Function reference • tern

Overview Pages

tern tern-package: tern Package

formatting_functions: Additional Formatting Functions

kaplan_meier: Kaplan-Meier Plot

Control Functions

Control functions capture options in lists, and take care of defaults (and if it makes sense also checks). They avoid cluttering of function signatures with long lists of single arguments.

control_coxph(): Control Function for CoxPH Model

control_coxreg(): Controls for Cox regression

control_incidence_rate(): Control function for incidence rate

control_lineplot_vars(): Control Function for g_lineplot Function

control_logistic(): Control Function for Logistic Regression Model Fitting

control_step(): Control Function for Subgroup Treatment Effect Pattern (STEP) Calculations

control_summarize_vars(): Control Function for Descriptive Statistics

control_surv_time(): Control Function for survfit Model for Survival Time

control_surv_timepoint(): Control Function for survfit Model for Patient's Survival Rate at time point

Statistics Functions

Statistics functions should do the computation of the numbers that are tabulated later. In order to separate computation from formatting, they should not take care of rcell type formatting themselves.

s_compare() a_compare() create_afun_compare() compare_vars(): Compare Variables Between Groups

h_count_cumulative() s_count_cumulative() a_count_cumulative() count_cumulative(): Cumulative Counts with Thresholds

s_count_nonmissing() d_count_missed_doses() s_count_missed_doses() a_count_missed_doses() count_missed_doses(): Counting Missed Doses

s_count_occurrences() a_count_occurrences() count_occurrences(): Occurrence Counts

h_append_grade_groups() s_count_occurrences_by_grade() a_count_occurrences_by_grade() count_occurrences_by_grade() summarize_occurrences_by_grade(): Occurrence Counts by Grade

s_count_patients_and_multiple_events() summarize_patients_events_in_cols(): Counting Patients and Events in Columns

s_count_patients_with_event() a_count_patients_with_event() count_patients_with_event() s_count_patients_with_flags() a_count_patients_with_flags() count_patients_with_flags(): Count the Number of Patients with a Particular Event

s_count_values() count_values() a_count_values(): Counting Specific Values

h_coxreg_univar_formulas() h_coxreg_multivar_formula() fit_coxreg_univar() tidy(<summary.coxph>) h_coxreg_univar_extract() tidy(<coxreg.univar>) fit_coxreg_multivar() h_coxreg_multivar_extract() tidy(<coxreg.multivar>) s_coxreg() summarize_coxreg(): Cox Proportional Hazards Regression

s_cox_univariate(): Cox regression including a single covariate - summarized results

d_onco_rsp_label() s_length_proportion() a_length_proportion() estimate_multinomial_response(): Estimation of Proportions per Level of Factor

s_num_patients() s_num_patients_content() summarize_num_patients(): Number of patients

or_glm() or_clogit() s_odds_ratio() a_odds_ratio() estimate_odds_ratio(): Odds Ratio Estimation

prop_wilson() prop_clopper_pearson() prop_wald() prop_agresti_coull() prop_jeffreys() s_proportion() estimate_proportion() a_proportion(): Estimation of Proportions

d_proportion_diff() prop_diff_wald() prop_diff_ha() prop_diff_nc() prop_diff_cmh() s_proportion_diff() a_proportion_diff() estimate_proportion_diff(): Proportion Difference

s_summary() a_summary() create_afun_summary() summarize_vars(): Summarize Variables

Formatted Analysis functions

These have the same arguments as the corresponding statistics functions, and can be further customized by calling rtables::make_afun() on them. They are used as afun in rtables::analyze().

h_count_cumulative() s_count_cumulative() a_count_cumulative() count_cumulative(): Cumulative Counts with Thresholds

s_count_nonmissing() d_count_missed_doses() s_count_missed_doses() a_count_missed_doses() count_missed_doses(): Counting Missed Doses

s_count_occurrences() a_count_occurrences() count_occurrences(): Occurrence Counts

h_append_grade_groups() s_count_occurrences_by_grade() a_count_occurrences_by_grade() count_occurrences_by_grade() summarize_occurrences_by_grade(): Occurrence Counts by Grade

s_count_patients_with_event() a_count_patients_with_event() count_patients_with_event() s_count_patients_with_flags() a_count_patients_with_flags() count_patients_with_flags(): Count the Number of Patients with a Particular Event

or_glm() or_clogit() s_odds_ratio() a_odds_ratio() estimate_odds_ratio(): Odds Ratio Estimation

prop_wilson() prop_clopper_pearson() prop_wald() prop_agresti_coull() prop_jeffreys() s_proportion() estimate_proportion() a_proportion(): Estimation of Proportions

s_compare() a_compare() create_afun_compare() compare_vars(): Compare Variables Between Groups

s_summary() a_summary() create_afun_summary() summarize_vars(): Summarize Variables

