Create Common TLGs Used in Clinical Trials

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Documentation for package ‘tern’ version 0.9.8

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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A B C D E F G H I K L M O P R S T U misc

tern-package

tern Package

-- A --

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_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'
as_factor_keep_attributes	Factor utilities
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

-- B --

bland_altman

Bland-Altman plot

-- C --

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	Factor utilities
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

-- D --

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

-- E --

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

-- F --

factor_utils	Factor utilities
fct_collapse_only	Factor utilities
fct_discard	Factor utilities
fct_explicit_na_if	Factor utilities
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

-- G --

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

-- H --

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_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_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 functions for tabulation of a single biomarker result
h_tab_rsp_one_biomarker	Helper functions for tabulation of a single biomarker result
h_tab_surv_one_biomarker	Helper functions for tabulation of a single biomarker result
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

-- I --

imputation_rule	Apply 1/3 or 1/2 imputation rule to data
individual_patient_plot	Individual patient plots

-- K --

kaplan_meier	Kaplan-Meier plot
keep_content_rows	Occurrence table pruning
keep_rows	Occurrence table pruning

-- L --

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

-- M --

month2day

Conversion of months to days

-- O --

odds_ratio	Odds ratio estimation
or_clogit	Helper functions for odds ratio estimation
or_glm	Helper functions for odds ratio estimation

-- P --

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

-- R --

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

-- S --

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_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_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

-- T --

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

-- U --

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

-- misc --

!-method	Class for 'CombinationFunction'
&-method	Class for 'CombinationFunction'
|-method	Class for 'CombinationFunction'