Package index • junco

junco Analysis Functions

The following functions are the Analysis functions used used to create common table layouts.

column_stats(): Statistics within the column space
a_combo_prop_diff_pval_mf(): Combined Proportion, Risk Difference, and Risk Difference Test Analysis Function with Method Selection Based on the Mantel-Fleiss Criterion
s_eair100_levii_j() a_eair100_j(): Exposure-Adjusted Incidence Rate
s_diff_means() a_diff_means() stable: Difference in Means
a_freq_combos_j(): Analysis function count and percentage in column design controlled by combosdf
s_freq_j() a_freq_j() a_freq_j_with_exclude(): Analysis/statistical function for count and percentage in core columns and (optional) relative risk columns
a_freq_subcol_j(): Analysis function count and percentage with extra column-subsetting in selected columns (controlled by subcol_* arguments)
a_freq_resp_var_j(): Analysis Function for Response Variables
a_maxlev(): Calculate Count and Percentage of the Maximum Level of an Ordered Factor per Subject.
a_proportion_ci_factor(): Formatted Analysis Function For Proportion Confidence Interval for Factor
a_proportion_ci_logical(): Formatted Analysis Function For Proportion Confidence Interval for Logical
a_proportion_diff_mf() s_proportion_diff_mf() stable: Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion
a_test_proportion_diff_mf() s_test_proportion_diff_mf() stable: Test of Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion
a_summarize_aval_chg_diff_j(): Analysis function 3-column presentation
s_summarize_ex_j() a_summarize_ex_j(): Tabulation for Exposure Tables
s_summarize_mmrm() a_summarize_mmrm() a_summarize_mmrm_with_exclude() stable: Dynamic tabulation of MMRM results with tables
a_summary_j_with_exclude() stable: Wrappers Around tern::a_summary() with Row Split Exclusion
a_summary_subset() c_summary_subset_label() stable: Wrappers Around tern::a_summary() with Optional Subsetting and Labels
a_sum_ratio_j() stable: Analysis Function: Sum and Ratio of Sums
a_two_tier() a_three_tier(): Two Tier Analysis Function
analyze_values(): Shortcut Layout Function for Standard Continuous Variable Analysis
rbmi_ancova(): Analysis of Covariance
rbmi_ancova_single(): Implements an Analysis of Covariance (ANCOVA)
build_formula(): Building Model Formula
c_proportion_logical(): c_function for proportion of TRUE in logical vector
cmp_cfun(): Summary Analysis Function for Compliance Columns
cmp_post_fun() cmp_split_fun(): Split Function for Compliance Columns
a_cond_proportion_j() s_cond_proportion_j() d_cond_proportion_j() experimental: Conditional proportion with adaptive CI (exact vs. Wald)
find_missing_chg_after_avisit(): Helper for Finding AVISIT after which CHG are all Missing
fit_ancova(): ANCOVA Analysis
fit_mmrm_j(): MMRM Analysis
h_tidy_pool() s_rbmi_lsmeans() a_rbmi_lsmeans() stable: Tabulation of RBMI Results
tidy(<tern_model>) s_lsmeans() a_lsmeans() stable: Tabulation of Least Square Means Results
or_glm_j() or_clogit_j() or_cmh() stable: Helper functions for odds ratio estimation
rbmi_mmrm(): MMRM Analysis for Imputed Datasets
a_event_free() s_event_free(): Workaround statistics function to time point survival estimate with CI
a_odds_ratio_j() s_odds_ratio_j() stable: Odds ratio estimation
a_proportion_diff_j(): Proportion difference estimation
prop_post_fun() prop_split_fun(): Split Function for Proportion Analysis Columns
prop_ratio_cmh(): Relative Risk CMH Statistic
prop_table_afun(): Formatted Analysis Function for Proportion Analysis
a_relative_risk() s_relative_risk(): Relative risk estimation
resp01_a_comp_stat_factor(): Formatted Analysis Function for Comparative Statistic in Response Tables (RESP01)
resp01_a_comp_stat_logical(): Formatted Analysis Function for Comparative Statistic in Response Tables (RESP01)
resp01_acfun(): Formatted Analysis and Content Summary Function for Response Tables (RESP01)
resp01_counts_cfun(): Content Row Function for Counts of Subgroups in Response Tables (RESP01)
resp01_split_fun_fct(): Split Function Factory for the Response Tables (RESP01)
response_by_var(): Count denom fraction statistic
s_ancova_j(): Junco Extended ANCOVA Function
s_proportion_factor(): s_function for proportion of factor levels
s_proportion_logical(): s_function for proportion of TRUE in logical vector
a_summarize_ancova_j() s_summarize_ancova_j(): ANCOVA Summary Function
s_summary_diff() experimental: Descriptive Statistics for Univariate Data with Optional Reference Comparison
summarize_coxreg_multivar(): Layout Generating Function for TEFOS03 and Related Cox Regression Layouts
lsmeans_wide_first_split_fun_fct() lsmeans_wide_second_split_fun_fct() lsmeans_wide_cfun() summarize_lsmeans_wide(): Layout Generating Function for LS Means Wide Table Layouts
summarize_row_counts(): Layout Creating Function Adding Row Counts
rbmi_mmrm_single_info(): Extract Single Visit Information from a Fitted MMRM for Multiple Imputation Analysis
rbmi_pool(): Pool analysis results obtained from the imputed datasets
a_cmhrms_j() s_cmhrms_j() a_cmhrms_j_with_exclude(): Cochran-Mantel-Haenszel Row Mean Scores test
pool_rubin_scalar(): Pool a scalar estimate across imputations
pool_z_stat(): Pool z statistics across imputations
resp_multiple_imputation(): Calculate results across binary-imputation scenarios
a_test_proportion_diff() stable: Difference test for two proportions

junco Formatting Functions

The following functions are the junco formatting functions used to create common table layouts.

