Man pages for tern
Create Common TLGs Used in Clinical Trials
| abnormal | Count patients with abnormal range values |
| abnormal_by_baseline | Count patients with abnormal analysis range values by... |
| abnormal_by_marked | Count patients with marked laboratory abnormalities |
| abnormal_by_worst_grade | Count patients by most extreme post-baseline toxicity grade... |
| abnormal_lab_worsen_by_baseline | Count patients with toxicity grades that have worsened from... |
| 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 |
| afun_riskdiff | Analysis function to calculate risk difference column values |
| afun_selected_stats | Get selected statistics names |
| analyze_colvars_functions | Analyze functions in columns |
| analyze_functions | Analyze functions |
| analyze_variables | Analyze variables |
| analyze_vars_in_cols | Analyze numeric variables in columns |
| append_varlabels | Add variable labels to top left corner in table |
| apply_auto_formatting | Apply automatic formatting |
| argument_convention | Standard arguments |
| arrange_grobs | Arrange multiple grobs |
| as.rtable | Convert to 'rtable' |
| assertions | Additional assertions to use with 'checkmate' |
| bins_percent_labels | Labels for bins in percent |
| cfun_by_flag | Constructor for content functions given a data frame with... |
| check_diff_prop_ci | Check proportion difference arguments |
| check_same_n | Check element dimension |
| c_label_n | Content row function to add row total to labels |
| c_label_n_alt | Content row function to add 'alt_counts_df' row total to... |
| clogit_with_tryCatch | Wrapper function of survival::clogit |
| combination_function | Class for 'CombinationFunction' |
| combine_counts | Combine counts |
| combine_groups | Reference and treatment group combination |
| combine_vectors | Element-wise combination of two vectors |
| compare_variables | 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_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)... |
| control_surv_time | Control function for 'survfit' models for survival time |
| control_surv_timepoint | Control function for 'survfit' models for patients' survival... |
| count_cumulative | Cumulative counts of numeric variable by thresholds |
| count_missed_doses | Count number of patients with missed doses by thresholds |
| count_occurrences | Count occurrences |
| count_occurrences_by_grade | Count occurrences by grade |
| count_patients_events_in_cols | Count patient events in columns |
| 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 |
| 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... |
| decorate_grob | Add titles, footnotes, page Number, and a bounding box to a... |
| decorate_grob_factory | Update page number |
| 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,... |
| desctools_binom | Confidence intervals for a difference of binomials |
| df2gg | Convert 'data.frame' object to 'ggplot' object |
| df_explicit_na | Encode categorical missing values in a data frame |
| d_onco_rsp_label | Description of standard oncology response |
| dot-is_equal_float | Utility function to check if a float value is equal to... |
| d_pkparam | Generate PK reference dataset |
| d_proportion | Description of the proportion summary |
| d_proportion_diff | Description of method used for proportion comparison |
| draw_grob | Draw 'grob' |
| d_rsp_subgroups_colvars | Labels for column variables in binary response by subgroup... |
| d_survival_subgroups_colvars | Labels for column variables in survival duration by subgroup... |
| d_test_proportion_diff | Description of the difference test between two proportions |
| empty_vector_if_na | Return an empty numeric if all elements are 'NA'. |
| estimate_coef | Hazard ratio estimation in interactions |
| estimate_multinomial_rsp | Estimate proportions of each level of a variable |
| estimate_proportion | Proportion estimation |
| ex_data | Simulated CDISC data for examples |
| explicit_na | Missing data |
| extract_by_name | Extract elements by name |
| extract_rsp_biomarkers | Prepare response data estimates for multiple biomarkers in a... |
| extract_rsp_subgroups | Prepare response data for population subgroups in data frames |
| extract_survival_biomarkers | Prepare survival data estimates for multiple biomarkers in a... |
| extract_survival_subgroups | Prepare survival data for population subgroups in data frames |
| extreme_format | Format extreme values |
| factor_utils | Factor utilities |
| f_conf_level | Utility function to create label for confidence interval |
| fit_coxreg | Fitting functions for Cox proportional hazards regression |
| fit_logistic | Fit for logistic regression |
| fit_rsp_step | Subgroup treatment effect pattern (STEP) fit for binary... |
| fit_survival_step | Subgroup treatment effect pattern (STEP) fit for survival... |
| forest_viewport | Create a viewport tree for the forest plot |
| 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... |
| format_fraction_threshold | Format fraction with lower threshold |
| format_sigfig | Format numeric values by significant figures |
| formatting_functions | Formatting functions |
| format_xx | Format XX as a formatting function |
| f_pval | Utility function to create label for p-value |
| g_bland_altman | Bland-Altman plot |
| get_covariates | Utility function to return a named list of covariate names |
| get_smooths | Smooth function with optional grouping |
| 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 |
