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"unique_fraction" as a new statistic supported by
s_freq_j() and a_freq_j() (#519).lowercase_words argument to
string_to_title() to keep specified words lowercase
(#524)..cell_footnotes and .row_footnotes
arguments to format_stats() (#470).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).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).get_ref_info() to accept ref_path = NULL
(#359).junco_get_stats() to inherit any default stats
from tern that are not explicitly defined in junco.get_ref_info() so that is works in the presence
of “overall” column (#332)tt_to_tlgrtf() lost titles in
certain cases (#373)def_colwidths() when a column label
is too long (#281)h_get_cur_trt_grp() (#295).h_get_trtvar_refpath() with
h_get_cur_trt_grp() (#295).get_ref_info() for matching column split paths
(#295).factor_by_order()
(#425).in_ref_col() to in_column() and
renamed its ref_path argument to
col_path.in_ref_col() to accept
ref_path = NULL (#404).cur_col_split_path() and
in_column() to support custom analysis functions that
depend on the current column split context (#404).label argument in
c_summary_subset_label().a_summary_subset().prepend_label_cell(); Only
RowsVerticalSection is now supported.filter_df_prior_afun(),
a_summary_diff_mvars(),
a_summary_diff_mvars_label().a_coxph_hr for
tern:::a_coxph_pairwise() and s_coxph_hr for
tern:::s_coxph_pairwise() #158rbmi test to make tests shorter
(#323)test-tt_to_tblfile
(#323)h_ancova for the tern
onea_eair100_j and introduce
scaling factor num_p_year (default = 100) (#361)a_freq_resp_var_j
(#236)dplyr from junco and replaced by
base R #201assertthat by checkmate for
consistency #201stringi from dependencies #201rbmi_analyse(),
make_rbmi_cluster(), par_lapply() for
rbmi equivalent functions #367a_kaplan_meier() for
tern::a_surv_time()range_with_cens_info from
"Min, max" (junco) to
"Min - Max (with censoring)" and the argument from
lsmean_diffci to lsmean_diff_with_cis_coxph_hr() for
tern:::a_coxph_pairwise()a_freq_j() when
label_map option is used in a rowsplit with no data on a
character analysis var #386roxygen2 8.0.0a_eair100_j and introduce
scaling factor num_p_year (default = 100) (#361)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)insightsengineering urls to
pharmaversepostfun_eq5d into
stats_in_cols_setup.var in s_freq_j
(#453).id argument in
a_freq_j() and s_freq_j() (#424).jjcsformat_percentage() for formatting percentage
values (#519).a_combo_prop_diff_pval_mf() for proportions, risk
differences, and risk difference tests with adaptive Mantel-Fleiss-based
method selection (#517).s_test_proportion_diff_mf() and
a_test_proportion_diff_mf() adaptive test of stratified
response-proportion differences using the Mantel–Fleiss criterion
(#457).s_proportion_diff_mf() and
a_proportion_diff_mf() adaptive estimation of stratified
response-proportion differences using the Mantel–Fleiss criterion
(#456).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).a_sum_ratio_j() analysis function for computing
sum, unique-row sum, and their ratios against a denominator column.strict_match() for uniquely matching a value in
the odd or even positions of a character vector.categorize_pval() for assigning p-values to
validated, user-defined categories.pool_rubin_scalar() and
pool_z_stat() for pooling scalar estimates and z statistics
across imputations.resp_multiple_imputation() to impute missing
binary responses across scenarios and pool CMH risk-difference and
p-value results.label_map in
a_freq_j (#235)tern methods for difference in proportions in
a_freq_j and a_freq_resp_var_j :
cmh_sato, cmh_mn,
uncond_exact_diff (#389)a_summary_j_with_exclude() to allow
tern::a_summary() analyses to be skipped for selected row
split levels.a_summarize_mmrm_with_exclude() to allow MMRM
summaries to be skipped for selected row split levels.rightside() to extract the right-hand side of a
formula as a scalar character value.a_three_tier() as extension to
a_two_tier().format_sigfig_j() as
alternative to tern::format_sigfig(). (#436)make_multicomp_splfun(),
grouped_cols_w_diffs(),
grouped_cols_w_subgrps(),
shift_tbl_col_struct(), and
some_v_all_col_struct().fmt_spec_single_d, fmt_spec_df_d,
fmt_spec_var_d. (#474)get_fmt_details and
compare_fmt_specs for reviewing format specification
objects.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.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).leftside(), postfun_eq5d
ac_blank_line and tt_to_tblfilett_to_flextable_j() to have correct
left-indentation in header col 1 (#171) and footer first line starting
with newline (#171)a_freq_j(), a_freq_resp_var_j() and
a_eair100_j() (#195)insert_keepNext_vertical_pagination()
(#218)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)c_summary_subset_label(): removed
.spl_context argument and renamed subset_expr
to filter_expr.a_summary_j() to
a_summary_subset() and updated its purpose, implementation,
and arguments.junco_utils_default_stats_formats_labels.r file.s_diff_mean_ci() to
s_diff_means(), and added new statistics to
s_diff_means().safe_t_test() from
a_summarize_aval_chg_diff.R to a new file
safe_t_test.R,add_blank_line_rcells() from
s_functions.R to blank_line.R.n for s_ancova_j into
n_fit, to differentiate between these two statistics for
combined function s_summarize_ancova_j() (#117)junco_default_labels_startdefault_stats_formats_labelstt_to_flextable_j() and
export_as_docx_j()export_TLG_as_docx(),
which now calls export_as_docx_j() and
export_graph_as_docx() (#173)export_as_docx_j() and
export_graph_as_docx() still exist but are now internal,
i.e. not exportedcran = TRUEtheme_docx_default_j,
tt_to_flextable_j and export_TLG_as_docxa_diff_means(), which is based on the existing
s_diff_means().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).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
returnedtt_to_tlgrtf() and export_as_docx_j()export_TLG_as_docx() and
tt_to_flextable_j() (#213)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.vars argument
of fit_mmrm_j() to enable fitting an overall MMRM with
subgroup interaction terms.lsmeans_wide_cfun,
lsmeans_wide_first_split_fun_fct,
lsmeans_wide_second_split_fun_fctlifecycle to suggestscountsource in
h_a_freq_dataprep altdf_subset (#200)tt_to_tlgrtf(), when exporting an empty listing
do not lose Title and Footerstt_to_tlgrtf() argument
label_width_ins which was not applying the change in the
row label column width (#166).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)
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.