A B C D E F G H I K L M O P R S T U misc
| tern-package | tern Package |
| add_riskdiff | Split function to configure risk difference column |
| add_rowcounts | Layout-creating function to add row total counts |
| aesi_label | Labels for adverse event baskets |
| analyze_colvars_functions | Analyze functions in columns |
| analyze_functions | Analyze functions |
| analyze_num_patients | Count number of patients |
| analyze_variables | Analyze variables |
| analyze_vars | Analyze variables |
| analyze_vars_in_cols | Analyze numeric variables in columns |
| append_varlabels | Add variable labels to top left corner in table |
| arrange_grobs | Arrange multiple grobs |
| as.rtable | Convert to 'rtable' |
| as.rtable.data.frame | Convert to 'rtable' |
| a_count_occurrences | Count occurrences |
| a_count_occurrences_by_grade | Count occurrences by grade |
| a_count_patients_with_event | Count the number of patients with a particular event |
| a_count_patients_with_flags | Count the number of patients with particular flags |
| a_count_values | Count specific values |
| a_coxreg | Cox proportional hazards regression |
| a_length_proportion | Estimate proportions of each level of a variable |
| a_odds_ratio | Odds ratio estimation |
| a_proportion | Proportion estimation |
| a_proportion_diff | Proportion difference estimation |
| a_summary | Analyze variables |
| bland_altman | Bland-Altman plot |
| CombinationFunction | Class for 'CombinationFunction' |
| CombinationFunction-class | Class for 'CombinationFunction' |
| combination_function | Class for 'CombinationFunction' |
| combine_counts | Combine counts |
| combine_groups | Reference and treatment group combination |
| combine_levels | Combine factor levels |
| combine_vectors | Element-wise combination of two vectors |
| compare_variables | Compare variables between groups |
| compare_vars | Compare variables between groups |
| control_analyze_vars | Control function for descriptive statistics |
| control_annot | Control functions for Kaplan-Meier plot annotation tables |
| control_coxph | Control function for Cox-PH model |
| control_coxph_annot | Control functions for Kaplan-Meier plot annotation tables |
| control_coxreg | Control function for Cox regression |
| control_incidence_rate | Control function for incidence rate |
| control_lineplot_vars | Control function for 'g_lineplot()' |
| control_logistic | Control function for logistic regression model fitting |
| control_riskdiff | Control function for risk difference column |
| control_step | Control function for subgroup treatment effect pattern (STEP) calculations |
| control_surv_med_annot | Control functions for Kaplan-Meier plot annotation tables |
| control_surv_time | Control function for 'survfit' models for survival time |
| control_surv_timepoint | Control function for 'survfit' models for patients' survival rate at time points |
| count_occurrences | Count occurrences |
| count_occurrences_by_grade | Count occurrences by grade |
| count_patients_with_event | Count the number of patients with a particular event |
| count_patients_with_flags | Count the number of patients with particular flags |
| count_values | Count specific values |
| cox_regression | Cox proportional hazards regression |
| cox_regression_inter | Cox regression helper function for interactions |
| cut_quantile_bins | Cut numeric vector into empirical quantile bins |
| day2month | Conversion of days to months |
| decorate_grob | Add titles, footnotes, page Number, and a bounding box to a grid grob |
| decorate_grob_set | Decorate set of 'grob's and add page numbering |
| default_na_str | Default string replacement for 'NA' values |
| default_stats_formats_labels | Get default statistical methods and their associated formats, labels, and indent modifiers |
| df_explicit_na | Encode categorical missing values in a data frame |
| draw_grob | Draw 'grob' |
| d_count_abnormal_by_baseline | Description function for 's_count_abnormal_by_baseline()' |
| d_count_cumulative | Description of cumulative count |
| d_count_missed_doses | Description function that calculates labels for 's_count_missed_doses()' |
| d_onco_rsp_label | Description of standard oncology response |
| d_pkparam | Generate PK reference dataset |