Analyze Functions

Analyze Functions are used in combination with the rtables layout functions, in the pipeline which creates the table.

s_compare() a_compare() create_afun_compare() compare_vars(): Compare Variables Between Groups

s_count_abnormal() a_count_abnormal() count_abnormal(): Patient Counts with Abnormal Range Values

d_count_abnormal_by_baseline() s_count_abnormal_by_baseline() a_count_abnormal_by_baseline() count_abnormal_by_baseline(): Patient Counts with Abnormal Range Values by Baseline Status

s_count_abnormal_by_marked() a_count_abnormal_by_marked() count_abnormal_by_marked(): Count patients with marked laboratory abnormalities

s_count_abnormal_by_worst_grade() a_count_abnormal_by_worst_grade() count_abnormal_by_worst_grade(): Patient Counts with the Most Extreme Post-baseline Toxicity Grade per Direction of Abnormality

h_adlb_worsen() h_worsen_counter() s_count_abnormal_lab_worsen_by_baseline() a_count_abnormal_lab_worsen_by_baseline() count_abnormal_lab_worsen_by_baseline(): Patient Counts for Laboratory Events (Worsen From Baseline) by Highest Grade Post-Baseline

h_count_cumulative() s_count_cumulative() a_count_cumulative() count_cumulative(): Cumulative Counts with Thresholds

s_count_nonmissing() d_count_missed_doses() s_count_missed_doses() a_count_missed_doses() count_missed_doses(): Counting Missed Doses

s_count_occurrences() a_count_occurrences() count_occurrences(): Occurrence Counts

h_append_grade_groups() s_count_occurrences_by_grade() a_count_occurrences_by_grade() count_occurrences_by_grade() summarize_occurrences_by_grade(): Occurrence Counts by Grade

s_count_patients_with_event() a_count_patients_with_event() count_patients_with_event() s_count_patients_with_flags() a_count_patients_with_flags() count_patients_with_flags(): Count the Number of Patients with a Particular Event

s_count_values() count_values() a_count_values(): Counting Specific Values

s_incidence_rate() a_incidence_rate() estimate_incidence_rate() h_incidence_rate_normal() h_incidence_rate_normal_log() h_incidence_rate_exact() h_incidence_rate_byar() h_incidence_rate(): Incidence rate

d_onco_rsp_label() s_length_proportion() a_length_proportion() estimate_multinomial_response(): Estimation of Proportions per Level of Factor

or_glm() or_clogit() s_odds_ratio() a_odds_ratio() estimate_odds_ratio(): Odds Ratio Estimation

prop_wilson() prop_clopper_pearson() prop_wald() prop_agresti_coull() prop_jeffreys() s_proportion() estimate_proportion() a_proportion(): Estimation of Proportions

d_proportion_diff() prop_diff_wald() prop_diff_ha() prop_diff_nc() prop_diff_cmh() s_proportion_diff() a_proportion_diff() estimate_proportion_diff(): Proportion Difference

extract_rsp_biomarkers() tabulate_rsp_biomarkers(): Tabulate Biomarker Effects on Binary Response by Subgroup

h_ancova() s_ancova() a_ancova() summarize_ancova(): Summary for analysis of covariance (ANCOVA).

s_change_from_baseline() a_change_from_baseline() summarize_change(): Summarize the Change from Baseline or Absolute Baseline Values

summarize_colvars(): Summarize Variables in Columns

h_coxreg_univar_formulas() h_coxreg_multivar_formula() fit_coxreg_univar() tidy(<summary.coxph>) h_coxreg_univar_extract() tidy(<coxreg.univar>) fit_coxreg_multivar() h_coxreg_multivar_extract() tidy(<coxreg.multivar>) s_coxreg() summarize_coxreg(): Cox Proportional Hazards Regression

