Create Common Tables and Listings Used in Clinical Trials

Documentation for package ‘junco’ version 0.1.1

Help Pages

-- A --

analyze_values	Shortcut Layout Function for Standard Continuous Variable Analysis
a_coxph_hr	Workaround statistics function to add HR with CI
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_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_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

-- 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
cmp_cfun	Summary Analysis Function for Compliance Columns (TEFSCNCMP01 e.g.)
cmp_post_fun	Split Function for Compliance Columns (TEFSCNCMP01 e.g.)
cmp_split_fun	Split Function for Compliance Columns (TEFSCNCMP01 e.g.)
column_stats	Statistics within the column space
cond_rm_facets	Conditional Removal of Facets
count_fraction	Formatting count 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

-- D --

def_colwidths	Define Column Widths
d_test_proportion_diff_j	Description of the difference test between two proportions

-- E --

Workaround statistics function to time point survival estimate with CI

-- F --

find_missing_chg_after_avisit	Helper for Finding AVISIT after which CHG are all Missing
fit_ancova	'ANCOVA' Analysis
fit_mmrm_j	'MMRM' Analysis
format_xx_fct	Function factory for xx style formatting

-- 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

-- H --

h_a_freq_dataprep	A Frequency Data Preparation Function
h_a_freq_prepinrows	Frequency Preparation in Rows
h_colexpr_substr	Extract Substring from Column Expression
h_create_altdf	Create Alternative Data Frame
h_denom_parentdf	Get Denominator Parent Data Frame
h_df_add_newlevels	Add New Levels to Data Frame
h_get_label_map	Get Label Map
h_get_trtvar_refpath	Get Treatment Variable Reference Path
h_odds_ratio	Helper functions for odds ratio estimation
h_subset_combo	Subset Combination
h_tidy_pool	Tabulation of RBMI Results
h_update_factor	Update Factor
h_upd_dfrow	Update Data Frame Row

-- I --

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

-- J --

jjcsformat_count_denom_fraction	Formatting count, denominator and fraction values
jjcsformat_count_fraction	Formatting count and fraction values
jjcsformat_fraction_count_denom	Formatting fraction, count and denominator values
jjcsformat_pval_fct	Function factory for p-value formatting
jjcsformat_range_fct	Function factory for range with censoring information formatting
jjcsformat_xx	Formatting of values
jjcs_num_formats	Numeric Formatting Function
jj_complex_scorefun	Complex Scoring Function
jj_uc_map	Unicode Mapping Table

-- K --

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

-- L --

Define Column Widths

-- M --

make_combo_splitfun	Split Function Helper
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
prop_diff	Proportion difference estimation
prop_post_fun	Split Function for Proportion Analysis Columns (TEFCGIS08 e.g.)
prop_ratio_cmh	Relative Risk CMH Statistic
prop_split_fun	Split Function for Proportion Analysis Columns (TEFCGIS08 e.g.)
prop_table_afun	Formatted Analysis Function for Proportion Analysis (TEFCGIS08 e.g.)

-- 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
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
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_coxph_hr	Workaround statistics function to add HR with CI
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

-- T --

tabulate_lsmeans	Tabulation of Least Square Means Results
tabulate_rbmi	Tabulation of RBMI Results
tidy.tern_model	Tabulation of Least Square Means Results
tt_to_tbldf	Create TableTree as DataFrame via gentlg
tt_to_tlgrtf	TableTree to .rtf Conversion