| d_proportion | Description of the proportion summary |
| d_proportion_diff | Description of method used for proportion comparison |
| d_rsp_subgroups_colvars | Labels for column variables in binary response by subgroup table |
| d_survival_subgroups_colvars | Labels for column variables in survival duration by subgroup table |
| d_test_proportion_diff | Description of the difference test between two proportions |
| estimate_multinomial_response | Estimate proportions of each level of a variable |
| estimate_multinomial_rsp | Estimate proportions of each level of a variable |
| estimate_odds_ratio | Odds ratio estimation |
| estimate_proportion | Proportion estimation |
| estimate_proportion_diff | Proportion difference estimation |
| explicit_na | Missing data |
| extract_rsp_biomarkers | Prepare response data estimates for multiple biomarkers in a single data frame |
| extract_rsp_subgroups | Prepare response data for population subgroups in data frames |
| extract_survival_biomarkers | Prepare survival data estimates for multiple biomarkers in a single data frame |
| extract_survival_subgroups | Prepare survival data for population subgroups in data frames |
| extreme_format | Format extreme values |
| ex_data | Simulated CDISC data for examples |
| fct_collapse_only | Collapse factor levels and keep only those new group levels |
| fct_discard | Discard specified levels of a factor |
| fct_explicit_na_if | Insertion of explicit missing values in a factor |
| fit_coxreg | Fitting functions for Cox proportional hazards regression |
| fit_coxreg_multivar | Fitting functions for Cox proportional hazards regression |
| fit_coxreg_univar | Fitting functions for Cox proportional hazards regression |
| fit_logistic | Fit for logistic regression |
| fit_rsp_step | Subgroup treatment effect pattern (STEP) fit for binary (response) outcome |
| fit_survival_step | Subgroup treatment effect pattern (STEP) fit for survival outcome |
| forest_viewport | Create a viewport tree for the forest plot |
| formatting_functions | Formatting functions |
| format_auto | Format automatically using data significant digits |
| format_count_fraction | Format count and fraction |
| format_count_fraction_fixed_dp | Format count and percentage with fixed single decimal place |
| format_count_fraction_lt10 | Format count and fraction with special case for count < 10 |
| format_extreme_values | Format a single extreme value |
| format_extreme_values_ci | Format extreme values part of a confidence interval |
| format_fraction | Format fraction and percentage |
| format_fraction_fixed_dp | Format fraction and percentage with fixed single decimal place |
| format_fraction_threshold | Format fraction with lower threshold |
| format_sigfig | Format numeric values by significant figures |
| format_xx | Format XX as a formatting function |
| f_conf_level | Utility function to create label for confidence interval |
| f_pval | Utility function to create label for p-value |
| get_formats_from_stats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| get_indents_from_stats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| get_labels_from_stats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| get_smooths | Smooth function with optional grouping |
| get_stats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| get_stat_names | Get default statistical methods and their associated formats, labels, and indent modifiers |
| groups_list_to_df | Convert list of groups to a data frame |
| g_bland_altman | Bland-Altman plot |
| g_forest | Create a forest plot from an 'rtable' |
| g_ipp | Individual patient plots |
| g_km | Kaplan-Meier plot |
| g_lineplot | Line plot with optional table |
| g_step | Create a STEP graph |
| g_waterfall | Horizontal waterfall plot |
| has_counts_difference | Occurrence table pruning |
| has_count_in_any_col | Occurrence table pruning |
| has_count_in_cols | Occurrence table pruning |
| has_fractions_difference | Occurrence table pruning |
| has_fraction_in_any_col | Occurrence table pruning |
| has_fraction_in_cols | Occurrence table pruning |
| h_adlb_abnormal_by_worst_grade | Helper function to prepare ADLB for 'count_abnormal_by_worst_grade()' |
| h_adlb_worsen | Helper function to prepare ADLB with worst labs |
