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"h_step_rsp_formula", "h_step_survival_est", "h_step_survival_formula", "h_step_trt_effect", "h_step_window", "h_surv_to_coxreg_variables", "h_survtime_df", "h_survtime_subgroups_df", "h_tab_one_biomarker", "h_tab_rsp_one_biomarker", "h_tab_surv_one_biomarker", "h_tbl_coxph_pairwise", "h_tbl_median_surv", "h_worsen_counter", "h_xticks", "has_count_in_any_col", "has_count_in_cols", "has_counts_difference", "has_fraction_in_any_col", "has_fraction_in_cols", "has_fractions_difference", "imputation_rule", "keep_content_rows", "keep_rows", "labels_or_names", "labels_use_control", "level_order", "logistic_regression_cols", "logistic_summary_by_flag", "month2day", "or_clogit", "or_glm", "prop_agresti_coull", "prop_clopper_pearson", "prop_diff_cmh", "prop_diff_ha", "prop_diff_nc", "prop_diff_strat_nc", "prop_diff_wald", "prop_jeffreys", "prop_strat_wilson", "prop_wald", "prop_wilson", "range_noinf", "reapply_varlabels", "ref_group_position", "rtable2gg", "s_bland_altman", "s_compare", "s_count_occurrences", "s_count_occurrences_by_grade", "s_count_patients_with_event", "s_count_patients_with_flags", "s_count_values", "s_coxreg", "s_length_proportion", "s_num_patients", "s_num_patients_content", "s_odds_ratio", "s_proportion", "s_proportion_diff", "s_summary", "s_surv_timepoint", "s_test_proportion_diff", "sas_na", "score_occurrences", "score_occurrences_cols", "score_occurrences_cont_cols", "score_occurrences_subtable", "set_default_drop_na", "set_default_na_str", "split_cols_by_groups", "stack_grobs", "stat_mean_ci", "stat_mean_pval", "stat_median_ci", "stat_propdiff_ci", "strata_normal_quantile", "summarize_ancova", "summarize_change", "summarize_colvars", "summarize_coxreg", "summarize_glm_count", "summarize_logistic", "summarize_num_patients", "summarize_occurrences", "summarize_occurrences_by_grade", "summarize_patients_events_in_cols", "summarize_patients_exposure_in_cols", "summary_formats", "summary_labels", "surv_time", "surv_timepoint", "tabulate_rsp_biomarkers", "tabulate_rsp_subgroups", "tabulate_survival_biomarkers", "tabulate_survival_subgroups", "tern_default_formats", "tern_default_labels", "tern_default_stats", "test_proportion_diff", "to_n", "to_string_matrix", "univariate", "update_weights_strat_wilson" ], "_datasets": [ { "name": "tern_ex_adae", "title": "Simulated CDISC data for examples", "object": "tern_ex_adae", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "STUDYID", "COUNTRY", "SITEID", "SUBJID", "AGE", "SEX", "ARMCD", "ARM", "ACTARMCD", "ACTARM", "RACE", "TRTSDTM", "TRTEDTM", "EOSDY", "STRATA1", "STRATA2", "BMRKR1", "BMRKR2", "REGION1", "SAFFL", "USUBJID", "AEBODSYS", "AELLT", "AEDECOD", "AEHLT", "AEHLGT", "AETOXGR", "AESOC", "AESER", "AEREL", "AETERM", "AESEV", "ASTDTM", "AESEQ", "ASEQ", "AEOUT", "TRTEMFL", "CQ01NAM", "SMQ01NAM", "SMQ01SC", "SMQ02NAM", "SMQ02SC" ], "rows": 541, "table": true, "tojson": true }, { "name": "tern_ex_adlb", "title": "Simulated CDISC data for examples", "object": "tern_ex_adlb", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "STUDYID", "COUNTRY", "SITEID", "SUBJID", "AGE", "SEX", "ARMCD", "ARM", "ACTARMCD", "ACTARM", "RACE", "TRTSDTM", "TRTEDTM", "EOSDY", "STRATA1", "STRATA2", "BMRKR1", "BMRKR2", "REGION1", "SAFFL", "USUBJID", "PARAM", "AVISIT", "AVAL", "LBCAT", "PARAMCD", "AVALU", "AVISITN", "ABLFL2", "ABLFL", "BASE", "BASETYPE", "ANRIND", "ANRLO", "ANRHI", "DTYPE", "ATOXGR", "BTOXGR", "ATOXDSCL", "ATOXDSCH", "ADTM", "ASPID", "LBSEQ", "ONTRTFL", "WORS01FL", "WGRHIFL", "WGRLOFL", "WGRHIVFL", "WGRLOVFL", "ANL01FL" ], "rows": 4200, "table": true, "tojson": true }, { "name": "tern_ex_adpp", "title": "Simulated CDISC data for examples", "object": "tern_ex_adpp", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "STUDYID", "COUNTRY", "SITEID", "SUBJID", "AGE", "SEX", "ARMCD", "ARM", "ACTARMCD", "ACTARM", "RACE", "TRTSDTM", "TRTEDTM", "EOSDY", "STRATA1", "STRATA2", "BMRKR1", "BMRKR2", "REGION1", "SAFFL", "USUBJID", "PARAM", "AVAL", "PARAMCD", "AVALU" ], "rows": 522, "table": true, "tojson": true }, { "name": "tern_ex_adrs", "title": "Simulated CDISC data for examples", "object": "tern_ex_adrs", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "STUDYID", "COUNTRY", "SITEID", "SUBJID", "AGE", "SEX", "ARMCD", "ARM", "ACTARMCD", "ACTARM", "RACE", "TRTSDTM", "TRTEDTM", "EOSDY", "STRATA1", "STRATA2", "BMRKR1", "BMRKR2", "REGION1", "SAFFL", "USUBJID", "AVISIT", "PARAMCD", "PARAM", "AVALC", "AVAL", "ADTM", "AVISITN", "DTHFL" ], "rows": 1600, "table": true, "tojson": true }, { "name": "tern_ex_adsl", "title": "Simulated CDISC data for examples", "object": "tern_ex_adsl", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "STUDYID", "COUNTRY", "SITEID", "SUBJID", "AGE", "SEX", "ARMCD", "ARM", "ACTARMCD", "ACTARM", "RACE", "TRTSDTM", "TRTEDTM", "EOSDY", "STRATA1", "STRATA2", "BMRKR1", "BMRKR2", "REGION1", "SAFFL", "USUBJID" ], "rows": 200, "table": true, "tojson": true }, { "name": "tern_ex_adtte", "title": "Simulated CDISC data for examples", "object": "tern_ex_adtte", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "STUDYID", "COUNTRY", "SITEID", "SUBJID", "AGE", "SEX", "ARMCD", "ARM", "ACTARMCD", "ACTARM", "RACE", "TRTSDTM", "TRTEDTM", "EOSDY", "STRATA1", "STRATA2", "BMRKR1", "BMRKR2", "REGION1", "SAFFL", "USUBJID", "PARAMCD", "PARAM", "CNSR", "AVAL", "AVALU", "ADTM", "lgTMATRSK" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "tern-package", "title": "tern Package", "topics": [ "tern-package", "tern" ] }, { "page": "add_riskdiff", "title": "Split function to configure risk difference column", "topics": [ "add_riskdiff" ] }, { "page": "add_rowcounts", "title": "Layout-creating function to add row total counts", "topics": [ "add_rowcounts" ] }, { "page": "aesi_label", "title": "Labels for adverse event baskets", "topics": [ "aesi_label" ] }, { "page": "analyze_colvars_functions", "title": "Analyze functions in columns", "topics": [ "analyze_colvars_functions" ] }, { "page": "analyze_functions", "title": "Analyze functions", "topics": [ "analyze_functions" ] }, { "page": "analyze_variables", "title": "Analyze variables", "topics": [ "analyze_variables", "analyze_vars", "a_summary", "s_summary", "s_summary.character", "s_summary.factor", "s_summary.logical", "s_summary.numeric" ] }, { "page": "analyze_vars_in_cols", "title": "Analyze numeric variables in columns", "topics": [ "analyze_vars_in_cols" ] }, { "page": "append_varlabels", "title": "Add variable labels to top left corner in table", "topics": [ "append_varlabels" ] }, { "page": "arrange_grobs", "title": "Arrange multiple grobs", "topics": [ "arrange_grobs" ] }, { "page": "as.rtable", "title": "Convert to 'rtable'", "topics": [ "as.rtable", "as.rtable.data.frame" ] }, { "page": "check_diff_prop_ci", "title": "Check proportion difference arguments", "topics": [ "check_diff_prop_ci" ] }, { "page": "clogit_with_tryCatch", "title": "Wrapper function of survival::clogit", "topics": [ "clogit_with_tryCatch" ] }, { "page": "combination_function", "title": "Class for 'CombinationFunction'", "topics": [ "!,CombinationFunction-method", "&,CombinationFunction,CombinationFunction-method", "CombinationFunction", "CombinationFunction-class", "combination_function", "|,CombinationFunction,CombinationFunction-method" ] }, { "page": "combine_counts", "title": "Combine