool() #22
Add functionality to a_freq_j() to process val = NULL from levels specified in label_map, as well as the modified version a_freq_j_with_exclude() that allows to exclude the analysis from specified row splits. #95
Add a_cmhrms_j() to support p-value from CMH row mean score test, as well as the modified version a_cmhrms_j_with_exclude() that allows to exclude the analysis from specified row splits. #97
Added standard error (SE) column for each treatment arm’s least square (LS) means estimate to the summarize_lsmeans_wide() layout.
Added the internal function do_exclude_split() to facilitate the exclusion of specified row splits from analysis functions.
Remove some unused functions (jj_uc_map, postfun_cog, column_N, non_blank_sentinel, null_fn, unicodify
Add extra check for existence of .alt_df_full when layout has risk difference column and a row-split (h_create_alt_df) #120.
Add docx exporter for Tables, Listings and Figures.
Add alignments argument in tt_to_tlgrtf()
Removed s_test_proportion_diff() and corresponding helper functions, as they are now available as needed in the tern package.
Added cmh_sato and cmh_mn (Cochran-Mantel-Haenszel stratified proportion difference estimation with Sato variance and Miettinen Nurminen method, respectively) method options to the s_proportion_diff_j() function.
Added formatting function round type (#76)
Fixed bug in s_summarize_desc_j function to handle sparse data (zero variance) cases (#78)

0.1.1 - 2025-07-28

Added

First release of the junco package for Table and Listing (TL) Reporting
Functions to produce tables and listings in R
Built on the rtables package framework
Integration with formatters, rtables, tidytlg, and tern packages

Changed

Initial CRAN release

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.