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tern

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install.packages('tern')

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1,791

Version

0.9.6

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 (0.9.6)

Count patients with abnormal range values

Analysis function to calculate risk difference column values

abnormal_by_baseline

Count patients with abnormal analysis range values by baseline status

Layout-creating function to add row total counts

abnormal_by_marked

Count patients with marked laboratory abnormalities

Convert to rtable

as_factor_keep_attributes

Conversion of a vector to a factor

afun_selected_stats

Get selected statistics names

Additional assertions to use with checkmate

abnormal_by_worst_grade_worsen

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

Labels for adverse event baskets

abnormal_by_worst_grade

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

check_diff_prop_ci

Check proportion difference arguments

argument_convention

Standard arguments

bins_percent_labels

Labels for bins in percent

analyze_variables

Analyze variables

append_varlabels

Add variable labels to top left corner in table

apply_auto_formatting

Apply automatic formatting

Split function to configure risk difference column

Arrange multiple grobs

Check element dimension

analyze_colvars_functions

Analyze functions in columns

combine_vectors

Element-wise combination of two vectors

analyze_vars_in_cols

Analyze numeric variables in columns

control_surv_timepoint

Control function for survfit models for patients' survival rate at time points

control_lineplot_vars

Control function for g_lineplot()

cox_regression_inter

Cox regression helper function for interactions

control_surv_time

Control function for survfit models for survival time

cut_quantile_bins

Cut numeric vector into empirical quantile bins

control_incidence_rate

Control function for incidence rate

combination_function

Class for CombinationFunction

Conversion of days to months

analyze_functions

Analyze functions

Control function for subgroup treatment effect pattern (STEP) calculations

count_cumulative

Cumulative counts of numeric variable by thresholds

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

compare_variables

Compare variables between groups

Bland-Altman analysis

Content row function to add row total to labels

Control function for Cox regression

Control function for Cox-PH model

count_patients_with_event

Count the number of patients with a particular event

Combine factor levels

d_onco_rsp_label

Description of standard oncology response

control_logistic

Control function for logistic regression model fitting

count_occurrences_by_grade

Count occurrences by grade

d_survival_subgroups_colvars

Labels for column variables in survival duration by subgroup table

Reference and treatment group combination

d_count_missed_doses

Description function that calculates labels for s_count_missed_doses()

count_patients_events_in_cols

Count patient events in columns

Count specific values

control_riskdiff

Control function for risk difference column

estimate_multinomial_rsp

Estimate proportions of each level of a variable

Description of the proportion summary

extract_rsp_biomarkers

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

d_test_proportion_diff

Description of the difference test between two proportions

Hazard ratio estimation in interactions

Generate PK reference dataset

Cox proportional hazards regression

extract_by_name

Extract elements by name

Utility function to create label for confidence interval

Fit for logistic regression

Fitting functions for Cox proportional hazards regression

count_patients_with_flags

Count the number of patients with particular flags

Format extreme values

default_stats_formats_labels

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

Default string replacement for NA values

Content row function to add alt_counts_df row total to labels

desctools_binom

Confidence intervals for a difference of binomials

format_extreme_values_ci

Format extreme values part of a confidence interval

forest_viewport

Create a viewport tree for the forest plot

Constructor for content functions given a data frame with flag input

control_analyze_vars

Control function for descriptive statistics

format_fraction

Format fraction and percentage

Horizontal waterfall plot

Utility function to return a named list of covariate names

Helper function to return results of a linear model

h_adsl_adlb_merge_using_worst_flag

Helper function for deriving analysis datasets for select laboratory tables

extract_rsp_subgroups

Prepare response data for population subgroups in data frames

Convert data.frame object to ggplot object

Discard specified levels of a factor

Helper function to format the optional g_lineplot table

Format automatically using data significant digits

h_count_cumulative

Helper function for s_count_cumulative()

Line plot with optional table

Create a STEP graph

Helper function to create simple line plot over time

Format XX as a formatting function

formatting_functions

Formatting functions

Create a forest plot from an rtable

Format numeric values by significant figures

Obtain column indices

h_append_grade_groups

Helper function for s_count_occurrences_by_grade()