| h_adsl_adlb_merge_using_worst_flag | Helper function for deriving analysis datasets for select laboratory tables |
| h_ancova | Helper function to return results of a linear model |
| h_append_grade_groups | Helper function for 's_count_occurrences_by_grade()' |
| h_col_indices | Obtain column indices |
| h_count_cumulative | Helper function for 's_count_cumulative()' |
| h_coxph_df | Helper functions for tabulating survival duration by subgroup |
| h_coxph_subgroups_df | Helper functions for tabulating survival duration by subgroup |
| h_coxreg_extract_interaction | Cox regression helper function for interactions |
| h_coxreg_inter_effect | Cox regression helper function for interactions |
| h_coxreg_inter_effect.character | Cox regression helper function for interactions |
| h_coxreg_inter_effect.factor | Cox regression helper function for interactions |
| h_coxreg_inter_effect.numeric | Cox regression helper function for interactions |
| h_coxreg_inter_estimations | Cox regression helper function for interactions |
| h_coxreg_multivar_extract | Helper functions for Cox proportional hazards regression |
| h_coxreg_multivar_formula | Helper functions for Cox proportional hazards regression |
| h_coxreg_mult_cont_df | Helper functions for tabulating biomarker effects on survival by subgroup |
| h_coxreg_univar_extract | Helper functions for Cox proportional hazards regression |
| h_coxreg_univar_formulas | Helper functions for Cox proportional hazards regression |
| h_cox_regression | Helper functions for Cox proportional hazards regression |
| h_data_plot | Helper function to tidy survival fit data |
| h_decompose_gg | 'ggplot' decomposition |
| h_format_row | Helper function to format the optional 'g_lineplot' table |
| h_format_threshold | Format extreme values |
| h_get_format_threshold | Format extreme values |
| h_get_interaction_vars | Helper functions for multivariate logistic regression |
| h_ggkm | Helper function to create a KM plot |
| h_glm_interaction_extract | Helper functions for multivariate logistic regression |
| h_glm_inter_term_extract | Helper functions for multivariate logistic regression |
| h_glm_simple_term_extract | Helper functions for multivariate logistic regression |
| h_grob_coxph | Helper function to create Cox-PH grobs |
| h_grob_median_surv | Helper function to create survival estimation grobs |
| h_grob_tbl_at_risk | Helper function to create patient-at-risk grobs |
| h_grob_y_annot | Helper function to create grid object with y-axis annotation |
| h_g_ipp | Helper function to create simple line plot over time |
| h_interaction_coef_name | Helper functions for multivariate logistic regression |
| h_interaction_term_labels | Helper functions for multivariate logistic regression |
| h_km_layout | Helper function to prepare a KM layout |
| h_logistic_inter_terms | Helper functions for multivariate logistic regression |
| h_logistic_mult_cont_df | Helper functions for tabulating biomarker effects on binary response by subgroup |
| h_logistic_regression | Helper functions for multivariate logistic regression |
| h_logistic_simple_terms | Helper functions for multivariate logistic regression |
| h_map_for_count_abnormal | Helper function to create a map data frame for 'trim_levels_to_map()' |
| h_odds_ratio | Helper functions for odds ratio estimation |
| h_odds_ratio_df | Helper functions for tabulating binary response by subgroup |
| h_odds_ratio_subgroups_df | Helper functions for tabulating binary response by subgroup |
| h_or_cat_interaction | Helper functions for multivariate logistic regression |
| h_or_cont_interaction | Helper functions for multivariate logistic regression |
| h_or_interaction | Helper functions for multivariate logistic regression |
| h_pkparam_sort | Sort pharmacokinetic data by 'PARAM' variable |
| h_ppmeans | Function to return the estimated means using predicted probabilities |
| h_proportions | Helper functions for calculating proportion confidence intervals |
| h_proportion_df | Helper functions for tabulating binary response by subgroup |
| h_proportion_subgroups_df | Helper functions for tabulating binary response by subgroup |
| h_prop_diff | Helper functions to calculate proportion difference |
