Create Common Tables and Listings Used in Clinical Trials
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Documentation for package ‘junco’ version 0.1.7
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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_combo_prop_diff_pval_mf | Combined Proportion, Risk Difference, and Risk Difference Test Analysis Function with Method Selection Based on the Mantel-Fleiss Criterion |
| a_cond_proportion_j | Conditional proportion with adaptive CI (exact vs. Wald) |
| a_coxph_hr | a_coxph_hr |
| a_diff_means | Difference in Means |
| 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_kaplan_meier | a_kaplan_meier |
| 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_proportion_diff_mf | Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion |
| 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_summarize_mmrm_with_exclude | Dynamic tabulation of MMRM results with tables |
| a_summary_j | Wrappers Around 'tern::a_summary()' with Row Split Exclusion |
| a_summary_j_with_exclude | Wrappers Around 'tern::a_summary()' with Row Split Exclusion |
| a_summary_subset | Wrappers Around 'tern::a_summary()' with Optional Subsetting and Labels |
| a_sum_ratio_j | Analysis Function: Sum and Ratio of Sums |
| a_test_proportion_diff | Difference test for two proportions |
| a_test_proportion_diff_mf | Test of Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion |
| a_three_tier | Two Tier Analysis Function |
| 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 --
| categorize_pval | Categorize p-values |
| 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 |
| compare_fmt_specs | Utilities for reviewing format specification objects |
| cond_proportion_j | Conditional proportion with adaptive CI (exact vs. Wald) |
| 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 |
| create_colspan_map | Creation of Column Spanning Mapping Dataframe |
| create_colspan_var | Creation of Column Spanning Variables |
| cur_col_split_path | Utilities for the Current Column Split Path |
| cur_col_split_path_utils | Utilities for the Current Column Split Path |
| c_proportion_logical | c_function for proportion of 'TRUE' in logical vector |
| c_summary_subset_label | Wrappers Around 'tern::a_summary()' with Optional Subsetting and Labels |
-- D --
| def_colwidths | Define Column Widths |
| diff_means | Difference in Means |
| do_exclude_split | Predicate to Check if Split Should be Excluded |
| d_cond_proportion_j | Conditional proportion with adaptive CI (exact vs. Wald) |
-- 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 --
| factor_by_order | Create a factor with levels ordered by a separate ordering vector |
| find_missing_chg_after_avisit | Helper for Finding AVISIT after which CHG are all Missing |
| fit_ancova | 'ANCOVA' Analysis |
| fit_mmrm_j | 'MMRM' Analysis |
| fmt_spec_d | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
| fmt_spec_df_d | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
| fmt_spec_single_d | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
| fmt_spec_var_d | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
| fmt_utils | Utilities for reviewing format specification objects |
-- G --
| get_fmt_details | Utilities for reviewing format specification objects |
| get_mmrm_lsmeans | Extract Least Square Means from 'MMRM' |
| get_ref_info | Obtain reference group information from split context. |
| 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 |
| grouped_cols_w_subgrps | Standard Column Structure With Grouped Treatments and Difference Columns |
-- H --
| 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 |
| in_column | Utilities for the Current Column Split Path |
-- 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_denom_fraction_legacy | 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 | Formatting function for percentage values |
| jjcsformat_fraction_count_denom | Formatting functions for count and fraction, and for count denominator and fraction values |
| jjcsformat_fraction_count_denom_legacy | 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 |
| junco_def_d_all | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
| junco_def_d_alt1 | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
| junco_def_d_alt2 | Utilities for processing d-style string formatting specifications (eg "xx.dx") |
-- 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 |
| pool_rubin_scalar | Pool a scalar estimate across imputations |
| pool_z_stat | Pool z statistics across imputations |
| prepend_label_cell | Prepend a Label Row to a RowsVerticalSection Object |
| proportion_diff_mf | Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion |
| 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 |
| resp_multiple_imputation | Calculate results across binary-imputation scenarios |
| rightside | Extract the right-hand side of a formula |
| 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 |
| shift_tbl_col_struct | Create Column Structure for a J&J-Style Shift Table |
| some_v_all_col_struct | Standard All vs Some (e.g. Related AEs) column structure |
| stats_in_cols_setup | Function factory to be used as Post-processing split function for setup of stats in column structure |
| string_to_title | Title Case Conversion |
| 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 |
| summary_subset | Wrappers Around 'tern::a_summary()' with Optional Subsetting and Labels |
| s_ancova_j | Junco Extended ANCOVA Function |
| s_cmhrms_j | Cochran-Mantel-Haenszel Row Mean Scores test |
| s_cond_proportion_j | Conditional proportion with adaptive CI (exact vs. Wald) |
| s_diff_means | Difference in Means |
| 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_mf | Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion |
| 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 |
| s_test_proportion_diff_mf | Test of Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion |
-- T --
| tabulate_lsmeans | Tabulation of Least Square Means Results |
| tabulate_rbmi | Tabulation of RBMI Results |
| test_proportion_diff_mf | Test of Proportion Difference with Method Selection Based on the Mantel-Fleiss Criterion |
| 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 |