R: Create Common Tables and Listings Used in Clinical Trials

# Create Common Tables and Listings Used in Clinical Trials

## Documentation for package ‘junco’ version 0.1.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M O P R S T

## -- A --

ac_blank_line | Analysis and Content Summary Function Producing Blank Line
analyze_values | Shortcut Layout Function for Standard Continuous Variable Analysis
a_cmhrms_j | Cochran-Mantel-Haenszel Row Mean Scores test
a_cmhrms_j_with_exclude | Cochran-Mantel-Haenszel Row Mean Scores test
a_coxph_hr | Workaround statistics function to add HR with CI
a_eair100_j | Exposure-Adjusted Incidence Rate
a_event_free | Workaround statistics function to time point survival estimate with CI
a_freq_combos_j | Analysis function count and percentage in column design controlled by combosdf
a_freq_j | Analysis/statistical function for count and percentage in core columns and (optional) relative risk columns
a_freq_j_with_exclude | Analysis/statistical function for count and percentage in core columns and (optional) relative risk columns
a_freq_resp_var_j | Analysis Function for Response Variables
a_freq_subcol_j | Analysis function count and percentage with extra column-subsetting in selected columns (controlled by subcol_* arguments)
a_lsmeans | Tabulation of Least Square Means Results
a_maxlev | Calculate Count and Percentage of the Maximum Level of an Ordered Factor per Subject.
a_odds_ratio_j | Odds ratio estimation
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_j | Proportion difference estimation
a_rbmi_lsmeans | Tabulation of RBMI Results
a_relative_risk | Relative risk estimation
a_summarize_ancova_j | ANCOVA Summary Function
a_summarize_aval_chg_diff_j | Analysis function 3-column presentation
a_summarize_ex_j | Tabulation for Exposure Tables
a_summarize_mmrm | Dynamic tabulation of MMRM results with tables
a_summary_diff_mvars | Descriptive Statistics for Multiple Univariate Variables with Optional Reference-Based Comparison
a_summary_diff_mvars_label | Descriptive Statistics for Multiple Univariate Variables with Optional Reference-Based Comparison
a_summary_j | Wrapper around 'tern::a_summary()' with junco-specific defaults
a_test_proportion_diff | Difference test for two proportions
a_two_tier | Two Tier Analysis Function

## -- B --

bspt_pruner | Pruning Function for pruning based on a fraction and/or a difference from the control arm
build_formula | Building Model Formula

## -- C --

check_wrap_nobreak | Check Word Wrapping
cmhrms | Cochran-Mantel-Haenszel Row Mean Scores test
cmp_cfun | Summary Analysis Function for Compliance Columns
cmp_post_fun | Split Function for Compliance Columns
cmp_split_fun | Split Function for Compliance Columns
column_stats | Statistics within the column space
cond_rm_facets | Conditional Removal of Facets
count and fraction related formatting functions | Formatting functions for count and fraction, and for count denominator and fraction values
count_pruner | Count Pruner
coxph_hr | Workaround statistics function to add HR with CI
create_colspan_map | Creation of Column Spanning Mapping Dataframe
create_colspan_var | Creation of Column Spanning Variables
c_proportion_logical | c_function for proportion of 'TRUE' in logical vector
c_summary_subset_label | Summary Statistics for Filtered Data with Label

## -- D --

def_colwidths | Define Column Widths
do_exclude_split | Predicate to Check if Split Should be Excluded

## -- E --

event_free | Workaround statistics function to time point survival estimate with CI
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

## -- F --

filter_df_prior_afun | Filter Data Prior To Analysis Function
find_missing_chg_after_avisit | Helper for Finding AVISIT after which CHG are all Missing
fit_ancova | 'ANCOVA' Analysis
fit_mmrm_j | 'MMRM' Analysis

## -- G --

get_mmrm_lsmeans | Extract Least Square Means from 'MMRM'
get_ref_info | Obtain Reference Information for a Global Reference Group
get_titles_from_file | Get Titles/Footers For Table From Sources
get_visit_levels | Get Visit Levels in Order Defined by Numeric Version
grouped_cols_w_diffs | Standard Column Structure With Grouped Treatments and Difference Columns

## -- H --

h_get_trtvar_refpath | Get Treatment Variable Reference Path
h_odds_ratio | Helper functions for odds ratio estimation
h_tidy_pool | Tabulation of RBMI Results

## -- I --

inches_to_spaces | Conversion of inches to spaces.
insert_blank_line | Insertion of Blank Lines in a Layout