| h_response_biomarkers_subgroups | Helper functions for tabulating biomarker effects on binary response by subgroup |
| h_response_subgroups | Helper functions for tabulating binary response by subgroup |
| h_rsp_to_logistic_variables | Helper functions for tabulating biomarker effects on binary response by subgroup |
| h_simple_term_labels | Helper functions for multivariate logistic regression |
| h_split_by_subgroups | Split data frame by subgroups |
| h_split_param | Split parameters |
| h_stack_by_baskets | Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. |
| h_step | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_step_rsp_est | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_step_rsp_formula | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_step_survival_est | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_step_survival_formula | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_step_trt_effect | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_step_window | Helper functions for subgroup treatment effect pattern (STEP) calculations |
| h_survival_biomarkers_subgroups | Helper functions for tabulating biomarker effects on survival by subgroup |
| h_survival_duration_subgroups | Helper functions for tabulating survival duration by subgroup |
| h_survtime_df | Helper functions for tabulating survival duration by subgroup |
| h_survtime_subgroups_df | Helper functions for tabulating survival duration by subgroup |
| h_surv_to_coxreg_variables | Helper functions for tabulating biomarker effects on survival by subgroup |
| h_tab_one_biomarker | Helper function for tabulation of a single biomarker result |
| h_tab_rsp_one_biomarker | Helper functions for tabulating biomarker effects on binary response by subgroup |
| h_tab_surv_one_biomarker | Helper functions for tabulating biomarker effects on survival by subgroup |
| h_tbl_coxph_pairwise | Helper function for generating a pairwise Cox-PH table |
| h_tbl_median_surv | Helper function for survival estimations |
| h_worsen_counter | Helper function to analyze patients for 's_count_abnormal_lab_worsen_by_baseline()' |
| h_xticks | Helper function to calculate x-tick positions |
| imputation_rule | Apply 1/3 or 1/2 imputation rule to data |
| individual_patient_plot | Individual patient plots |
| kaplan_meier | Kaplan-Meier plot |
| keep_content_rows | Occurrence table pruning |
| keep_rows | Occurrence table pruning |
| labels_use_control | Update labels according to control specifications |
| level_order | Custom split functions |
| logistic_regression_cols | Logistic regression multivariate column layout function |
| logistic_summary_by_flag | Logistic regression summary table |
| month2day | Conversion of months to days |
| odds_ratio | Odds ratio estimation |
| or_clogit | Helper functions for odds ratio estimation |
| or_glm | Helper functions for odds ratio estimation |
| prop_agresti_coull | Helper functions for calculating proportion confidence intervals |
| prop_clopper_pearson | Helper functions for calculating proportion confidence intervals |
| prop_diff | Proportion difference estimation |
| prop_diff_cmh | Helper functions to calculate proportion difference |
| prop_diff_ha | Helper functions to calculate proportion difference |
| prop_diff_nc | Helper functions to calculate proportion difference |
| prop_diff_strat_nc | Helper functions to calculate proportion difference |
| prop_diff_wald | Helper functions to calculate proportion difference |
| prop_jeffreys | Helper functions for calculating proportion confidence intervals |
| prop_strat_wilson | Helper functions for calculating proportion confidence intervals |
| prop_wald | Helper functions for calculating proportion confidence intervals |
| prop_wilson | Helper functions for calculating proportion confidence intervals |
| prune_occurrences | Occurrence table pruning |
| reapply_varlabels | Reapply variable labels |
| ref_group_position | Custom split functions |
| response_biomarkers_subgroups | Tabulate biomarker effects on binary response by subgroup |
| rtable2gg | Convert 'rtable' objects to 'ggplot' objects |
| sas_na | Convert strings to 'NA' |
| score_occurrences | Occurrence table sorting |
| score_occurrences_cols | Occurrence table sorting |