fit_logistic() h_get_interaction_vars() h_interaction_coef_name() h_or_cat_interaction() h_or_cont_interaction() h_or_interaction() h_simple_term_labels() h_interaction_term_labels() h_glm_simple_term_extract() h_glm_interaction_extract() h_glm_inter_term_extract() h_logistic_simple_terms() h_logistic_inter_terms() tidy(<glm>) logistic_regression_cols() logistic_summary_by_flag() summarize_logistic(): Multi-variable logistic regression table

s_num_patients() s_num_patients_content() summarize_num_patients(): Number of patients

s_count_patients_and_multiple_events() summarize_patients_events_in_cols(): Counting Patients and Events in Columns

s_count_patients_sum_exposure() summarize_patients_exposure_in_cols(): Counting Patients Summing Exposure Across All Patients in Columns

summary_in_cols() summarize_vars_in_cols(): Summary numeric variables in columns

s_summary() a_summary() create_afun_summary() summarize_vars(): Summarize Variables

extract_rsp_subgroups() a_response_subgroups() tabulate_rsp_subgroups(): Tabulate Binary Response by Subgroup

extract_survival_biomarkers() tabulate_survival_biomarkers(): Tabulate Biomarker Effects on Survival by Subgroup

extract_survival_subgroups() a_survival_subgroups() tabulate_survival_subgroups(): Tabulate Survival Duration by Subgroup

prop_chisq() prop_schouten() prop_fisher() prop_cmh() s_test_proportion_diff() a_test_proportion_diff() test_proportion_diff(): Difference Test for Two Proportions

Analysis Helper Functions

These functions are useful to help definining the analysis.

`add_footnotes<-`() `add_footnotes<-`(): Add Footnotes

footnotes() footnotes(): Retrieve Footnotes

`footnotes<-`() `footnotes<-`(): Assign Footnotes

h_adlb_worsen() h_worsen_counter() s_count_abnormal_lab_worsen_by_baseline() a_count_abnormal_lab_worsen_by_baseline() count_abnormal_lab_worsen_by_baseline(): Patient Counts for Laboratory Events (Worsen From Baseline) by Highest Grade Post-Baseline

h_adsl_adlb_merge_using_worst_flag(): Helper Function for Deriving Analysis Datasets for LBT13 and LBT14

h_ancova() s_ancova() a_ancova() summarize_ancova(): Summary for analysis of covariance (ANCOVA).

h_append_grade_groups() s_count_occurrences_by_grade() a_count_occurrences_by_grade() count_occurrences_by_grade() summarize_occurrences_by_grade(): Occurrence Counts by Grade

h_col_indices(): Obtain Column Indices

h_count_cumulative() s_count_cumulative() a_count_cumulative() count_cumulative(): Cumulative Counts with Thresholds

h_survtime_df() h_survtime_subgroups_df() h_coxph_df() h_coxph_subgroups_df(): Helper Functions for Tabulating Survival Duration by Subgroup

h_coxreg_inter_effect() h_coxreg_extract_interaction() h_coxreg_inter_estimations(): Cox Regression Helper: Interactions

h_surv_to_coxreg_variables() h_coxreg_mult_cont_df() h_tab_surv_one_biomarker(): Helper Functions for Tabulating Biomarker Effects on Survival by Subgroup

h_coxreg_univar_formulas() h_coxreg_multivar_formula() fit_coxreg_univar() tidy(<summary.coxph>) h_coxreg_univar_extract() tidy(<coxreg.univar>) fit_coxreg_multivar() h_coxreg_multivar_extract() tidy(<coxreg.multivar>) s_coxreg() summarize_coxreg(): Cox Proportional Hazards Regression

h_decompose_gg(): ggplot Decomposition

h_get_format_threshold() h_format_threshold() format_extreme_values() format_extreme_values_ci(): Formatting Extreme Values

h_format_row(): Helper function to get the right formatting in the optional table in g_lineplot.

fit_logistic() h_get_interaction_vars() h_interaction_coef_name() h_or_cat_interaction() h_or_cont_interaction() h_or_interaction() h_simple_term_labels() h_interaction_term_labels() h_glm_simple_term_extract() h_glm_interaction_extract() h_glm_inter_term_extract() h_logistic_simple_terms() h_logistic_inter_terms() tidy(<glm>) logistic_regression_cols() logistic_summary_by_flag() summarize_logistic(): Multi-variable logistic regression table

h_ggkm(): Helper function: KM plot

s_incidence_rate() a_incidence_rate() estimate_incidence_rate() h_incidence_rate_normal() h_incidence_rate_normal_log() h_incidence_rate_exact() h_incidence_rate_byar() h_incidence_rate(): Incidence rate

h_km_layout(): Helper: KM Layout

h_rsp_to_logistic_variables() h_logistic_mult_cont_df() h_tab_rsp_one_biomarker(): Helper Functions for Tabulating Biomarker Effects on Binary Response by Subgroup

h_map_for_count_abnormal(): Helper Function to create a map dataframe that can be used in trim_levels_to_map split function.