| groups_list_to_df | Convert list of groups to a data frame |
| g_step | Create a STEP graph |
| g_waterfall | Horizontal waterfall plot |
| h_adlb_abnormal_by_worst_grade | Helper function to prepare ADLB for... |
| 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... |
| h_ancova | Helper function to return results of a linear model |
| h_append_grade_groups | Helper function for 's_count_occurrences_by_grade()' |
| h_biomarkers_subgroups | Helper functions for tabulation of a single biomarker result |
| h_col_indices | Obtain column indices |
| h_count_cumulative | Helper function for 's_count_cumulative()' |
| 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_ggkm | Helper function to create a KM plot |
| h_g_ipp | Helper function to create simple line plot over time |
| h_glm_count | Helper functions for Poisson models |
| 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_incidence_rate | Helper functions for incidence rate |
| h_km_layout | Helper function to prepare a KM layout |
| h_logistic_regression | Helper functions for multivariate logistic regression |
| h_map_for_count_abnormal | Helper function to create a map data frame for... |
| h_odds_ratio | Helper functions for odds ratio estimation |
| h_pkparam_sort | Sort pharmacokinetic data by 'PARAM' variable |
| h_ppmeans | Function to return the estimated means using predicted... |
| h_prop_diff | Helper functions to calculate proportion difference |
| h_prop_diff_test | Helper functions to test proportion differences |
| h_proportions | Helper functions for calculating proportion confidence... |
| h_response_biomarkers_subgroups | Helper functions for tabulating biomarker effects on binary... |
| h_response_subgroups | Helper functions for tabulating binary response by subgroup |
| 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... |
| h_step | Helper functions for subgroup treatment effect pattern (STEP)... |
| h_survival_biomarkers_subgroups | Helper functions for tabulating biomarker effects on survival... |
| h_survival_duration_subgroups | Helper functions for tabulating survival duration 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... |
| h_xticks | Helper function to calculate x-tick positions |
| imputation_rule | Apply 1/3 or 1/2 imputation rule to data |
| incidence_rate | Incidence rate estimation |
| labels_or_names | Labels or names of list elements |
| labels_use_control | Update labels according to control specifications |
| logistic_regression_cols | Logistic regression multivariate column layout function |
| logistic_summary_by_flag | Logistic regression summary table |
| make_names | Make names without dots |
| month2day | Conversion of months to days |
| muffled_car_anova | Muffled 'car::Anova' |
| n_available | Number of available (non-missing entries) in a vector |
| odds_ratio | Odds ratio estimation |
| prop_diff | Proportion difference estimation |
| prop_diff_test | Difference test for two proportions |
| prune_occurrences | Occurrence table pruning |
| range_noinf | Re-implemented 'range()' default S3 method for numerical... |
| reapply_varlabels | Reapply variable labels |
| response_biomarkers_subgroups | Tabulate biomarker effects on binary response by subgroup |
| response_subgroups | Tabulate binary response by subgroup |
| rtable2gg | Convert 'rtable' objects to 'ggplot' objects |
| rtables_access | Helper functions for accessing information from 'rtables' |
| sas_na | Convert strings to 'NA' |
| s_bland_altman | Bland-Altman analysis |
| score_occurrences | Occurrence table sorting |
| s_cox_multivariate | Multivariate Cox model - summarized results |
| split_cols_by_groups | Split columns by groups of levels |
| split_text_grob | Split text according to available text width |
| 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 |
| study_arm | Indicate study arm variable in formula |
| summarize_ancova | Summarize analysis of covariance (ANCOVA) results |
| summarize_change | Summarize change from baseline values or absolute baseline... |
| summarize_colvars | Summarize variables in columns |
| summarize_functions | Summarize functions |
| summarize_glm_count | Summarize Poisson negative binomial regression |
| summarize_logistic | Multivariate logistic regression table |
| summarize_num_patients | Count number of patients |
| summarize_patients_exposure_in_cols | Count number of patients and sum exposure across all patients... |
| survival_biomarkers_subgroups | Tabulate biomarker effects on survival by subgroup |
| survival_coxph_pairwise | Analyze a pairwise Cox-PH model |
| survival_duration_subgroups | Tabulate survival duration by subgroup |
| survival_time | Survival time analysis |
| survival_timepoint | Survival time point analysis |
| tern-package | tern Package |
| tidy_coxreg | Custom tidy methods for Cox regression |
| tidy.glm | Custom tidy method for binomial GLM results |
| tidy.step | Custom tidy method for STEP results |
| to_n | Replicate entries of a vector if required |
| to_string_matrix | Convert table into matrix of strings |
| try_car_anova | 'tryCatch' around 'car::Anova' |
| univariate | Univariate formula special term |
| unlist_and_blank_na | Blank for missing input |
| update_weights_strat_wilson | Helper function for the estimation of weights for... |
| util_handling_additional_fun_params | Utilities to handle extra arguments in analysis functions |
| utils_split_funs | Custom split functions |