| score_occurrences_cont_cols | Occurrence table sorting |
| score_occurrences_subtable | Occurrence table sorting |
| set_default_na_str | Default string replacement for 'NA' values |
| split_cols_by_groups | Split columns by groups of levels |
| stack_grobs | Stack multiple grobs |
| stat_mean_ci | Confidence interval for mean |
| stat_mean_pval | p-Value of the mean |
| stat_median_ci | Confidence interval for median |
| stat_propdiff_ci | Proportion difference and confidence interval |
| strata_normal_quantile | Helper function for the estimation of stratified quantiles |
| summarize_colvars | Summarize variables in columns |
| summarize_coxreg | Cox proportional hazards regression |
| summarize_functions | Summarize functions |
| summarize_logistic | Multivariate logistic regression table |
| summarize_num_patients | Count number of patients |
| summarize_occurrences | Count occurrences |
| summarize_occurrences_by_grade | Count occurrences by grade |
| summary_formats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| summary_labels | Get default statistical methods and their associated formats, labels, and indent modifiers |
| survival_biomarkers_subgroups | Tabulate biomarker effects on survival by subgroup |
| s_bland_altman | Bland-Altman analysis |
| s_compare | Compare variables between groups |
| s_compare.character | Compare variables between groups |
| s_compare.factor | Compare variables between groups |
| s_compare.logical | Compare variables between groups |
| s_compare.numeric | Compare variables between groups |
| s_count_occurrences | Count occurrences |
| s_count_occurrences_by_grade | Count occurrences by grade |
| s_count_patients_with_event | Count the number of patients with a particular event |
| s_count_patients_with_flags | Count the number of patients with particular flags |
| s_count_values | Count specific values |
| s_count_values.character | Count specific values |
| s_count_values.factor | Count specific values |
| s_count_values.logical | Count specific values |
| s_coxreg | Cox proportional hazards regression |
| s_length_proportion | Estimate proportions of each level of a variable |
| s_num_patients | Count number of patients |
| s_num_patients_content | Count number of patients |
| s_odds_ratio | Odds ratio estimation |
| s_proportion | Proportion estimation |
| s_proportion_diff | Proportion difference estimation |
| s_summary | Analyze variables |
| s_summary.character | Analyze variables |
| s_summary.factor | Analyze variables |
| s_summary.logical | Analyze variables |
| s_summary.numeric | Analyze variables |
| tabulate_rsp_biomarkers | Tabulate biomarker effects on binary response by subgroup |
| tabulate_survival_biomarkers | Tabulate biomarker effects on survival by subgroup |
| tern | tern Package |
| tern_default_formats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| tern_default_labels | Get default statistical methods and their associated formats, labels, and indent modifiers |
| tern_default_stats | Get default statistical methods and their associated formats, labels, and indent modifiers |
| tern_ex_adae | Simulated CDISC data for examples |
| tern_ex_adlb | Simulated CDISC data for examples |
| tern_ex_adpp | Simulated CDISC data for examples |
| tern_ex_adrs | Simulated CDISC data for examples |
| tern_ex_adsl | Simulated CDISC data for examples |
| tern_ex_adtte | Simulated CDISC data for examples |
| tidy.coxreg.multivar | Custom tidy methods for Cox regression |
| tidy.coxreg.univar | Custom tidy methods for Cox regression |
| tidy.glm | Custom tidy method for binomial GLM results |
| tidy.step | Custom tidy method for STEP results |
| tidy.summary.coxph | Custom tidy methods for Cox regression |
| tidy_coxreg | Custom tidy methods for Cox regression |
| to_n | Replicate entries of a vector if required |
| to_string_matrix | Convert table into matrix of strings |
| univariate | Univariate formula special term |
| update_weights_strat_wilson | Helper function for the estimation of weights for 'prop_strat_wilson()' |
| utils_split_funs | Custom split functions |
| !-method | Class for 'CombinationFunction' |
| &-method | Class for 'CombinationFunction' |
| |-method | Class for 'CombinationFunction' |