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tern

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install.packages('tern')

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1,648

Version

0.9.8

License

Apache License 2.0

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Repository

https://github.com/insightsengineering/tern/

Homepage

https://insightsengineering.github.io/tern/

Maintainer

Joe Zhu

Last Published

April 14th, 2025

Functions in tern (0.9.8)

Labels for adverse event baskets

afun_selected_stats

Get selected statistics names

Count patients with abnormal range values

Split function to configure risk difference column

Layout-creating function to add row total counts

abnormal_by_baseline

Count patients with abnormal analysis range values by baseline status

Analysis function to calculate risk difference column values

abnormal_by_worst_grade

Count patients by most extreme post-baseline toxicity grade per direction of abnormality

abnormal_by_marked

Count patients with marked laboratory abnormalities

abnormal_lab_worsen_by_baseline

Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline

analyze_colvars_functions

Analyze functions in columns

append_varlabels

Add variable labels to top left corner in table

analyze_variables

Analyze variables

Arrange multiple grobs

Additional assertions to use with checkmate

Convert to rtable

analyze_functions

Analyze functions

analyze_vars_in_cols

Analyze numeric variables in columns

apply_auto_formatting

Apply automatic formatting

argument_convention

Standard arguments

combine_vectors

Element-wise combination of two vectors

combination_function

Class for CombinationFunction

Reference and treatment group combination

check_diff_prop_ci

Check proportion difference arguments

bins_percent_labels

Labels for bins in percent

Check element dimension

Content row function to add alt_counts_df row total to labels

Content row function to add row total to labels

Constructor for content functions given a data frame with flag input

compare_variables

Compare variables between groups

control_riskdiff

Control function for risk difference column

control_incidence_rate

Control function for incidence rate

Control function for Cox regression

Control function for subgroup treatment effect pattern (STEP) calculations

control_logistic

Control function for logistic regression model fitting

control_lineplot_vars

Control function for g_lineplot()

control_analyze_vars

Control function for descriptive statistics

Control functions for Kaplan-Meier plot annotation tables

Control function for Cox-PH model

count_patients_with_flags

Count the number of patients with particular flags

count_patients_with_event

Count the number of patients with a particular event

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_by_grade

Count occurrences by grade

count_patients_events_in_cols

Count patient events in columns

Count specific values

count_occurrences

Count occurrences

count_missed_doses

Count number of patients with missed doses by thresholds

count_cumulative

Cumulative counts of numeric variable by thresholds

d_count_cumulative

Description of cumulative count

cox_regression_inter

Cox regression helper function for interactions

cut_quantile_bins

Cut numeric vector into empirical quantile bins

Description of the proportion summary

Generate PK reference dataset

d_onco_rsp_label

Description of standard oncology response

d_proportion_diff

Description of method used for proportion comparison

Cox proportional hazards regression

d_count_abnormal_by_baseline

Description function for s_count_abnormal_by_baseline()

d_count_missed_doses

Description function that calculates labels for s_count_missed_doses()

decorate_grob_set

Decorate set of grobs and add page numbering

d_test_proportion_diff

Description of the difference test between two proportions

Default string replacement for NA values

default_stats_formats_labels

Get default statistical methods and their associated formats, labels, and indent modifiers

desctools_binom

Confidence intervals for a difference of binomials

Conversion of days to months

d_survival_subgroups_colvars

Labels for column variables in survival duration by subgroup table

d_rsp_subgroups_colvars

Labels for column variables in binary response by subgroup table

.is_equal_float

Utility function to check if a float value is equal to another float value

estimate_multinomial_rsp

Estimate proportions of each level of a variable

estimate_proportion

Proportion estimation

empty_vector_if_na

Return an empty numeric if all elements are NA.

Encode categorical missing values in a data frame

Hazard ratio estimation in interactions

Convert data.frame object to ggplot object

Utility function to create label for confidence interval

Utility function to create label for p-value

Factor utilities

Add titles, footnotes, page Number, and a bounding box to a grid grob

decorate_grob_factory

Update page number

Simulated CDISC data for examples

extract_by_name

Extract elements by name

extract_rsp_subgroups

Prepare response data for population subgroups in data frames

extract_rsp_biomarkers

Prepare response data estimates for multiple biomarkers in a single data frame

extract_survival_subgroups

Prepare survival data for population subgroups in data frames

Format extreme values

Fitting functions for Cox proportional hazards regression

format_count_fraction_lt10

Format count and fraction with special case for count < 10

format_count_fraction_fixed_dp

Format count and percentage with fixed single decimal place

extract_survival_biomarkers

Prepare survival data estimates for multiple biomarkers in a single data frame

Format automatically using data significant digits

fit_survival_step

Subgroup treatment effect pattern (STEP) fit for survival outcome

forest_viewport

Create a viewport tree for the forest plot

Bland-Altman plot

Create a forest plot from an rtable

format_extreme_values

Format a single extreme value

format_extreme_values_ci

Format extreme values part of a confidence interval

formatting_functions

Formatting functions

Format XX as a formatting function

format_count_fraction

Format count and fraction

format_fraction_threshold

Format fraction with lower threshold

Fit for logistic regression

format_fraction_fixed_dp

Format fraction and percentage with fixed single decimal place

Subgroup treatment effect pattern (STEP) fit for binary (response) outcome

format_fraction

Format fraction and percentage

Individual patient plots

Kaplan-Meier plot

Format numeric values by significant figures

h_adsl_adlb_merge_using_worst_flag

Helper function for deriving analysis datasets for select laboratory tables

Smooth function with optional grouping

Line plot with optional table

groups_list_to_df

Convert list of groups to a data frame

Create a STEP graph

Utility function to return a named list of covariate names

ggplot decomposition

h_append_grade_groups

Helper function for s_count_occurrences_by_grade()