Helper function to create a KM plot

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

fct_explicit_na_if

Insertion of explicit missing values in a factor

decorate_grob_set

Decorate set of grobs and add page numbering

decorate_grob_factory

Update page number

h_tab_one_biomarker

Helper function for tabulation of a single biomarker result

Helper functions for Poisson models

h_logistic_regression

Helper functions for multivariate logistic regression

h_map_for_count_abnormal

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

Control functions for Kaplan-Meier plot annotation tables

h_stack_by_baskets

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

Helper functions for subgroup treatment effect pattern (STEP) calculations

h_cox_regression

Helper functions for Cox proportional hazards regression

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

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

Conversion of months to days

count_missed_doses

Count number of patients with missed doses by thresholds

format_count_fraction_lt10

Format count and fraction with special case for count < 10

count_occurrences

Count occurrences

format_extreme_values

Format a single extreme value

d_count_abnormal_by_baseline

Description function for s_count_abnormal_by_baseline()

reapply_varlabels

Reapply variable labels

response_biomarkers_subgroups

Tabulate biomarker effects on binary response by subgroup

muffled_car_anova

Muffled car::Anova

h_tbl_coxph_pairwise

Helper function for generating a pairwise Cox-PH table

Helper function to create Cox-PH grobs

Helper functions for odds ratio estimation

Individual patient plots

ggplot decomposition

h_grob_median_surv

Helper function to create survival estimation grobs

Helper function to tidy survival fit data

Kaplan-Meier plot

Sort pharmacokinetic data by PARAM variable

d_count_cumulative

Description of cumulative count

d_proportion_diff

Description of method used for proportion comparison

Confidence interval for mean

Stack multiple grobs

empty_vector_if_na

Return an empty numeric if all elements are NA.

Odds ratio estimation

score_occurrences

Occurrence table sorting

summarize_colvars

Summarize variables in columns

Convert strings to NA

Custom tidy method for binomial GLM results

summarize_change

Summarize change from baseline values or absolute baseline values

h_split_by_subgroups

Split data frame by subgroups

labels_use_control

Update labels according to control specifications

Indicate study arm variable in formula

d_rsp_subgroups_colvars

Labels for column variables in binary response by subgroup table

Encode categorical missing values in a data frame

Split parameters

Helper function to calculate x-tick positions

summarize_ancova

Summarize analysis of covariance (ANCOVA) results

fit_survival_step

Subgroup treatment effect pattern (STEP) fit for survival outcome

.is_equal_float

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

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

format_fraction_fixed_dp

Format fraction and percentage with fixed single decimal place

format_fraction_threshold

Format fraction with lower threshold

estimate_proportion

Proportion estimation

logistic_regression_cols

Logistic regression multivariate column layout function

extract_survival_subgroups

Prepare survival data for population subgroups in data frames

Simulated CDISC data for examples

extract_survival_biomarkers

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

Proportion difference estimation

survival_coxph_pairwise

Analyze a pairwise Cox-PH model

survival_duration_subgroups

Tabulate survival duration by subgroup

imputation_rule

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

p-Value of the mean

Confidence interval for median

Survival time analysis

summarize_logistic

Multivariate logistic regression table

summarize_num_patients

Count number of patients

update_weights_strat_wilson

Helper function for the estimation of weights for prop_strat_wilson()

utils_split_funs

Custom split functions

Difference test for two proportions

survival_timepoint

Survival time point analysis

Helper function to prepare a KM layout

h_incidence_rate

Helper functions for incidence rate

prune_occurrences

Occurrence table pruning

Utility function to create label for p-value

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

Helper functions for calculating proportion confidence intervals

h_prop_diff_test

Helper functions to test proportion differences

format_count_fraction

Format count and fraction

fct_collapse_only

Collapse factor levels and keep only those new group levels

Smooth function with optional grouping

format_count_fraction_fixed_dp

Format count and percentage with fixed single decimal place

h_tbl_median_surv

Helper function for survival estimations

survival_biomarkers_subgroups

Tabulate biomarker effects on survival by subgroup

summarize_patients_exposure_in_cols

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

groups_list_to_df

Convert list of groups to a data frame

Helper functions for accessing information from rtables

s_cox_multivariate

Multivariate Cox model - summarized results

h_adlb_abnormal_by_worst_grade

Helper function to prepare ADLB for count_abnormal_by_worst_grade()

tryCatch around car::Anova

h_worsen_counter

Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline()

Ungroup non-numeric statistics

Make names without dots

split_cols_by_groups

Split columns by groups of levels

stat_propdiff_ci

Proportion difference and confidence interval

logistic_summary_by_flag

Logistic regression summary table

split_text_grob

Split text according to available text width

strata_normal_quantile

Helper function for the estimation of stratified quantiles

Custom tidy method for STEP results

Helper function to prepare ADLB with worst labs

Helper function to create grid object with y-axis annotation

Function to return the estimated means using predicted probabilities

h_grob_tbl_at_risk

Helper function to create patient-at-risk grobs

Custom tidy methods for Cox regression

Helper functions to calculate proportion difference

Incidence rate estimation

Univariate formula special term

unlist_and_blank_na

Blank for missing input

labels_or_names

Labels or names of list elements

response_subgroups

Tabulate binary response by subgroup

Replicate entries of a vector if required

summarize_functions

Summarize functions

summarize_glm_count

Summarize Poisson negative binomial regression

Convert rtable objects to ggplot objects

to_string_matrix

Convert table into matrix of strings