jjcsformat_xx() jjcsformat_pval_fct() jjcsformat_range_fct(): Utility for specifying custom formats
jjcs_num_formats(): Numeric Formatting Function
jjcsformat_cnt_den_fract_fct() jjcsformat_count_fraction() jjcsformat_count_denom_fraction() jjcsformat_count_denom_fraction_legacy() jjcsformat_fraction_count_denom() jjcsformat_fraction_count_denom_legacy(): Formatting functions for count and fraction, and for count denominator and fraction values
jjcsformat_fraction() experimental: Formatting function for percentage values
ac_blank_line(): Analysis and Content Summary Function Producing Blank Line
insert_blank_line(): Insertion of Blank Lines in a Layout
format_sigfig_j() modified_signif_j() experimental: Format numeric values by significant figures.
fmt_spec_single_d() fmt_spec_df_d() fmt_spec_var_d() junco_def_d_all junco_def_d_alt1 junco_def_d_alt2 experimental: Utilities for processing d-style string formatting specifications (eg "xx.dx")
get_fmt_details() compare_fmt_specs() experimental: Utilities for reviewing format specification objects

junco Sorting Functions and Pruning Functions

The following functions are the junco sorting and pruning functions used to create common table layouts.

bspt_pruner(): Pruning Function for pruning based on a fraction and/or a difference from the control arm
count_pruner(): Count Pruner
jj_complex_scorefun(): Complex Scoring Function
keep_non_null_rows(): Pruning Function to accommodate removal of completely NULL rows within a table
remove_rows(): Pruning function to remove specific rows of a table regardless of counts
safe_prune_table(): Safely Prune Table With Empty Table Message If Needed

junco Splitting Functions

The following functions are junco column spanning functions used to create common table layouts.

cond_rm_facets(): Conditional Removal of Facets
create_colspan_map(): Creation of Column Spanning Mapping Dataframe
create_colspan_var(): Creation of Column Spanning Variables
grouped_cols_w_diffs() grouped_cols_w_subgrps(): Standard Column Structure With Grouped Treatments and Difference Columns
shift_tbl_col_struct(): Create Column Structure for a J&J-Style Shift Table
do_exclude_split(): Predicate to Check if Split Should be Excluded
make_combo_splitfun(): Split Function Helper
make_multicomp_splfun() make_dflt_comp_map(): Make Multi-comparator Split Function
stats_in_cols_setup(): Function factory to be used as Post-processing split function for setup of stats in column structure
real_add_overall_facet(): Add Overall Facet
some_v_all_col_struct(): Standard All vs Some (e.g. Related AEs) column structure

junco Functions For titles/footnotes

The following utility functions help to add titles/footnotes.

listing_column_widths() def_colwidths(): Define Column Widths
get_titles_from_file(): Get Titles/Footers For Table From Sources
set_titles(): Set Output Titles

junco Miscellaneous Functions

The following functions are other miscellaneous junco functions used to create common table layouts.

categorize_pval(): Categorize p-values
cur_col_split_path() in_column() stable: Utilities for the Current Column Split Path
get_mmrm_lsmeans(): Extract Least Square Means from MMRM
get_ref_info() stable: Obtain reference group information from split context.
get_visit_levels(): Get Visit Levels in Order Defined by Numeric Version
leftside(): Extract the left-hand side of a formula
rightside(): Extract the right-hand side of a formula
remove_col_count(): Removal of Unwanted Column Counts
rm_levels(): Removal of Levels

junco Functions For generating .rtfs, .docxs and HTMLs

The following utility functions help to generate the .rtfs, .docxs and HTMLs.

tt_to_tlgrtf(): TableTree to .rtf Conversion
tt_to_flextable_j(): Convert a TableTree or a listing_df object to a flextable
export_as_docx_j(): Export a VTableTree or a listing_df object into docx
export_graph_as_docx(): export_graph_as_docx
export_TLG_as_docx(): Export a TLG (Table, Listing, Graph) to .docx format
theme_docx_default_j(): Obtain the default theme for the docx

Deprecated Functions

The following functions are deprecated and should not be used in new code.

a_coxph_hr() deprecated: a_coxph_hr
rbmi_analyse() deprecated: Analyse Multiple Imputed Datasets
make_rbmi_cluster() deprecated: Create a rbmi ready cluster
par_lapply() deprecated: Parallelise Lapply
a_kaplan_meier() deprecated: a_kaplan_meier