Horizontal waterfall plot

h_count_cumulative

Helper function for s_count_cumulative()

Helper function to format the optional g_lineplot table

Helper function to prepare ADLB with worst labs

Obtain column indices

h_adlb_abnormal_by_worst_grade

Helper function to prepare ADLB for count_abnormal_by_worst_grade()

h_cox_regression

Helper functions for Cox proportional hazards regression

Helper function to tidy survival fit data

Helper function to create simple line plot over time

Helper function to create a KM plot

Helper function to return results of a linear model

h_biomarkers_subgroups

Helper functions for tabulation of a single biomarker result

h_map_for_count_abnormal

Helper function to create a map data frame for trim_levels_to_map()

h_incidence_rate

Helper functions for incidence rate

Helper function to prepare a KM layout

h_grob_median_surv

Helper function to create survival estimation grobs

Helper function to create grid object with y-axis annotation

h_grob_tbl_at_risk

Helper function to create patient-at-risk grobs

Helper functions for Poisson models

h_logistic_regression

Helper functions for multivariate logistic regression

Helper functions for odds ratio estimation

Helper function to create Cox-PH grobs

h_stack_by_baskets

Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records.

Helper functions for calculating proportion confidence intervals

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

Split parameters

h_split_by_subgroups

Split data frame by subgroups

Helper functions to calculate proportion difference

h_prop_diff_test

Helper functions to test proportion differences

Sort pharmacokinetic data by PARAM variable

Function to return the estimated means using predicted probabilities

Incidence rate estimation

Helper functions for subgroup treatment effect pattern (STEP) calculations

Helper function to calculate x-tick positions

imputation_rule

Apply 1/3 or 1/2 imputation rule to data

h_survival_biomarkers_subgroups

Helper functions for tabulating biomarker effects on survival by subgroup

labels_or_names

Labels or names of list elements

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_tbl_coxph_pairwise

Helper function for generating a pairwise Cox-PH table

Number of available (non-missing entries) in a vector

h_survival_duration_subgroups

Helper functions for tabulating survival duration by subgroup

Odds ratio estimation

Conversion of months to days

Proportion difference estimation

Difference test for two proportions

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 without dots

muffled_car_anova

Muffled car::Anova

response_biomarkers_subgroups

Tabulate biomarker effects on binary response by subgroup

reapply_varlabels

Reapply variable labels

Helper functions for accessing information from rtables

prune_occurrences

Occurrence table pruning

Re-implemented range() default S3 method for numerical objects

response_subgroups

Tabulate binary response by subgroup

Convert rtable objects to ggplot objects

Bland-Altman analysis

s_cox_multivariate

Multivariate Cox model - summarized results

Convert strings to NA

Confidence interval for mean

strata_normal_quantile

Helper function for the estimation of stratified quantiles

Indicate study arm variable in formula

Confidence interval for median

stat_propdiff_ci

Proportion difference and confidence interval

score_occurrences

Occurrence table sorting

split_cols_by_groups

Split columns by groups of levels

Stack multiple grobs

p-Value of the mean

split_text_grob

Split text according to available text width

summarize_glm_count

Summarize Poisson negative binomial regression

survival_biomarkers_subgroups

Tabulate biomarker effects on survival by subgroup

summarize_logistic

Multivariate logistic regression table

summarize_change

Summarize change from baseline values or absolute baseline values

summarize_ancova

Summarize analysis of covariance (ANCOVA) results

summarize_num_patients

Count number of patients

summarize_colvars

Summarize variables in columns

summarize_functions

Summarize functions

survival_coxph_pairwise

Analyze a pairwise Cox-PH model

summarize_patients_exposure_in_cols

Count number of patients and sum exposure across all patients in columns

Custom tidy method for STEP results

Custom tidy method for binomial GLM results

Replicate entries of a vector if required

Custom tidy methods for Cox regression

to_string_matrix

Convert table into matrix of strings

tryCatch around car::Anova

Survival time analysis

survival_timepoint

Survival time point analysis

survival_duration_subgroups

Tabulate survival duration by subgroup

update_weights_strat_wilson

Helper function for the estimation of weights for prop_strat_wilson()

Univariate formula special term

unlist_and_blank_na

Blank for missing input

util_handling_additional_fun_params

Utilities to handle extra arguments in analysis functions

utils_split_funs

Custom split functions