h_proportion_df() h_proportion_subgroups_df() h_odds_ratio_df() h_odds_ratio_subgroups_df(): Helper Functions for Tabulating Binary Response by Subgroup

h_pkparam_sort(): Sort PK PARAM variable

h_recycle() desctools_binom() desctools_binomci(): Confidence Intervals for a Difference of Binomials

h_split_by_subgroups(): Split Dataframe 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_window() h_step_trt_effect() h_step_survival_formula() h_step_survival_est() h_step_rsp_formula() h_step_rsp_est(): Helper Functions for Subgroup Treatment Effect Pattern (STEP) Calculations

h_tab_one_biomarker(): Helper Function for Tabulation of a Single Biomarker Result

h_tbl_coxph_pairwise(): Helper Function: Pairwise CoxPH table

h_tbl_median_surv(): Helper Function: Survival Estimations

or_glm() or_clogit() s_odds_ratio() a_odds_ratio() estimate_odds_ratio(): Odds Ratio Estimation

d_proportion_diff() prop_diff_wald() prop_diff_ha() prop_diff_nc() prop_diff_cmh() s_proportion_diff() a_proportion_diff() estimate_proportion_diff(): Proportion Difference

Model Specific Functions

These functions help with fitting or extracting results from specific models.

estimate_coef(): Hazard Ratio Estimation in Interactions

extract_rsp_subgroups() a_response_subgroups() tabulate_rsp_subgroups(): Tabulate Binary Response by Subgroup

extract_survival_biomarkers() tabulate_survival_biomarkers(): Tabulate Biomarker Effects on Survival by Subgroup

extract_survival_subgroups() a_survival_subgroups() tabulate_survival_subgroups(): Tabulate Survival Duration by Subgroup

h_coxreg_univar_formulas() h_coxreg_multivar_formula() fit_coxreg_univar() tidy(<summary.coxph>) h_coxreg_univar_extract() tidy(<coxreg.univar>) fit_coxreg_multivar() h_coxreg_multivar_extract() tidy(<coxreg.multivar>) s_coxreg() summarize_coxreg(): Cox Proportional Hazards Regression

fit_logistic() h_get_interaction_vars() h_interaction_coef_name() h_or_cat_interaction() h_or_cont_interaction() h_or_interaction() h_simple_term_labels() h_interaction_term_labels() h_glm_simple_term_extract() h_glm_interaction_extract() h_glm_inter_term_extract() h_logistic_simple_terms() h_logistic_inter_terms() tidy(<glm>) logistic_regression_cols() logistic_summary_by_flag() summarize_logistic(): Multi-variable logistic regression table

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

get_smooths(): Smooth Function with Optional Grouping

pairwise(): Pairwise formula special term

g_step() tidy(<step>): Create a STEP Graph

univariate(): Univariate formula special term

Graphs

Functions that creates graphical type of the output.

g_forest(): Create a Forest Plot based on a Table

h_set_nest_theme() h_g_ipp() g_ipp(): Individual Patient Plots

g_km(): Kaplan-Meier Plot

g_lineplot(): Line plot with the optional table

g_step() tidy(<step>): Create a STEP Graph

g_waterfall(): Horizontal Waterfall Plot

rtables Helper Functions

These functions help to work with the new rtables package and might be moved there later.

add_rowcounts(): Layout Creating Function to Add Row Total Counts

append_varlabels(): Add Variable Labels to Top Left Corner in Table

as.rtable(): Convert to rtable

combine_groups(): Reference and Treatment Group Combination

combine_vectors(): Combine Two Vectors Element Wise

h_row_counts() h_row_fractions() h_col_counts() is_leaf_table() h_content_first_row(): rtables Access Helper Functions

h_col_indices(): Obtain Column Indices

split_cols_by_groups(): Split Columns by Groups of Levels

to_string_matrix(): Convert Table into Matrix of Strings

rtables Formatting Functions

These functions provide customized formatting rules to work with the rtables package.