## -- J --

jjcsformat_cnt_den_fract_fct | Formatting functions for count and fraction, and for count denominator and fraction values
jjcsformat_count_denom_fraction | Formatting functions for count and fraction, and for count denominator and fraction values
jjcsformat_count_fraction | Formatting functions for count and fraction, and for count denominator and fraction values
jjcsformat_fraction_count_denom | Formatting functions for count and fraction, and for count denominator and fraction values
jjcsformat_pval_fct | Utility for specifying custom formats
jjcsformat_range_fct | Utility for specifying custom formats
jjcsformat_xx | Utility for specifying custom formats
jjcs_num_formats | Numeric Formatting Function
jj_complex_scorefun | Complex Scoring Function

## -- K --

keep_non_null_rows | Pruning Function to accommodate removal of completely NULL rows within a table

## -- L --

leftside | Extract the left-hand side of a formula
listing_column_widths | Define Column Widths
lsmeans_wide_cfun | Layout Generating Function for LS Means Wide Table Layouts
lsmeans_wide_first_split_fun_fct | Layout Generating Function for LS Means Wide Table Layouts
lsmeans_wide_second_split_fun_fct | Layout Generating Function for LS Means Wide Table Layouts

## -- M --

make_combo_splitfun | Split Function Helper
make_dflt_comp_map | Make Multi-comparator Split Function
make_multicomp_splfun | Make Multi-comparator Split Function
make_rbmi_cluster | Create a 'rbmi' ready cluster

## -- O --

odds_ratio | Odds ratio estimation
or_clogit_j | Helper functions for odds ratio estimation
or_cmh | Helper functions for odds ratio estimation
or_glm_j | Helper functions for odds ratio estimation

## -- P --

par_lapply | Parallelise Lapply
postfun_eq5d | Post-processing split function for EQ-5D style column statistics
prepend_label_cell | Prepend Label Row to Analysis Output
prop_diff | Proportion difference estimation
prop_diff_test | Difference test for two proportions
prop_post_fun | Split Function for Proportion Analysis Columns
prop_ratio_cmh | Relative Risk CMH Statistic
prop_split_fun | Split Function for Proportion Analysis Columns
prop_table_afun | Formatted Analysis Function for Proportion Analysis

## -- R --

rbmi_analyse | Analyse Multiple Imputed Datasets
rbmi_ancova | Analysis of Covariance
rbmi_ancova_single | Implements an Analysis of Covariance (ANCOVA)
rbmi_mmrm | MMRM Analysis for Imputed Datasets
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
real_add_overall_facet | Add Overall Facet
relative_risk | Relative risk estimation
remove_col_count | Removal of Unwanted Column Counts
remove_rows | Pruning function to remove specific rows of a table regardless of counts
resp01_acfun | Formatted Analysis and Content Summary Function for Response Tables (RESP01)
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_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
rm_levels | Removal of Levels
rm_other_facets_fact | rm_other_facets_fact

## -- S --

safe_prune_table | Safely Prune Table With Empty Table Message If Needed
safe_t_test | Safe Wrapper for 'stats::t.test()'
set_titles | Set Output Titles
summarize_coxreg_multivar | Layout Generating Function for TEFOS03 and Related Cox Regression Layouts
summarize_lsmeans_wide | Layout Generating Function for LS Means Wide Table Layouts
summarize_mmrm | Dynamic tabulation of MMRM results with tables
summarize_row_counts | Layout Creating Function Adding Row Counts
s_ancova_j | Junco Extended ANCOVA Function
s_cmhrms_j | Cochran-Mantel-Haenszel Row Mean Scores test
s_coxph_hr | Workaround statistics function to add HR with CI
s_diff_mean_ci | Difference in Means with Confidence Interval
s_event_free | Workaround statistics function to time point survival estimate with CI
s_freq_j | Analysis/statistical function for count and percentage in core columns and (optional) relative risk columns
s_lsmeans | Tabulation of Least Square Means Results
s_odds_ratio_j | Odds ratio estimation
s_proportion_diff_j | Proportion difference estimation
s_proportion_factor | s_function for proportion of factor levels
s_proportion_logical | s_function for proportion of 'TRUE' in logical vector
s_rbmi_lsmeans | Tabulation of RBMI Results
s_relative_risk | Relative risk estimation
s_summarize_ancova_j | ANCOVA Summary Function
s_summarize_ex_j | Tabulation for Exposure Tables
s_summarize_mmrm | Dynamic tabulation of MMRM results with tables
s_summary_diff | Descriptive Statistics for Univariate Data with Optional Reference Comparison

## -- T --

tabulate_lsmeans | Tabulation of Least Square Means Results
tabulate_rbmi | Tabulation of RBMI Results
theme_docx_default_j | Obtain the default theme for the docx
tidy.tern_model | Tabulation of Least Square Means Results
tt_to_flextable_j | Convert a TableTree or a listing_df object to a flextable
tt_to_tbldf | Create TableTree as DataFrame via gentlg
tt_to_tlgrtf | TableTree to .rtf Conversion