counts", "topics": [ "combine_counts" ] }, { "page": "combine_groups", "title": "Reference and treatment group combination", "topics": [ "combine_groups" ] }, { "page": "combine_vectors", "title": "Element-wise combination of two vectors", "topics": [ "combine_vectors" ] }, { "page": "compare_variables", "title": "Compare variables between groups", "topics": [ "compare_variables", "compare_vars", "s_compare", "s_compare.character", "s_compare.factor", "s_compare.logical", "s_compare.numeric" ] }, { "page": "control_analyze_vars", "title": "Control function for descriptive statistics", "topics": [ "control_analyze_vars" ] }, { "page": "control_annot", "title": "Control functions for Kaplan-Meier plot annotation tables", "topics": [ "control_annot", "control_coxph_annot", "control_surv_med_annot" ] }, { "page": "control_coxph", "title": "Control function for Cox-PH model", "topics": [ "control_coxph" ] }, { "page": "control_coxreg", "title": "Control function for Cox regression", "topics": [ "control_coxreg" ] }, { "page": "control_incidence_rate", "title": "Control function for incidence rate", "topics": [ "control_incidence_rate" ] }, { "page": "control_lineplot_vars", "title": "Control function for 'g_lineplot()'", "topics": [ "control_lineplot_vars" ] }, { "page": "control_logistic", "title": "Control function for logistic regression model fitting", "topics": [ "control_logistic" ] }, { "page": "control_riskdiff", "title": "Control function for risk difference column", "topics": [ "control_riskdiff" ] }, { "page": "control_step", "title": "Control function for subgroup treatment effect pattern (STEP) calculations", "topics": [ "control_step" ] }, { "page": "control_surv_time", "title": "Control function for 'survfit' models for survival time", "topics": [ "control_surv_time" ] }, { "page": "control_surv_timepoint", "title": "Control function for 'survfit' models for patients' survival rate at time points", "topics": [ "control_surv_timepoint" ] }, { "page": "count_occurrences", "title": "Count occurrences", "topics": [ "a_count_occurrences", "count_occurrences", "summarize_occurrences", "s_count_occurrences" ] }, { "page": "count_occurrences_by_grade", "title": "Count occurrences by grade", "topics": [ "a_count_occurrences_by_grade", "count_occurrences_by_grade", "summarize_occurrences_by_grade", "s_count_occurrences_by_grade" ] }, { "page": "count_patients_with_event", "title": "Count the number of patients with a particular event", "topics": [ "a_count_patients_with_event", "count_patients_with_event", "s_count_patients_with_event" ] }, { "page": "count_patients_with_flags", "title": "Count the number of patients with particular flags", "topics": [ "a_count_patients_with_flags", "count_patients_with_flags", "s_count_patients_with_flags" ] }, { "page": "count_values", "title": "Count specific values", "topics": [ "a_count_values", "count_values", "s_count_values", "s_count_values.character", "s_count_values.factor", "s_count_values.logical" ] }, { "page": "cox_regression", "title": "Cox proportional hazards regression", "topics": [ "a_coxreg", "cox_regression", "summarize_coxreg", "s_coxreg" ] }, { "page": "cox_regression_inter", "title": "Cox regression helper function for interactions", "topics": [ "cox_regression_inter", "h_coxreg_extract_interaction", "h_coxreg_inter_effect", "h_coxreg_inter_effect.character", "h_coxreg_inter_effect.factor", "h_coxreg_inter_effect.numeric", "h_coxreg_inter_estimations" ] }, { "page": "cut_quantile_bins", "title": "Cut numeric vector into empirical quantile bins", "topics": [ "cut_quantile_bins" ] }, { "page": "d_count_abnormal_by_baseline", "title": "Description function for 's_count_abnormal_by_baseline()'", "topics": [ "d_count_abnormal_by_baseline" ] }, { "page": "d_count_cumulative", "title": "Description of cumulative count", "topics": [ "d_count_cumulative" ] }, { "page": "d_count_missed_doses", "title": "Description function that calculates labels for 's_count_missed_doses()'", "topics": [ "d_count_missed_doses" ] }, { "page": "d_onco_rsp_label", "title": "Description of standard oncology response", "topics": [ "d_onco_rsp_label" ] }, { "page": "d_pkparam", "title": "Generate PK reference dataset", "topics": [ "d_pkparam" ] }, { "page": "d_proportion", "title": "Description of the proportion summary", "topics": [ "d_proportion" ] }, { "page": "d_proportion_diff", "title": "Description of method used for proportion comparison", "topics": [ "d_proportion_diff" ] }, { "page": "d_rsp_subgroups_colvars", "title": "Labels for column variables in binary response by subgroup table", "topics": [ "d_rsp_subgroups_colvars" ] }, { "page": "d_survival_subgroups_colvars", "title": "Labels for column variables in survival duration by subgroup table", "topics": [ "d_survival_subgroups_colvars" ] }, { "page": "d_test_proportion_diff", "title": "Description of the difference test between two proportions", "topics": [ "d_test_proportion_diff" ] }, { "page": "day2month", "title": "Conversion of days to months", "topics": [ "day2month" ] }, { "page": "decorate_grob", "title": "Add titles, footnotes, page Number, and a bounding box to a grid grob", "topics": [ "decorate_grob" ] }, { "page": "decorate_grob_set", "title": "Decorate set of 'grob's and add page numbering", "topics": [ "decorate_grob_set" ] }, { "page": "default_na_str", "title": "Default string replacement for 'NA' values", "topics": [ "default_na_str", "set_default_na_str" ] }, { "page": "default_stats_formats_labels", "title": "Get default statistical methods and their associated formats, labels, and indent modifiers", "topics": [ "default_stats_formats_labels", "get_formats_from_stats", "get_indents_from_stats", "get_labels_from_stats", "get_stats", "get_stat_names", "summary_formats", "summary_labels", "tern_default_formats", "tern_default_labels", "tern_default_stats" ] }, { "page": "df_explicit_na", "title": "Encode categorical missing values in a data frame", "topics": [ "df_explicit_na" ] }, { "page": "draw_grob", "title": "Draw 'grob'", "topics": [ "draw_grob" ] }, { "page": "estimate_multinomial_rsp", "title": "Estimate proportions of each level of a variable", "topics": [ "a_length_proportion", "estimate_multinomial_response", "estimate_multinomial_rsp", "s_length_proportion" ] }, { "page": "estimate_proportion", "title": "Proportion estimation", "topics": [ "a_proportion", "estimate_proportion", "s_proportion" ] }, { "page": "ex_data", "title": "Simulated CDISC data for examples", "topics": [ "ex_data", "tern_ex_adae", "tern_ex_adlb", "tern_ex_adpp", "tern_ex_adrs", "tern_ex_adsl", "tern_ex_adtte" ] }, { "page": "explicit_na", "title": "Missing data", "topics": [ "default_drop_na", "explicit_na", "set_default_drop_na" ] }, { "page": "extract_rsp_biomarkers", "title": "Prepare response data estimates for multiple biomarkers in a single data frame", "topics": [ "extract_rsp_biomarkers" ] }, { "page": "extract_rsp_subgroups", "title": "Prepare response data for population subgroups in data frames", "topics": [ "extract_rsp_subgroups" ] }, { "page": "extract_survival_biomarkers", "title": "Prepare survival data estimates for multiple biomarkers in a single data frame", "topics": [ "extract_survival_biomarkers" ] }, { "page": "extract_survival_subgroups", "title": "Prepare survival data for population subgroups in data frames", "topics": [ "extract_survival_subgroups" ] }, { "page": "extreme_format", "title": "Format extreme values", "concept": [ "formatting functions" ], "topics": [ "extreme_format", "h_format_threshold", "h_get_format_threshold" ] }, { "page": "f_conf_level", "title": "Utility function to create label for confidence interval", "topics": [ "f_conf_level" ] }, { "page": "f_pval", "title": "Utility function to create label for p-value", "topics": [ "f_pval" ] }, { "page": "factor_utils", "title": "Factor utilities", "topics": [ "as_factor_keep_attributes", "combine_levels", "factor_utils", "fct_collapse_only", "fct_discard", "fct_explicit_na_if" ] }, { "page": "fit_coxreg", "title": "Fitting functions for Cox proportional hazards regression", "topics": [ "fit_coxreg", "fit_coxreg_multivar", "fit_coxreg_univar" ] }, { "page": "fit_logistic", "title": "Fit for logistic regression", "topics": [ "fit_logistic" ] }, { "page": "fit_rsp_step", "title": "Subgroup treatment effect pattern (STEP) fit for binary (response) outcome", "topics": [ "fit_rsp_step" ] }, { "page": "fit_survival_step", "title": "Subgroup treatment effect pattern (STEP) fit for survival outcome", "topics": [ "fit_survival_step" ] }, { "page": "forest_viewport", "title": "Create a viewport tree for the forest plot", "topics": [ "forest_viewport" ] }, { "page": "format_auto", "title": "Format automatically using data significant digits", "concept": [ "formatting functions" ], "topics": [ "format_auto" ] }, { "page": "format_count_fraction", "title": "Format count and fraction", "concept": [ "formatting functions" ], "topics": [ "format_count_fraction" ] }, { "page": "format_count_fraction_fixed_dp", "title": "Format count and percentage with fixed single decimal place", "concept": [ "formatting functions" ], "topics": [ "format_count_fraction_fixed_dp" ] }, { "page": "format_count_fraction_lt10", "title": "Format count and fraction with special case for count < 10", "concept": [ "formatting functions" ], "topics": [ "format_count_fraction_lt10" ] }, { "page": "format_extreme_values", "title": "Format a single extreme value", "concept": [ "formatting functions" ], "topics": [ "format_extreme_values" ] }, { "page": "format_extreme_values_ci", "title": "Format extreme values part of a confidence interval", "concept": [ "formatting functions" ], "topics": [ "format_extreme_values_ci" ] }, { "page": "format_fraction", "title": "Format fraction and percentage", "concept": [ "formatting functions" ], "topics": [ "format_fraction" ] }, { "page": "format_fraction_fixed_dp", "title": "Format fraction and percentage with fixed single decimal place", "concept": [ "formatting functions" ], "topics": [ "format_fraction_fixed_dp" ] }, { "page": "format_fraction_threshold", "title": "Format fraction with lower threshold", "concept": [ "formatting functions" ], "topics": [ "format_fraction_threshold" ] }, { "page": "format_sigfig", "title": "Format numeric values by significant figures", "concept": [ "formatting functions" ], "topics": [ "format_sigfig" ] }, { "page": "format_xx", "title": "Format XX as a formatting function", "concept": [ "formatting functions" ], "topics": [ "format_xx" ] }, { "page": "formatting_functions", "title": "Formatting functions", "concept": [ "formatting functions" ], "topics": [ "formatting_functions" ] }, { "page": "g_bland_altman", "title": "Bland-Altman plot", "topics": [ "bland_altman", "g_bland_altman" ] }, { "page": "g_forest", "title": "Create a forest plot from an 'rtable'", "topics": [ "g_forest" ] }, { "page": "g_ipp", "title": "Individual patient plots", "topics": [ "g_ipp", "individual_patient_plot" ] }, { "page": "g_km", "title": "Kaplan-Meier plot", "topics": [ "g_km", "kaplan_meier" ] }, { "page": "g_lineplot", "title": "Line plot with optional table", "topics": [ "g_lineplot" ] }, { "page": "g_step", "title": "Create a STEP graph", "topics": [ "g_step" ] }, { "page": "g_waterfall", "title": "Horizontal waterfall plot", "topics": [ "g_waterfall" ] }, { "page": "get_covariates", "title": "Utility function to return a named list of covariate names", "topics": [ "get_covariates" ] }, { "page": "get_smooths", "title": "Smooth function with optional grouping", "topics": [ "get_smooths" ] }, { "page": "groups_list_to_df", "title": "Convert list of groups to a data frame", "topics": [ "groups_list_to_df" ] }, { "page": "h_adlb_abnormal_by_worst_grade", "title": "Helper function to prepare ADLB for 'count_abnormal_by_worst_grade()'", "topics": [ "h_adlb_abnormal_by_worst_grade" ] }, { "page": "h_adlb_worsen", "title": "Helper function to prepare ADLB with worst labs", "topics": [ "h_adlb_worsen" ] }, { "page": "h_adsl_adlb_merge_using_worst_flag", "title": "Helper function for deriving analysis datasets for select laboratory tables", "topics": [ "h_adsl_adlb_merge_using_worst_flag" ] }, { "page": "h_ancova", "title": "Helper function to return results of a linear model", "topics": [ "h_ancova" ] }, { "page": "h_append_grade_groups", "title": "Helper function for 's_count_occurrences_by_grade()'", "topics": [ "h_append_grade_groups" ] }, { "page": "h_biomarkers_subgroups", "title": "Helper functions for tabulation of a single biomarker result", "topics": [ "h_biomarkers_subgroups", "h_tab_one_biomarker", "h_tab_rsp_one_biomarker", "h_tab_surv_one_biomarker" ] }, { "page": "h_col_indices", "title": "Obtain column indices", "topics": [ "h_col_indices" ] }, { "page": "h_count_cumulative", "title": "Helper function for 's_count_cumulative()'", "topics": [ "h_count_cumulative" ] }, { "page": "h_cox_regression", "title": "Helper functions for Cox proportional hazards regression", "topics": [ "h_coxreg_multivar_extract", "h_coxreg_multivar_formula", "h_coxreg_univar_extract", "h_coxreg_univar_formulas", "h_cox_regression" ] }, { "page": "h_data_plot", "title": "Helper function to tidy survival fit data", "topics": [ "h_data_plot" ] }, { "page": "h_decompose_gg", "title": "'ggplot' decomposition", "topics": [ "h_decompose_gg" ] }, { "page": "h_format_row", "title": "Helper function to format the optional 'g_lineplot' table", "topics": [ "h_format_row" ] }, { "page": "h_g_ipp", "title": "Helper function to create simple line plot over time", "topics": [ "h_g_ipp" ] }, { "page": "h_ggkm", "title": "Helper function to create a KM plot", "topics": [ "h_ggkm" ] }, { "page": "h_grob_coxph", "title": "Helper function to create Cox-PH grobs", "topics": [ "h_grob_coxph" ] }, { "page": "h_grob_median_surv", "title": "Helper function to create survival estimation grobs", "topics": [ "h_grob_median_surv" ] }, { "page": "h_grob_tbl_at_risk", "title": "Helper function to create patient-at-risk grobs", "topics": [ "h_grob_tbl_at_risk" ] }, { "page": "h_grob_y_annot", "title": "Helper function to create grid object with y-axis annotation", "topics": [ "h_grob_y_annot" ] }, { "page": "h_km_layout", "title": "Helper function to prepare a KM layout", "topics": [ "h_km_layout" ] }, { "page": "h_logistic_regression", "title": "Helper functions for multivariate logistic regression", "topics": [ "h_get_interaction_vars", "h_glm_interaction_extract", 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