format_count_fraction(): Formatting Count and Fraction

h_get_format_threshold() h_format_threshold() format_extreme_values() format_extreme_values_ci(): Formatting Extreme Values

format_fraction(): Formatting Fraction and Percentage

format_fraction_threshold(): Formatting Fraction with Lower Threshold

format_xx(): Formatting: XX as Formatting Function

rtables Scoring Functions

These functions can help with sorting of tables.

score_occurrences() score_occurrences_cols() score_occurrences_subtable() score_occurrences_cont_cols(): Occurrence Table Sorting

rtables Pruning Functions

These functions and classes help with flexible pruning of tables.

`&`(<CombinationFunction>,<CombinationFunction>) `|`(<CombinationFunction>,<CombinationFunction>) `!`(<CombinationFunction>): Combination Functions Class

keep_rows() keep_content_rows() has_count_in_cols() has_count_in_any_col() has_fraction_in_cols() has_fraction_in_any_col() has_fractions_difference() has_counts_difference(): Occurrence Table Pruning

Graphs Helper Functions

These functions are useful to modify graphs.

arrange_grobs(): Arrange Multiple Grobs

decorate_grob(): Add Titles, Footnotes, Page Number, and a Bounding Box to a Grid Grob

decorate_grob_factory(): Update Page Number

decorate_grob_set(): Decorate Set of grobs and Add Page Numbering

draw_grob(): Draw grob

h_set_nest_theme() h_g_ipp() g_ipp(): Individual Patient Plots

h_grob_coxph(): Helper Function: CoxPH Grob

h_grob_median_surv(): Helper Function: Survival Estimation Grob

h_grob_tbl_at_risk(): Helper: Patient-at-Risk Grobs

h_grob_y_annot(): Helper: Grid Object with y-axis Annotation

h_xticks(): Helper function: x tick positions

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

Data Helper Functions

These functions are used by other functions to derive data.

aesi_label(): Labels for Adverse Event Baskets

as_factor_keep_attributes(): Conversion of a Vector to a Factor

bins_percent_labels(): Labels for Bins in Percent

combine_levels(): Combine Factor Levels

cut_quantile_bins(): Cutting Numeric Vector into Empirical Quantile Bins

day2month(): Conversion of Days to Months

month2day(): Conversion of Months to Days

df_explicit_na(): Encode Categorical Missing Values in a Data Frame

d_onco_rsp_label() s_length_proportion() a_length_proportion() estimate_multinomial_response(): Estimation of Proportions per Level of Factor

d_count_abnormal_by_baseline() s_count_abnormal_by_baseline() a_count_abnormal_by_baseline() count_abnormal_by_baseline(): Patient Counts with Abnormal Range Values by Baseline Status

s_count_nonmissing() d_count_missed_doses() s_count_missed_doses() a_count_missed_doses() count_missed_doses(): Counting Missed Doses

d_count_cumulative(): Description of Cumulative Count

d_pkparam(): Generate PK reference dataset

d_proportion(): Description of the Proportion Summary

d_proportion_diff() prop_diff_wald() prop_diff_ha() prop_diff_nc() prop_diff_cmh() s_proportion_diff() a_proportion_diff() estimate_proportion_diff(): Proportion Difference

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

explicit_na(): Missing Data

fct_collapse_only(): Collapsing of Factor Levels and Keeping Only Those New Group Levels

fct_discard(): Discard Certain Levels from a Factor

fct_explicit_na_if(): Insertion of Explicit Missings in a Factor

f_conf_level(): Utility function to create label for confidence interval

f_pval(): Utility function to create label for p-value

h_data_plot(): Helper function: tidy survival fit

sas_na(): Convert Strings to NA

to_n(): Replicate Entries of a Vector if Required

Assertion Functions

These functions supplement those in the checkmate package.

assert_list_of_variables() assert_df_with_variables() assert_valid_factor() assert_df_with_factors() assert_proportion_value(): Additional Assertions for checkmate

Deprecated Functions

These functions already are or will eventually be removed.

color_palette(): Deprecated by nestcolor::color_palette: Color Palettes Used in NEST

h_set_nest_theme() h_g_ipp() g_ipp(): Individual Patient Plots

s_cox_univariate(): Cox regression including a single covariate - summarized results